Query psy3013
Match_columns 151
No_of_seqs 113 out of 337
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 23:16:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3013.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3013hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00471 60S ribosomal protein 100.0 6E-61 1.3E-65 372.4 9.3 118 33-151 1-119 (134)
2 KOG3418|consensus 100.0 4.3E-52 9.4E-57 323.2 6.7 119 33-151 1-121 (136)
3 PF01777 Ribosomal_L27e: Ribos 99.9 2.9E-29 6.3E-34 181.8 -7.6 68 84-151 1-70 (85)
4 COG2163 RPL14A Ribosomal prote 99.8 7.5E-20 1.6E-24 141.0 2.4 117 33-151 1-118 (125)
5 PRK04333 50S ribosomal protein 99.2 1.2E-11 2.7E-16 89.5 5.6 62 36-123 3-64 (84)
6 PTZ00065 60S ribosomal protein 98.8 9.3E-09 2E-13 80.3 6.6 65 34-124 5-69 (130)
7 KOG3421|consensus 96.2 0.0063 1.4E-07 48.3 4.0 64 34-124 4-67 (136)
8 PF00467 KOW: KOW motif; Inte 95.9 0.009 1.9E-07 35.6 2.9 26 39-64 1-26 (32)
9 PF01159 Ribosomal_L6e: Riboso 95.7 0.0023 5E-08 48.6 -0.3 47 102-149 4-54 (108)
10 smart00739 KOW KOW (Kyprides, 95.6 0.019 4.2E-07 31.9 3.2 26 37-62 2-27 (28)
11 CHL00141 rpl24 ribosomal prote 93.3 0.14 3E-06 37.0 3.9 42 33-80 5-46 (83)
12 PRK01191 rpl24p 50S ribosomal 92.6 0.22 4.7E-06 38.7 4.4 39 36-80 45-83 (120)
13 PRK12281 rplX 50S ribosomal pr 92.6 0.21 4.6E-06 35.6 4.0 40 36-81 6-45 (76)
14 PRK00004 rplX 50S ribosomal pr 92.0 0.26 5.6E-06 36.9 4.1 41 36-82 4-44 (105)
15 TIGR01079 rplX_bact ribosomal 91.4 0.31 6.7E-06 36.5 4.0 41 36-82 3-43 (104)
16 PTZ00194 60S ribosomal protein 90.9 0.38 8.2E-06 38.5 4.2 40 36-81 46-85 (143)
17 TIGR01080 rplX_A_E ribosomal p 90.1 0.53 1.1E-05 36.1 4.2 39 36-80 41-79 (114)
18 KOG1694|consensus 89.9 0.17 3.7E-06 40.6 1.5 23 25-47 22-44 (152)
19 COG0198 RplX Ribosomal protein 84.2 1.7 3.7E-05 33.1 4.0 39 36-82 4-42 (104)
20 COG2163 RPL14A Ribosomal prote 77.5 1.6 3.4E-05 34.1 1.8 53 51-123 7-66 (125)
21 KOG1999|consensus 65.2 5.7 0.00012 40.3 2.9 43 20-62 443-485 (1024)
22 PF13234 rRNA_proc-arch: rRNA- 59.0 9.2 0.0002 31.7 2.8 31 33-63 69-99 (268)
23 KOG1708|consensus 50.2 22 0.00048 30.6 3.7 73 36-118 72-153 (236)
24 TIGR00405 L26e_arch ribosomal 49.0 37 0.0008 25.6 4.4 28 35-62 85-112 (145)
25 KOG3418|consensus 48.0 2.2 4.8E-05 34.0 -2.4 52 33-84 77-132 (136)
26 PF15591 Imm17: Immunity prote 46.3 38 0.00083 24.6 3.9 27 48-76 21-47 (74)
27 PRK05609 nusG transcription an 46.1 36 0.00078 26.2 4.1 27 35-61 125-151 (181)
28 TIGR00922 nusG transcription t 45.0 42 0.0009 25.8 4.3 27 35-61 118-144 (172)
29 COG1471 RPS4A Ribosomal protei 38.1 30 0.00064 30.1 2.7 25 37-61 174-198 (241)
30 PF01929 Ribosomal_L14e: Ribos 38.0 21 0.00045 25.6 1.5 19 106-124 4-22 (77)
31 PRK08559 nusG transcription an 33.6 89 0.0019 24.2 4.5 28 36-63 94-121 (153)
32 PRK04313 30S ribosomal protein 33.5 39 0.00084 29.1 2.7 24 37-60 172-195 (237)
33 PTZ00118 40S ribosomal protein 32.9 38 0.00081 29.6 2.5 23 37-59 175-197 (262)
34 PLN00036 40S ribosomal protein 32.9 41 0.00088 29.4 2.7 25 37-61 175-199 (261)
35 PTZ00223 40S ribosomal protein 30.2 49 0.0011 29.1 2.8 24 37-60 172-195 (273)
36 PRK09014 rfaH transcriptional 30.0 96 0.0021 23.7 4.1 27 35-61 108-134 (162)
37 PF14789 THDPS_M: Tetrahydrodi 29.5 24 0.00052 22.8 0.6 12 72-83 30-41 (41)
38 PF12268 DUF3612: Protein of u 27.7 64 0.0014 26.8 2.9 14 71-84 89-102 (178)
39 TIGR01955 RfaH transcriptional 26.7 1.2E+02 0.0025 22.9 4.0 27 35-61 107-133 (159)
40 PF05257 CHAP: CHAP domain; I 23.2 1.9E+02 0.0041 20.8 4.4 38 33-77 59-98 (124)
41 cd04822 PA_M28_1_3 PA_M28_1_3: 22.6 1E+02 0.0022 24.4 3.1 13 36-48 44-56 (151)
42 COG5137 Histone chaperone invo 22.1 78 0.0017 27.8 2.5 22 40-61 91-112 (279)
No 1
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=100.00 E-value=6e-61 Score=372.43 Aligned_cols=118 Identities=42% Similarity=0.776 Sum_probs=116.1
Q ss_pred hhcceeccEEEEEecccccCceEEEEEecCCCCCCcccceeEEeccccCchhhhhhhhhhhhhhccccccceEeeeccee
Q psy3013 33 MGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKTLFKKRSKIKPFLKVLNYNHL 112 (151)
Q Consensus 33 m~k~lkpGkVVIvL~GRyAGkKaVivk~~D~Gt~dr~y~~aLVaGIdryP~kVt~~M~kkki~KRskiK~FvK~vN~nHl 112 (151)
|+|||+||+|||||+||||||||||||++||||+||||+|||||||||||++||++||+++++|||++|||||++|||||
T Consensus 1 M~K~~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdryP~kVtk~M~kkki~KRskiK~FvK~vNynHl 80 (134)
T PTZ00471 1 MTKFLKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYPKKVVRGMSKRTIARRSQVGVFLRVVNHKHF 80 (134)
T ss_pred CCccccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeecccchhhhhhccHHHHHHHhccccceEEEeecee
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeceeecCCCCCccCcc-cCCchhhHHHHHHHHhhhccC
Q psy3013 113 MPTRYTYPDMQEKLQPKE-LKDPMKKKKIRFQIRMKFEEK 151 (151)
Q Consensus 113 mpTRY~vdi~~d~~v~~~-fk~~~~kk~akk~~k~~Feer 151 (151)
|||||+||++ +++++++ |+||++|++|++++++.|||+
T Consensus 81 mPTRY~vdi~-~~~v~~~~~~d~~~k~~ar~~~k~~feer 119 (134)
T PTZ00471 81 LPTRYNMDMS-KELRGRINVSDASKKARSKQLVKKLFQAR 119 (134)
T ss_pred cccceeeecc-ccccCHHHhhChHHHHHHHHHHHHHHHHH
Confidence 9999999999 8889999 999999999999999999985
No 2
>KOG3418|consensus
Probab=100.00 E-value=4.3e-52 Score=323.22 Aligned_cols=119 Identities=62% Similarity=0.996 Sum_probs=116.2
Q ss_pred hhcceeccEEEEEecccccCceEEEEEecCCCCCCcccceeEEeccccCchhhhhhhhhhhhhhccccccceEeeeccee
Q psy3013 33 MGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKTLFKKRSKIKPFLKVLNYNHL 112 (151)
Q Consensus 33 m~k~lkpGkVVIvL~GRyAGkKaVivk~~D~Gt~dr~y~~aLVaGIdryP~kVt~~M~kkki~KRskiK~FvK~vN~nHl 112 (151)
|++||+||+||+||+||||||||||||++|||++|+||+|||||||||||++||++||++++++|||+++|+|+||||||
T Consensus 1 m~kflkPgkvv~v~sG~yAg~KaVivk~~Ddg~~d~p~~h~LvAgi~ryP~kvt~~~gkkk~~krsk~k~flKv~ny~hl 80 (136)
T KOG3418|consen 1 MAKFLKPGKVVLVLSGRYAGKKAVIVKNIDDGTEDKPYGHALVAGVDRYPRKVTKSMGKKKLAKRSKVKPFLKVINYNHL 80 (136)
T ss_pred CcccccCCcEEEeecccccCccEEEEeecccCCccCCCceeeeeehhhccccccccccchhhhhcccceeEEEEeecccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeceeecCCCC-CccCcc-cCCchhhHHHHHHHHhhhccC
Q psy3013 113 MPTRYTYPDMQE-KLQPKE-LKDPMKKKKIRFQIRMKFEEK 151 (151)
Q Consensus 113 mpTRY~vdi~~d-~~v~~~-fk~~~~kk~akk~~k~~Feer 151 (151)
|||||++|++++ ..+++| |++|++|..|+++++..|||+
T Consensus 81 MptRy~vdv~~~k~v~~kdv~~~p~~K~~a~~~~k~kfeer 121 (136)
T KOG3418|consen 81 MPTRYTVDVLALKTVINKDVFRDPVKKGTAIKEAKVKFEER 121 (136)
T ss_pred cCcceEEeehhhhccccHHhhhChhhhhhhhhHHHHHHHHH
Confidence 999999999976 669999 999999999999999999985
No 3
>PF01777 Ribosomal_L27e: Ribosomal L27e protein family; InterPro: IPR001141 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein, L27 is found in fungi, plants, algae and vertebrates [, ]. The family has a specific signature at the C terminus.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_a 4A1B_N 4A19_N 4A18_N 4A1D_N 3IZR_a.
Probab=99.93 E-value=2.9e-29 Score=181.84 Aligned_cols=68 Identities=59% Similarity=0.880 Sum_probs=59.8
Q ss_pred hhhhhhhhhhhhhccccccceEeeecceeeeeceeecCCCC-CccCcc-cCCchhhHHHHHHHHhhhccC
Q psy3013 84 KVTKRMNKTLFKKRSKIKPFLKVLNYNHLMPTRYTYPDMQE-KLQPKE-LKDPMKKKKIRFQIRMKFEEK 151 (151)
Q Consensus 84 kVt~~M~kkki~KRskiK~FvK~vN~nHlmpTRY~vdi~~d-~~v~~~-fk~~~~kk~akk~~k~~Feer 151 (151)
+||++||+++++|||+||||||+|||||||||||+||++++ ++|+++ |+||++|++|+++++..|||+
T Consensus 1 KVtk~Mskkk~~KRskiK~FvK~iNynHlmPTRY~vd~~~~k~~v~~~~l~~~~~kk~a~k~~k~~feer 70 (85)
T PF01777_consen 1 KVTKKMSKKKIAKRSKIKPFVKVINYNHLMPTRYSVDIPDDKTVVNKDALKDPSKKKKAKKEIKKKFEER 70 (85)
T ss_dssp ---SSSSSCHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHTT--HHHHHHHHHHHHHHH
T ss_pred CccccccHHHHHHhhcceeeEEEeeccceEeeeeeeechhhhcccCHHHHhChHHHHHHHHHHHHHHHHH
Confidence 69999999999999999999999999999999999999554 779999 999999999999999999985
No 4
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=99.77 E-value=7.5e-20 Score=141.03 Aligned_cols=117 Identities=21% Similarity=0.239 Sum_probs=104.5
Q ss_pred hhcceeccEEEEEecccccCceEEEEEecCCCCCCcccceeEEeccccCchhhhhhhhhhhhhhccccccceEeeeccee
Q psy3013 33 MGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKTLFKKRSKIKPFLKVLNYNHL 112 (151)
Q Consensus 33 m~k~lkpGkVVIvL~GRyAGkKaVivk~~D~Gt~dr~y~~aLVaGIdryP~kVt~~M~kkki~KRskiK~FvK~vN~nHl 112 (151)
|++++.||+||++++|||||+++|||+++||+ .-.+.++++++|+.+++.+++..++-+.+....+-.++.++.++||.
T Consensus 1 ~~~~l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~i~gp~~v~gv~r~r~n~~~l~~t~~~~~~~rg~~~~~v~~~~~a 79 (125)
T COG2163 1 MRASLEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVLITGPKKVKGVPRRRINIKHLEPTDKVIDLVRGASDEKVKKANEA 79 (125)
T ss_pred CCccccCCeEEEEecceeCCceEEEEEEccCC-EEEEeCCccccCCccccccceeeeccceeeeecccccHHHHHHHHHh
Confidence 67899999999999999999999999999999 66788888889999999999999999999999999999999999999
Q ss_pred eeeceeecCCCCCccCcc-cCCchhhHHHHHHHHhhhccC
Q psy3013 113 MPTRYTYPDMQEKLQPKE-LKDPMKKKKIRFQIRMKFEEK 151 (151)
Q Consensus 113 mpTRY~vdi~~d~~v~~~-fk~~~~kk~akk~~k~~Feer 151 (151)
++++|..|.+- +.+..+ ++.+..+-+..+..+..|||+
T Consensus 80 ~~~~~~~~~~~-~~~~~k~~~~~~~~~~r~~~~k~~~~~~ 118 (125)
T COG2163 80 AGVLAKLDKSA-KNLETKKVREPLTDAERFKVMKLVKEER 118 (125)
T ss_pred hhhhccccccc-hhhhhhhhhcccchHHHHHHHHHHHHHH
Confidence 99999998887 444444 888888877777777777764
No 5
>PRK04333 50S ribosomal protein L14e; Validated
Probab=99.24 E-value=1.2e-11 Score=89.55 Aligned_cols=62 Identities=34% Similarity=0.510 Sum_probs=52.1
Q ss_pred ceeccEEEEEecccccCceEEEEEecCCCCCCcccceeEEeccccCchhhhhhhhhhhhhhccccccceEeeecceeeee
Q psy3013 36 IMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKTLFKKRSKIKPFLKVLNYNHLMPT 115 (151)
Q Consensus 36 ~lkpGkVVIvL~GRyAGkKaVivk~~D~Gt~dr~y~~aLVaGIdryP~kVt~~M~kkki~KRskiK~FvK~vN~nHlmpT 115 (151)
-+++|+||++++||++|+.+|||+.+|++ ++||+| |.. |. .+| |..|.+||.+|
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d~~-------~vlVdg----~~~-~~-------~~r-------k~kn~khl~lt 56 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIIDKN-------FVLVTG----PSL-TG-------VKR-------RRCNIKHLEPT 56 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEecCC-------EEEEEC----CCc-CC-------CCC-------eeechHHEEEe
Confidence 47899999999999999999999999998 999999 643 21 112 36899999999
Q ss_pred ceeecCCC
Q psy3013 116 RYTYPDMQ 123 (151)
Q Consensus 116 RY~vdi~~ 123 (151)
...++++.
T Consensus 57 ~~ki~~~~ 64 (84)
T PRK04333 57 DKKVDIEK 64 (84)
T ss_pred eEEEECCC
Confidence 99998754
No 6
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=98.83 E-value=9.3e-09 Score=80.27 Aligned_cols=65 Identities=20% Similarity=0.304 Sum_probs=55.3
Q ss_pred hcceeccEEEEEecccccCceEEEEEecCCCCCCcccceeEEeccccCchhhhhhhhhhhhhhccccccceEeeecceee
Q psy3013 34 GKIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKTLFKKRSKIKPFLKVLNYNHLM 113 (151)
Q Consensus 34 ~k~lkpGkVVIvL~GRyAGkKaVivk~~D~Gt~dr~y~~aLVaGIdryP~kVt~~M~kkki~KRskiK~FvK~vN~nHlm 113 (151)
..|+.+||||++..|.|+||-||||..+|.. .+||-| | ..|. + +| .++|++||.
T Consensus 5 ~rfVEiGRVvli~~Gp~~GKL~vIVDIID~n-------RvLVDG----P-~~tg-V------~R-------q~i~~k~l~ 58 (130)
T PTZ00065 5 KRFVEPGRLCLIQYGPDAGKLCFIVDIVTPT-------RVLVDG----A-FITG-V------KR-------QSIPLKRLK 58 (130)
T ss_pred ccceeeceEEEEecCCCCCCEEEEEEEEcCC-------eEEEeC----C-CcCC-c------ce-------eEEeccceE
Confidence 3689999999999999999999999999998 899999 8 3332 1 12 269999999
Q ss_pred eeceeecCCCC
Q psy3013 114 PTRYTYPDMQE 124 (151)
Q Consensus 114 pTRY~vdi~~d 124 (151)
+|.+.++|+-.
T Consensus 59 LT~~~v~i~r~ 69 (130)
T PTZ00065 59 LTDEKIKINRG 69 (130)
T ss_pred EccEEEecCCC
Confidence 99999999853
No 7
>KOG3421|consensus
Probab=96.22 E-value=0.0063 Score=48.31 Aligned_cols=64 Identities=25% Similarity=0.396 Sum_probs=53.8
Q ss_pred hcceeccEEEEEecccccCceEEEEEecCCCCCCcccceeEEeccccCchhhhhhhhhhhhhhccccccceEeeecceee
Q psy3013 34 GKIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKTLFKKRSKIKPFLKVLNYNHLM 113 (151)
Q Consensus 34 ~k~lkpGkVVIvL~GRyAGkKaVivk~~D~Gt~dr~y~~aLVaGIdryP~kVt~~M~kkki~KRskiK~FvK~vN~nHlm 113 (151)
+.+...|+|+++..|-|+||=++||..+|+. .+||-| |+-.-.+ +.+|++-+.
T Consensus 4 ~r~veVGrva~v~~G~~~GkL~AIVdviDqn-------r~lvDG----p~t~v~r----------------q~~~~~~~~ 56 (136)
T KOG3421|consen 4 KRFVEVGRVALVSFGPDAGKLVAIVDVIDQN-------RALVDG----PCTGVPR----------------QAMNLKCLQ 56 (136)
T ss_pred hhhhhcceEEEEEecCCCceEEEEEEeecch-------hhhccC----cccccch----------------hhcchhhee
Confidence 4578899999999999999999999999997 899999 6432110 268999999
Q ss_pred eeceeecCCCC
Q psy3013 114 PTRYTYPDMQE 124 (151)
Q Consensus 114 pTRY~vdi~~d 124 (151)
-|-|.++++..
T Consensus 57 LT~~~~kfp~g 67 (136)
T KOG3421|consen 57 LTDFVLKFPRG 67 (136)
T ss_pred eeeeeEecccC
Confidence 99999999875
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=95.93 E-value=0.009 Score=35.62 Aligned_cols=26 Identities=23% Similarity=0.443 Sum_probs=24.0
Q ss_pred ccEEEEEecccccCceEEEEEecCCC
Q psy3013 39 AGKIVLVLSGRYAGRKAVVLKTYDDG 64 (151)
Q Consensus 39 pGkVVIvL~GRyAGkKaVivk~~D~G 64 (151)
+|..|.|++|+|+|+.+.|++..++.
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 68899999999999999999988876
No 9
>PF01159 Ribosomal_L6e: Ribosomal protein L6e ; InterPro: IPR000915 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes mammalian ribosomal protein L6 (L6 was previously known as TAX-responsive enhancer element binding protein 107); Caenorhabditis elegans ribosomal protein L6 (R151.3); Saccharomyces cerevisiae (Baker's yeast) ribosomal protein YL16A/YL16B; and Mesembryanthemum crystallinum (Common ice plant) ribosomal protein YL16-like. These proteins have 175 (yeast) to 287 (mammalian) amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A18_E 4A1D_E 4A19_E 4A1B_E 3IZR_G 3O58_F 3O5H_F 3IZS_G.
Probab=95.73 E-value=0.0023 Score=48.61 Aligned_cols=47 Identities=17% Similarity=0.014 Sum_probs=32.9
Q ss_pred cceEeeecceeeeeceeecCCC-C--CccCcc-cCCchhhHHHHHHHHhhhc
Q psy3013 102 PFLKVLNYNHLMPTRYTYPDMQ-E--KLQPKE-LKDPMKKKKIRFQIRMKFE 149 (151)
Q Consensus 102 ~FvK~vN~nHlmpTRY~vdi~~-d--~~v~~~-fk~~~~kk~akk~~k~~Fe 149 (151)
+.+++||++|+++|+..||++. + +.++++ |+.+.+++ .++....+|+
T Consensus 4 VPLRRVnQ~yVIATSTkvDis~v~ip~~~~D~YF~~~~~~k-~k~~e~~~f~ 54 (108)
T PF01159_consen 4 VPLRRVNQAYVIATSTKVDISGVKIPEKIDDAYFKRKKKKK-KKKGEGDFFA 54 (108)
T ss_dssp --SEEESSCCCEECSCESCHCCHHH-CCTTGSSSCHCCCCH-HHHHHCHCCH
T ss_pred CcceecccceEEEEeeEEeccccchhhccchHHHHhhhhcc-ccccHHHHHh
Confidence 3466999999999999999983 3 668888 87666333 3344555554
No 10
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=95.58 E-value=0.019 Score=31.92 Aligned_cols=26 Identities=27% Similarity=0.521 Sum_probs=23.2
Q ss_pred eeccEEEEEecccccCceEEEEEecC
Q psy3013 37 MKAGKIVLVLSGRYAGRKAVVLKTYD 62 (151)
Q Consensus 37 lkpGkVVIvL~GRyAGkKaVivk~~D 62 (151)
+++|..|.|+.|.|+|..++|++...
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 57899999999999999999998653
No 11
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=93.27 E-value=0.14 Score=37.02 Aligned_cols=42 Identities=29% Similarity=0.405 Sum_probs=35.5
Q ss_pred hhcceeccEEEEEecccccCceEEEEEecCCCCCCcccceeEEecccc
Q psy3013 33 MGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDR 80 (151)
Q Consensus 33 m~k~lkpGkVVIvL~GRyAGkKaVivk~~D~Gt~dr~y~~aLVaGIdr 80 (151)
|.--+++|--|.|++|++.|+.+.|++.+.+.. .++|-|++.
T Consensus 5 ~~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~------~V~Vegvn~ 46 (83)
T CHL00141 5 KKMHVKIGDTVKIISGSDKGKIGEVLKIIKKSN------KVIVKGINI 46 (83)
T ss_pred eeCcccCCCEEEEeEcCCCCcEEEEEEEEcCCC------EEEEcCcEE
Confidence 334789999999999999999999999976653 699999765
No 12
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=92.59 E-value=0.22 Score=38.72 Aligned_cols=39 Identities=21% Similarity=0.360 Sum_probs=34.0
Q ss_pred ceeccEEEEEecccccCceEEEEEecCCCCCCcccceeEEecccc
Q psy3013 36 IMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDR 80 (151)
Q Consensus 36 ~lkpGkVVIvL~GRyAGkKaVivk~~D~Gt~dr~y~~aLVaGIdr 80 (151)
-++.|-.|.|++|.+.|+.+-|++...+.. .++|-||+.
T Consensus 45 ~IkkGD~V~VisG~~KGk~GkV~~V~~~~~------~V~VeGvn~ 83 (120)
T PRK01191 45 PVRKGDTVKVMRGDFKGEEGKVVEVDLKRG------RIYVEGVTV 83 (120)
T ss_pred eEeCCCEEEEeecCCCCceEEEEEEEcCCC------EEEEeCcEE
Confidence 489999999999999999999999976542 699999774
No 13
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=92.58 E-value=0.21 Score=35.58 Aligned_cols=40 Identities=25% Similarity=0.422 Sum_probs=34.5
Q ss_pred ceeccEEEEEecccccCceEEEEEecCCCCCCcccceeEEeccccC
Q psy3013 36 IMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRY 81 (151)
Q Consensus 36 ~lkpGkVVIvL~GRyAGkKaVivk~~D~Gt~dr~y~~aLVaGIdry 81 (151)
-+++|--|+|++|++.|+.+.|++.+.+.. .++|-|++..
T Consensus 6 ~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~------~V~Vegvn~~ 45 (76)
T PRK12281 6 KVKKGDMVKVIAGDDKGKTGKVLAVLPKKN------RVIVEGVKIA 45 (76)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCC------EEEEcCcEEE
Confidence 588999999999999999999999876542 6999997764
No 14
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=92.04 E-value=0.26 Score=36.87 Aligned_cols=41 Identities=27% Similarity=0.526 Sum_probs=35.1
Q ss_pred ceeccEEEEEecccccCceEEEEEecCCCCCCcccceeEEeccccCc
Q psy3013 36 IMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYP 82 (151)
Q Consensus 36 ~lkpGkVVIvL~GRyAGkKaVivk~~D~Gt~dr~y~~aLVaGIdryP 82 (151)
-+++|--|.|++|++.|+.+.|++.+.+.. .++|-||+.-.
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~------~V~Vegvn~~k 44 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPKKN------KVIVEGVNIVK 44 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCC------EEEEcCcEEEE
Confidence 578999999999999999999999987653 69999987543
No 15
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=91.45 E-value=0.31 Score=36.53 Aligned_cols=41 Identities=29% Similarity=0.501 Sum_probs=34.6
Q ss_pred ceeccEEEEEecccccCceEEEEEecCCCCCCcccceeEEeccccCc
Q psy3013 36 IMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYP 82 (151)
Q Consensus 36 ~lkpGkVVIvL~GRyAGkKaVivk~~D~Gt~dr~y~~aLVaGIdryP 82 (151)
-++.|--|.|++|+++|+.+.|++.+.+.. .++|-|++.-.
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~------~V~VegvN~~k 43 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKTN------KVIVEGVNMVK 43 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCC------EEEECCcEEEE
Confidence 478899999999999999999999986652 79999986543
No 16
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=90.89 E-value=0.38 Score=38.48 Aligned_cols=40 Identities=23% Similarity=0.291 Sum_probs=34.0
Q ss_pred ceeccEEEEEecccccCceEEEEEecCCCCCCcccceeEEeccccC
Q psy3013 36 IMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRY 81 (151)
Q Consensus 36 ~lkpGkVVIvL~GRyAGkKaVivk~~D~Gt~dr~y~~aLVaGIdry 81 (151)
-++-|-.|+|++|.++|+.+-|++.+.... .++|-||+.-
T Consensus 46 ~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~------~ViVEgvn~~ 85 (143)
T PTZ00194 46 PVRKDDEVMVVRGHHKGREGKVTAVYRKKW------VIHIEKITRE 85 (143)
T ss_pred eeecCCEEEEecCCCCCCceEEEEEEcCCC------EEEEeCeEEE
Confidence 488999999999999999999999975542 7999997643
No 17
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=90.12 E-value=0.53 Score=36.13 Aligned_cols=39 Identities=21% Similarity=0.363 Sum_probs=33.4
Q ss_pred ceeccEEEEEecccccCceEEEEEecCCCCCCcccceeEEecccc
Q psy3013 36 IMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDR 80 (151)
Q Consensus 36 ~lkpGkVVIvL~GRyAGkKaVivk~~D~Gt~dr~y~~aLVaGIdr 80 (151)
-++-|--|.|++|.++|+.+.|++...... .++|-||..
T Consensus 41 ~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~------~V~Vegvn~ 79 (114)
T TIGR01080 41 PVRKGDKVRIMRGDFKGHEGKVSKVDLKRY------RIYVEGVTK 79 (114)
T ss_pred eeecCCEEEEecCCCCCCEEEEEEEEcCCC------EEEEcCeEE
Confidence 588999999999999999999999975442 699999773
No 18
>KOG1694|consensus
Probab=89.94 E-value=0.17 Score=40.63 Aligned_cols=23 Identities=17% Similarity=0.453 Sum_probs=18.9
Q ss_pred hHhHhhhhhhcceeccEEEEEec
Q psy3013 25 LFCRHISKMGKIMKAGKIVLVLS 47 (151)
Q Consensus 25 ~f~~~~~~m~k~lkpGkVVIvL~ 47 (151)
++..+.+++++.+.||+|+|+|+
T Consensus 22 ~~~~~~~k~r~~l~~gtvliil~ 44 (152)
T KOG1694|consen 22 RYSAKPSKLRASLTPGTVLIILA 44 (152)
T ss_pred cccccchhhhhccCCCeeEEEec
Confidence 34445577899999999999998
No 19
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=84.23 E-value=1.7 Score=33.07 Aligned_cols=39 Identities=28% Similarity=0.476 Sum_probs=33.1
Q ss_pred ceeccEEEEEecccccCceEEEEEecCCCCCCcccceeEEeccccCc
Q psy3013 36 IMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYP 82 (151)
Q Consensus 36 ~lkpGkVVIvL~GRyAGkKaVivk~~D~Gt~dr~y~~aLVaGIdryP 82 (151)
-++-|-.|+|++|.+.|+.+.|++.+... ++|-|++.--
T Consensus 4 ~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~--------V~VEGvnv~k 42 (104)
T COG0198 4 KVKKGDTVKVIAGKDKGKEGKVLKVLPKK--------VVVEGVNVVK 42 (104)
T ss_pred ceecCCEEEEEecCCCCcceEEEEEecCe--------EEEECcEEEE
Confidence 46788999999999999999999998663 9999976543
No 20
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=77.48 E-value=1.6 Score=34.13 Aligned_cols=53 Identities=30% Similarity=0.395 Sum_probs=33.9
Q ss_pred cCceEEEEEecCCCCC-------CcccceeEEeccccCchhhhhhhhhhhhhhccccccceEeeecceeeeeceeecCCC
Q psy3013 51 AGRKAVVLKTYDDGTA-------DKQYGHALVAGIDRYPRKVTKRMNKTLFKKRSKIKPFLKVLNYNHLMPTRYTYPDMQ 123 (151)
Q Consensus 51 AGkKaVivk~~D~Gt~-------dr~y~~aLVaGIdryP~kVt~~M~kkki~KRskiK~FvK~vN~nHlmpTRY~vdi~~ 123 (151)
.|+=+|+++-=+-|.. |.. .++++| |..++. +-.+.+|++|++||...++++-
T Consensus 7 ~GrVvvv~~GR~aGkk~VIv~~iDd~--~v~i~g----p~~v~g--------------v~r~r~n~~~l~~t~~~~~~~r 66 (125)
T COG2163 7 VGRVVVVTAGRFAGKKVVIVKIIDDN--FVLITG----PKKVKG--------------VPRRRINIKHLEPTDKVIDLVR 66 (125)
T ss_pred CCeEEEEecceeCCceEEEEEEccCC--EEEEeC----CccccC--------------Cccccccceeeeccceeeeecc
Confidence 4666666666555532 111 455556 776664 2234689999999999888764
No 21
>KOG1999|consensus
Probab=65.16 E-value=5.7 Score=40.32 Aligned_cols=43 Identities=23% Similarity=0.339 Sum_probs=34.5
Q ss_pred hhhhhhHhHhhhhhhcceeccEEEEEecccccCceEEEEEecC
Q psy3013 20 SIFPFLFCRHISKMGKIMKAGKIVLVLSGRYAGRKAVVLKTYD 62 (151)
Q Consensus 20 ~~~~~~f~~~~~~m~k~lkpGkVVIvL~GRyAGkKaVivk~~D 62 (151)
.-+.=||--..+.++|.++||-.|=|++|||.|.-.+||+...
T Consensus 443 e~l~~pl~~~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvrVe~ 485 (1024)
T KOG1999|consen 443 EDLKGPLEVPASELRKYFEPGDHVKVIAGRYEGDTGLVVRVEQ 485 (1024)
T ss_pred ccCCCccccchHhhhhhccCCCeEEEEeccccCCcceEEEEeC
Confidence 3333444445566899999999999999999999999998765
No 22
>PF13234 rRNA_proc-arch: rRNA-processing arch domain; PDB: 4A4K_E 4A4Z_A 2XGJ_B 3L9O_A.
Probab=59.00 E-value=9.2 Score=31.66 Aligned_cols=31 Identities=19% Similarity=0.214 Sum_probs=25.1
Q ss_pred hhcceeccEEEEEecccccCceEEEEEecCC
Q psy3013 33 MGKIMKAGKIVLVLSGRYAGRKAVVLKTYDD 63 (151)
Q Consensus 33 m~k~lkpGkVVIvL~GRyAGkKaVivk~~D~ 63 (151)
..+||.|||||.|-.|-+...=||||+....
T Consensus 69 ~~~fL~~GRlV~v~~~~~~~~wgvvv~~~~~ 99 (268)
T PF13234_consen 69 CLPFLQPGRLVVVRDGDRDFGWGVVVNFAKK 99 (268)
T ss_dssp HHHHS-TTEEEEEEETTCEEEEEEEEEEEE-
T ss_pred HHHhCCCCCEEEEecCCCccceeEEEecccc
Confidence 5679999999999998888889999976543
No 23
>KOG1708|consensus
Probab=50.21 E-value=22 Score=30.63 Aligned_cols=73 Identities=19% Similarity=0.268 Sum_probs=50.8
Q ss_pred ceeccEEEEEecccccCceEEEEEecCCCCCCcccceeEEeccccCchhhhhhhhhhhhhhccc-cc---c-----ceEe
Q psy3013 36 IMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQYGHALVAGIDRYPRKVTKRMNKTLFKKRSK-IK---P-----FLKV 106 (151)
Q Consensus 36 ~lkpGkVVIvL~GRyAGkKaVivk~~D~Gt~dr~y~~aLVaGIdryP~kVt~~M~kkki~KRsk-iK---~-----FvK~ 106 (151)
.+.+|--|=||.||-+||-+.|++.+-+.+ -++|-|++-.= +.||..+---+-- ++ | =|+.
T Consensus 72 ~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s------~VvV~gln~k~----r~~gsekeg~pgtivk~EaPlhvsk~VmL 141 (236)
T KOG1708|consen 72 HFFFGDTVEVLVGKDKGKQGEVTQVIRHRS------WVVVKGLNTKY----RHMGSEKEGEPGTIVKSEAPLHVSKQVML 141 (236)
T ss_pred eEecCCEEEEEecccCCccceEEEEeecCc------eEEEcccchhh----hhhcccccCCCceEEeecCCceecceeEE
Confidence 368899999999999999999999998874 69999977433 4455443311111 00 1 2677
Q ss_pred eecceeeeecee
Q psy3013 107 LNYNHLMPTRYT 118 (151)
Q Consensus 107 vN~nHlmpTRY~ 118 (151)
|+.+-.-||+.-
T Consensus 142 vdp~d~q~te~~ 153 (236)
T KOG1708|consen 142 VDPEDDQPTEVE 153 (236)
T ss_pred ECccccCCceee
Confidence 778877788643
No 24
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=49.03 E-value=37 Score=25.61 Aligned_cols=28 Identities=32% Similarity=0.644 Sum_probs=24.9
Q ss_pred cceeccEEEEEecccccCceEEEEEecC
Q psy3013 35 KIMKAGKIVLVLSGRYAGRKAVVLKTYD 62 (151)
Q Consensus 35 k~lkpGkVVIvL~GRyAGkKaVivk~~D 62 (151)
..+++|-.|.|..|-|+|-.|+|++.-.
T Consensus 85 ~~~~~Gd~V~I~~GPf~G~~g~v~~~d~ 112 (145)
T TIGR00405 85 ESIKKGDIVEIISGPFKGERAKVIRVDE 112 (145)
T ss_pred cccCCCCEEEEeecCCCCCeEEEEEEcC
Confidence 3589999999999999999999998743
No 25
>KOG3418|consensus
Probab=47.97 E-value=2.2 Score=34.04 Aligned_cols=52 Identities=21% Similarity=0.202 Sum_probs=47.5
Q ss_pred hhcceeccEEEEEecccccCceEEEEEecCCCCCCcc----cceeEEeccccCchh
Q psy3013 33 MGKIMKAGKIVLVLSGRYAGRKAVVLKTYDDGTADKQ----YGHALVAGIDRYPRK 84 (151)
Q Consensus 33 m~k~lkpGkVVIvL~GRyAGkKaVivk~~D~Gt~dr~----y~~aLVaGIdryP~k 84 (151)
.+.+|.++-.|-+++=.+-+-++|.-++.+-++.-.+ |.+++-+|+++++..
T Consensus 77 y~hlMptRy~vdv~~~k~v~~kdv~~~p~~K~~a~~~~k~kfeer~k~gkn~wff~ 132 (136)
T KOG3418|consen 77 YNHLMPTRYTVDVLALKTVINKDVFRDPVKKGTAIKEAKVKFEERYKTGKNKWFFT 132 (136)
T ss_pred cccccCcceEEeehhhhccccHHhhhChhhhhhhhhHHHHHHHHHHHhCccccccc
Confidence 4567889999999999999999999999999999888 999999999999964
No 26
>PF15591 Imm17: Immunity protein 17
Probab=46.32 E-value=38 Score=24.64 Aligned_cols=27 Identities=19% Similarity=0.417 Sum_probs=19.4
Q ss_pred ccccCceEEEEEecCCCCCCcccceeEEe
Q psy3013 48 GRYAGRKAVVLKTYDDGTADKQYGHALVA 76 (151)
Q Consensus 48 GRyAGkKaVivk~~D~Gt~dr~y~~aLVa 76 (151)
-+++|++.|||--++++. .-|++.+++
T Consensus 21 ~ei~Gk~GVVlG~SeeD~--~~~gY~Vli 47 (74)
T PF15591_consen 21 AEIWGKRGVVLGISEEDG--GNFGYSVLI 47 (74)
T ss_pred hhhcCceeEEEEEecCCC--cEEEEEEEE
Confidence 489999999997776553 356665543
No 27
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=46.05 E-value=36 Score=26.21 Aligned_cols=27 Identities=22% Similarity=0.322 Sum_probs=24.5
Q ss_pred cceeccEEEEEecccccCceEEEEEec
Q psy3013 35 KIMKAGKIVLVLSGRYAGRKAVVLKTY 61 (151)
Q Consensus 35 k~lkpGkVVIvL~GRyAGkKaVivk~~ 61 (151)
..+++|.-|-|++|-++|-.+.|++..
T Consensus 125 ~~~~~Gd~VrI~~GPf~G~~g~v~~i~ 151 (181)
T PRK05609 125 VDFEVGEMVRVIDGPFADFNGTVEEVD 151 (181)
T ss_pred cCCCCCCEEEEeccCCCCCEEEEEEEe
Confidence 457899999999999999999999975
No 28
>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=45.01 E-value=42 Score=25.78 Aligned_cols=27 Identities=22% Similarity=0.187 Sum_probs=24.4
Q ss_pred cceeccEEEEEecccccCceEEEEEec
Q psy3013 35 KIMKAGKIVLVLSGRYAGRKAVVLKTY 61 (151)
Q Consensus 35 k~lkpGkVVIvL~GRyAGkKaVivk~~ 61 (151)
..+++|.-|.|..|-++|-.++|++..
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~ 144 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVD 144 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEc
Confidence 347899999999999999999999964
No 29
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=38.08 E-value=30 Score=30.07 Aligned_cols=25 Identities=28% Similarity=0.531 Sum_probs=22.1
Q ss_pred eeccEEEEEecccccCceEEEEEec
Q psy3013 37 MKAGKIVLVLSGRYAGRKAVVLKTY 61 (151)
Q Consensus 37 lkpGkVVIvL~GRyAGkKaVivk~~ 61 (151)
+.+|..+++..||++|+-+.|++..
T Consensus 174 fe~g~~~~vtgG~h~G~~G~I~~I~ 198 (241)
T COG1471 174 FEEGALVYVTGGRHVGRVGTIVEIE 198 (241)
T ss_pred cCCCcEEEEECCccccceEEEEEEE
Confidence 5689999999999999999998653
No 30
>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=37.95 E-value=21 Score=25.61 Aligned_cols=19 Identities=21% Similarity=0.217 Sum_probs=17.3
Q ss_pred eeecceeeeeceeecCCCC
Q psy3013 106 VLNYNHLMPTRYTYPDMQE 124 (151)
Q Consensus 106 ~vN~nHlmpTRY~vdi~~d 124 (151)
+||++||.+|.|.++|+-.
T Consensus 4 ~i~~k~l~LT~~~i~i~r~ 22 (77)
T PF01929_consen 4 VINLKRLHLTDFVIKIPRG 22 (77)
T ss_dssp EEECTSSEEEEEETTTTTT
T ss_pred eeeccceEeecEEEeccCC
Confidence 6999999999999999864
No 31
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=33.57 E-value=89 Score=24.19 Aligned_cols=28 Identities=32% Similarity=0.571 Sum_probs=25.0
Q ss_pred ceeccEEEEEecccccCceEEEEEecCC
Q psy3013 36 IMKAGKIVLVLSGRYAGRKAVVLKTYDD 63 (151)
Q Consensus 36 ~lkpGkVVIvL~GRyAGkKaVivk~~D~ 63 (151)
-+++|-.|-|..|-|+|-.|.|++...+
T Consensus 94 ~~~~G~~V~I~~Gpf~g~~g~V~~vd~~ 121 (153)
T PRK08559 94 GIKEGDIVELIAGPFKGEKARVVRVDES 121 (153)
T ss_pred CCCCCCEEEEeccCCCCceEEEEEEcCC
Confidence 3889999999999999999999987654
No 32
>PRK04313 30S ribosomal protein S4e; Validated
Probab=33.50 E-value=39 Score=29.06 Aligned_cols=24 Identities=13% Similarity=0.426 Sum_probs=21.7
Q ss_pred eeccEEEEEecccccCceEEEEEe
Q psy3013 37 MKAGKIVLVLSGRYAGRKAVVLKT 60 (151)
Q Consensus 37 lkpGkVVIvL~GRyAGkKaVivk~ 60 (151)
+.+|..|+|..|+.+|+=++|...
T Consensus 172 fe~G~l~~itgG~n~GriG~I~~i 195 (237)
T PRK04313 172 FEEGNLAIITGGKHVGEIGKIKEI 195 (237)
T ss_pred cCCCCEEEEECCeeeeeEEEEEEE
Confidence 568999999999999999998865
No 33
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=32.94 E-value=38 Score=29.59 Aligned_cols=23 Identities=22% Similarity=0.616 Sum_probs=21.3
Q ss_pred eeccEEEEEecccccCceEEEEE
Q psy3013 37 MKAGKIVLVLSGRYAGRKAVVLK 59 (151)
Q Consensus 37 lkpGkVVIvL~GRyAGkKaVivk 59 (151)
+.+|.+|+|..|+.+|+=++|+.
T Consensus 175 fe~G~l~~vtgG~n~GriG~I~~ 197 (262)
T PTZ00118 175 FEVGNLVMITGGHNVGRVGTIVS 197 (262)
T ss_pred cCCCCEEEEECCeeceeEEEEEE
Confidence 56899999999999999999987
No 34
>PLN00036 40S ribosomal protein S4; Provisional
Probab=32.93 E-value=41 Score=29.35 Aligned_cols=25 Identities=32% Similarity=0.571 Sum_probs=21.9
Q ss_pred eeccEEEEEecccccCceEEEEEec
Q psy3013 37 MKAGKIVLVLSGRYAGRKAVVLKTY 61 (151)
Q Consensus 37 lkpGkVVIvL~GRyAGkKaVivk~~ 61 (151)
+.+|..|+|..|+.+|+=++|+...
T Consensus 175 fe~G~l~~vtgG~n~GrvG~I~~i~ 199 (261)
T PLN00036 175 FDVGNLVMVTGGRNRGRVGVIKNRE 199 (261)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEE
Confidence 4689999999999999999987554
No 35
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=30.24 E-value=49 Score=29.10 Aligned_cols=24 Identities=29% Similarity=0.529 Sum_probs=21.7
Q ss_pred eeccEEEEEecccccCceEEEEEe
Q psy3013 37 MKAGKIVLVLSGRYAGRKAVVLKT 60 (151)
Q Consensus 37 lkpGkVVIvL~GRyAGkKaVivk~ 60 (151)
+.+|.+|+|..|+.+|+=++|...
T Consensus 172 fe~G~l~~vtgG~n~GriG~I~~i 195 (273)
T PTZ00223 172 NRNGKVVMVTGGANRGRIGEIVSI 195 (273)
T ss_pred cCCCCEEEEECCeeceeEEEEEEE
Confidence 468999999999999999998766
No 36
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=29.95 E-value=96 Score=23.67 Aligned_cols=27 Identities=22% Similarity=0.415 Sum_probs=24.0
Q ss_pred cceeccEEEEEecccccCceEEEEEec
Q psy3013 35 KIMKAGKIVLVLSGRYAGRKAVVLKTY 61 (151)
Q Consensus 35 k~lkpGkVVIvL~GRyAGkKaVivk~~ 61 (151)
..+++|.-|.|..|-++|--++|++.-
T Consensus 108 ~~~~~G~~V~I~~Gp~~g~eg~v~~~~ 134 (162)
T PRK09014 108 ETPKPGDKVIITEGAFEGLQAIYTEPD 134 (162)
T ss_pred cCCCCCCEEEEecCCCCCcEEEEEEeC
Confidence 357899999999999999999998864
No 37
>PF14789 THDPS_M: Tetrahydrodipicolinate N-succinyltransferase middle; PDB: 3R5A_F 3R5B_A 3R5C_B 3R5D_D 3FSY_C 3FSX_A 2RIJ_A.
Probab=29.51 E-value=24 Score=22.82 Aligned_cols=12 Identities=33% Similarity=0.720 Sum_probs=7.4
Q ss_pred eeEEeccccCch
Q psy3013 72 HALVAGIDRYPR 83 (151)
Q Consensus 72 ~aLVaGIdryP~ 83 (151)
++-|.|||++|+
T Consensus 30 ~~~V~~VDKFPR 41 (41)
T PF14789_consen 30 PLTVYSVDKFPR 41 (41)
T ss_dssp ---EEEEESS-B
T ss_pred CcEEEEEcCCCC
Confidence 688999999996
No 38
>PF12268 DUF3612: Protein of unknown function (DUF3612); InterPro: IPR022055 This domain family is found in bacteria, and is approximately 180 amino acids in length. The family is found in association with PF01381 from PFAM.
Probab=27.73 E-value=64 Score=26.77 Aligned_cols=14 Identities=50% Similarity=0.703 Sum_probs=12.0
Q ss_pred ceeEEeccccCchh
Q psy3013 71 GHALVAGIDRYPRK 84 (151)
Q Consensus 71 ~~aLVaGIdryP~k 84 (151)
+|+|-||||--|--
T Consensus 89 ~hVLCaGIDLNPAi 102 (178)
T PF12268_consen 89 NHVLCAGIDLNPAI 102 (178)
T ss_pred ceeEEecccCCHhH
Confidence 59999999999863
No 39
>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=26.71 E-value=1.2e+02 Score=22.86 Aligned_cols=27 Identities=26% Similarity=0.405 Sum_probs=24.2
Q ss_pred cceeccEEEEEecccccCceEEEEEec
Q psy3013 35 KIMKAGKIVLVLSGRYAGRKAVVLKTY 61 (151)
Q Consensus 35 k~lkpGkVVIvL~GRyAGkKaVivk~~ 61 (151)
..+++|--|.|..|=++|--++|++.-
T Consensus 107 ~~~~~G~~V~V~~GPf~g~~g~v~~~~ 133 (159)
T TIGR01955 107 TLPYKGDKVRITDGAFAGFEAIFLEPD 133 (159)
T ss_pred cCCCCCCEEEEeccCCCCcEEEEEEEC
Confidence 348899999999999999999999963
No 40
>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=23.22 E-value=1.9e+02 Score=20.78 Aligned_cols=38 Identities=32% Similarity=0.325 Sum_probs=26.5
Q ss_pred hhcceeccEEEEE--ecccccCceEEEEEecCCCCCCcccceeEEec
Q psy3013 33 MGKIMKAGKIVLV--LSGRYAGRKAVVLKTYDDGTADKQYGHALVAG 77 (151)
Q Consensus 33 m~k~lkpGkVVIv--L~GRyAGkKaVivk~~D~Gt~dr~y~~aLVaG 77 (151)
-....+||-|++. ..+...|+=|||.+..++| .+.+..
T Consensus 59 ~~~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~-------~i~v~e 98 (124)
T PF05257_consen 59 TGSTPQPGDIVVWDSGSGGGYGHVAIVESVNDGG-------TITVIE 98 (124)
T ss_dssp ECS---TTEEEEEEECTTTTT-EEEEEEEE-TTS-------EEEEEE
T ss_pred cCcccccceEEEeccCCCCCCCeEEEEEEECCCC-------EEEEEE
Confidence 3556899999998 6777889999999997777 577765
No 41
>cd04822 PA_M28_1_3 PA_M28_1_3: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 3. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subgroups; relatively litt
Probab=22.56 E-value=1e+02 Score=24.45 Aligned_cols=13 Identities=54% Similarity=0.634 Sum_probs=10.5
Q ss_pred ceeccEEEEEecc
Q psy3013 36 IMKAGKIVLVLSG 48 (151)
Q Consensus 36 ~lkpGkVVIvL~G 48 (151)
+=-.|||||+++|
T Consensus 44 iDVkGKIVlv~~g 56 (151)
T cd04822 44 LDVKGKIVLVLRH 56 (151)
T ss_pred CCCCCeEEEEEcC
Confidence 3357999999987
No 42
>COG5137 Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]
Probab=22.08 E-value=78 Score=27.81 Aligned_cols=22 Identities=41% Similarity=0.661 Sum_probs=18.7
Q ss_pred cEEEEEecccccCceEEEEEec
Q psy3013 40 GKIVLVLSGRYAGRKAVVLKTY 61 (151)
Q Consensus 40 GkVVIvL~GRyAGkKaVivk~~ 61 (151)
|--||+|+|||.|+--|-|--+
T Consensus 91 gvTvILlsc~Y~g~eFvRvGYy 112 (279)
T COG5137 91 GVTVILLSCRYKGQEFVRVGYY 112 (279)
T ss_pred ceeEEEEEEeecCceeEEEEEE
Confidence 7789999999999998887443
Done!