Query gi|254780262|ref|YP_003064675.1| 30S ribosomal protein S10 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 104
No_of_seqs 117 out of 758
Neff 5.8
Searched_HMMs 39220
Date Tue May 24 08:43:14 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780262.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01049 rpsJ_bact ribosomal 100.0 0 0 305.5 11.3 99 6-104 1-99 (99)
2 CHL00135 rps10 ribosomal prote 100.0 2.2E-42 0 268.2 13.2 103 2-104 3-105 (106)
3 PRK00596 rpsJ 30S ribosomal pr 100.0 2E-41 0 262.5 13.1 101 4-104 2-102 (102)
4 COG0051 RpsJ Ribosomal protein 100.0 7.1E-40 1.8E-44 253.5 12.6 101 4-104 2-102 (104)
5 PTZ00039 40S ribosomal protein 100.0 3.4E-39 8.7E-44 249.5 12.2 103 1-104 12-115 (115)
6 PRK12271 rps10p 30S ribosomal 100.0 1.1E-38 2.7E-43 246.7 12.5 98 6-104 2-100 (102)
7 pfam00338 Ribosomal_S10 Riboso 100.0 2.1E-35 5.3E-40 227.5 11.6 97 8-104 1-97 (97)
8 TIGR01046 S10_Arc_S20_Euk ribo 100.0 3.3E-31 8.4E-36 203.0 9.0 98 6-104 1-99 (99)
9 KOG3321 consensus 99.9 4.4E-28 1.1E-32 184.8 0.8 97 7-103 48-147 (175)
10 KOG0900 consensus 99.8 8.4E-20 2.1E-24 136.5 5.4 100 4-104 18-118 (121)
11 KOG4060 consensus 98.5 7.2E-07 1.8E-11 61.0 7.5 94 8-103 55-151 (176)
12 PRK05580 primosome assembly pr 56.3 18 0.00047 17.8 7.9 78 8-104 608-694 (699)
13 pfam05435 Phi-29_GP3 Phi-29 DN 49.4 20 0.00052 17.6 3.3 38 9-46 6-47 (266)
14 PHA00490 terminal protein 41.9 31 0.0008 16.5 3.4 38 9-46 6-47 (266)
15 pfam04743 consensus 33.3 18 0.00047 17.8 1.0 31 70-100 14-45 (160)
16 PRK00140 rplK 50S ribosomal pr 33.0 6.9 0.00018 20.3 -1.3 28 20-51 35-62 (142)
17 KOG3473 consensus 31.1 42 0.0011 15.7 2.5 44 4-47 54-98 (112)
18 COG2121 Uncharacterized protei 26.4 48 0.0012 15.4 2.1 20 52-71 153-172 (214)
19 TIGR01348 PDHac_trf_long pyruv 26.2 41 0.0011 15.8 1.8 20 14-33 625-646 (655)
20 TIGR01632 L11_bact ribosomal p 25.1 15 0.00037 18.4 -0.7 31 10-40 112-144 (144)
21 COG4784 Putative Zn-dependent 24.7 61 0.0016 14.8 4.3 68 15-89 61-128 (479)
22 KOG2934 consensus 22.7 14 0.00036 18.5 -1.2 21 39-59 127-147 (204)
23 pfam04533 Herpes_U44 Herpes vi 22.4 41 0.001 15.8 1.1 39 55-100 13-51 (211)
24 PRK01143 rpl11p 50S ribosomal 20.5 25 0.00063 17.1 -0.3 26 20-50 31-56 (163)
25 TIGR00004 TIGR00004 endoribonu 20.4 57 0.0014 15.0 1.5 34 71-104 91-125 (129)
26 COG0080 RplK Ribosomal protein 20.3 36 0.00091 16.1 0.5 27 20-51 34-60 (141)
27 pfam02399 Herpes_ori_bp Origin 20.1 68 0.0017 14.5 1.9 31 36-66 32-66 (829)
No 1
>TIGR01049 rpsJ_bact ribosomal protein S10; InterPro: IPR005731 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 of 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 , . Included in the family are one member each from Saccharomyces cerevisiae and Schizosaccharomyces pombe. These proteins lack an N-terminal mitochondrial transit peptide but contain additional sequence C-terminal to the ribosomal S10 protein region.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00 E-value=0 Score=305.52 Aligned_cols=99 Identities=57% Similarity=0.908 Sum_probs=97.8
Q ss_pred EEEEEEEEEECHHHHHHHHHHHHHHHHHHCCEECCCCCCCCEEEEEEEECCCCCCCCCHHHHHEEEEEEEEEEECCCHHH
Q ss_conf 48999999716889999999999999971880115648982136998730678986314235223344578797699899
Q gi|254780262|r 6 IRICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMRIYKRLLYIIKPTPQT 85 (104)
Q Consensus 6 ~kirIkl~s~d~~~Ld~~~~~i~~~a~~~g~~v~GpipLPtk~~~~tvlrSPhv~KksreqfE~r~hkRlI~i~~~~~~~ 85 (104)
|||||+|+|||+.+||++|++|+++|+++|+.++||+|||||+++|||||||||||+||||||+|+|+|||+|+++|++|
T Consensus 1 ~kiRIkLksyD~~~LD~s~~~Iv~t~~~~ga~~~GPiPLPTk~~~~TVLRSPHv~K~SREqFE~RtHkRLidI~~~~~~t 80 (99)
T TIGR01049 1 QKIRIKLKSYDHRLLDQSAKKIVETVKRTGAKVKGPIPLPTKKERYTVLRSPHVNKDSREQFEIRTHKRLIDIIDPTPKT 80 (99)
T ss_pred CCEEEEEEECCHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCEEEEEECCCCCCCCCCHHHHHEEEEEEEEEEECCHHH
T ss_conf 95267752058357889999999988861880247898997513788723775166670012110224577885079789
Q ss_pred HHHHHCCCCCCCCEEEEEC
Q ss_conf 9998647899984589989
Q gi|254780262|r 86 VDALMKLDIAAGVNVVIKL 104 (104)
Q Consensus 86 ~~~l~~~~lp~gV~i~i~~ 104 (104)
+|+||+++||+||+|+|++
T Consensus 81 ~daL~~ldLPaGVDv~Ik~ 99 (99)
T TIGR01049 81 IDALMKLDLPAGVDVEIKL 99 (99)
T ss_pred HHHHHCCCCCCCEEEEEEC
T ss_conf 8987504788861688748
No 2
>CHL00135 rps10 ribosomal protein S10; Validated
Probab=100.00 E-value=2.2e-42 Score=268.19 Aligned_cols=103 Identities=45% Similarity=0.753 Sum_probs=100.6
Q ss_pred CCCCEEEEEEEEEECHHHHHHHHHHHHHHHHHHCCEECCCCCCCCEEEEEEEECCCCCCCCCHHHHHEEEEEEEEEEECC
Q ss_conf 98864899999971688999999999999997188011564898213699873067898631423522334457879769
Q gi|254780262|r 2 TSRNIRICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMRIYKRLLYIIKP 81 (104)
Q Consensus 2 ~~~~~kirIkl~s~d~~~Ld~~~~~i~~~a~~~g~~v~GpipLPtk~~~~tvlrSPhv~KksreqfE~r~hkRlI~i~~~ 81 (104)
.+++|||||+|+|||+..||++|++|+++|+++|+.++||||||||+++|||+||||+||+||||||||+|||+|||+++
T Consensus 3 ~~~~~kiRIkL~S~d~~~Ld~~~~~I~~~ak~~g~~v~GPIpLPTk~~~~tvlrSPhv~k~srEqfE~R~HKRlIdi~~~ 82 (106)
T CHL00135 3 IKQQQKIRIKLKSYNHSLLNSSCEKIIDTAKRTNATAVGPIPLPTKRRIYCVLRSPHVDKDSREHFEIRTHKRIIDIYNP 82 (106)
T ss_pred CCCCCEEEEEEEECCHHHHHHHHHHHHHHHHHCCCEEECCCCCCEEEEEEEEEECCCCCCCCHHHEEEEEEEEEEEECCC
T ss_conf 54377089999967788999999999999998499577983398478999786189889962564143673589982189
Q ss_pred CHHHHHHHHCCCCCCCCEEEEEC
Q ss_conf 98999998647899984589989
Q gi|254780262|r 82 TPQTVDALMKLDIAAGVNVVIKL 104 (104)
Q Consensus 82 ~~~~~~~l~~~~lp~gV~i~i~~ 104 (104)
+++++++||+++||+||+|||++
T Consensus 83 ~~~ti~~l~~~~lp~gV~ieikl 105 (106)
T CHL00135 83 SSDTIDALMKLDLPSGVDIEIKL 105 (106)
T ss_pred CHHHHHHHHCCCCCCCCEEEEEE
T ss_conf 98999998678899997799997
No 3
>PRK00596 rpsJ 30S ribosomal protein S10; Reviewed
Probab=100.00 E-value=2e-41 Score=262.52 Aligned_cols=101 Identities=58% Similarity=0.909 Sum_probs=99.0
Q ss_pred CCEEEEEEEEEECHHHHHHHHHHHHHHHHHHCCEECCCCCCCCEEEEEEEECCCCCCCCCHHHHHEEEEEEEEEEECCCH
Q ss_conf 86489999997168899999999999999718801156489821369987306789863142352233445787976998
Q gi|254780262|r 4 RNIRICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMRIYKRLLYIIKPTP 83 (104)
Q Consensus 4 ~~~kirIkl~s~d~~~Ld~~~~~i~~~a~~~g~~v~GpipLPtk~~~~tvlrSPhv~KksreqfE~r~hkRlI~i~~~~~ 83 (104)
..|||||+|+|||+..||++|++|+++|+.+|++++||+||||++++|||+||||+||+||||||||+|||+|+++++++
T Consensus 2 ~~qkirI~L~s~d~~~Ld~~~~~i~~~a~~~g~~v~GPipLPtk~~~~tvlrSPhv~kksreqfE~RtHkRlI~i~~~t~ 81 (102)
T PRK00596 2 AKQKIRIRLKAFDHRLLDQSAKKIVETAKRTGAKVRGPIPLPTKKERFTVLRSPHVNKDSREQFEIRTHKRLIDIVDPTP 81 (102)
T ss_pred CCCEEEEEEEECCHHHHHHHHHHHHHHHHHHCCEECCCCCCCEEEEEEEEEECCCCCCCHHHHHHHHHHEEEEEEECCCH
T ss_conf 87669999997678899999999999999829904377269804689998637877975488885530048999857998
Q ss_pred HHHHHHHCCCCCCCCEEEEEC
Q ss_conf 999998647899984589989
Q gi|254780262|r 84 QTVDALMKLDIAAGVNVVIKL 104 (104)
Q Consensus 84 ~~~~~l~~~~lp~gV~i~i~~ 104 (104)
+++++||+++||+||+|||++
T Consensus 82 ~tv~~l~~~~lp~gV~iei~~ 102 (102)
T PRK00596 82 KTVDALMKLDLPAGVDVEIKL 102 (102)
T ss_pred HHHHHHHCCCCCCCCEEEEEC
T ss_conf 999998668899995799979
No 4
>COG0051 RpsJ Ribosomal protein S10 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.1e-40 Score=253.55 Aligned_cols=101 Identities=56% Similarity=0.878 Sum_probs=98.8
Q ss_pred CCEEEEEEEEEECHHHHHHHHHHHHHHHHHHCCEECCCCCCCCEEEEEEEECCCCCCCCCHHHHHEEEEEEEEEEECCCH
Q ss_conf 86489999997168899999999999999718801156489821369987306789863142352233445787976998
Q gi|254780262|r 4 RNIRICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMRIYKRLLYIIKPTP 83 (104)
Q Consensus 4 ~~~kirIkl~s~d~~~Ld~~~~~i~~~a~~~g~~v~GpipLPtk~~~~tvlrSPhv~KksreqfE~r~hkRlI~i~~~~~ 83 (104)
++|||||+|+|||+..||.+|.+|+++|+++|+.++||+|||||+.+||++||||+||+||||||||+|||+|||.++++
T Consensus 2 ~~~kirI~L~s~d~~~LD~~~~~Ive~akrtg~~v~GPiPLPTk~~~~tvlrsP~~~k~s~e~fEmr~HkRlidi~~~~~ 81 (104)
T COG0051 2 KKQKIRIRLKSFDHRLLDQVCREIVETAKRTGADVKGPIPLPTKRERVTVLRSPHGEKDSREQFEMRTHKRLIDIVDPTP 81 (104)
T ss_pred CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCEEECCCCCCCCEEEEEEEECCCCCCCHHHHHHHHEEEEEEEEECCCH
T ss_conf 97459999861887789999999999999729803388569971289998767887874077762201106888646997
Q ss_pred HHHHHHHCCCCCCCCEEEEEC
Q ss_conf 999998647899984589989
Q gi|254780262|r 84 QTVDALMKLDIAAGVNVVIKL 104 (104)
Q Consensus 84 ~~~~~l~~~~lp~gV~i~i~~ 104 (104)
+++++||++++|+||+|||++
T Consensus 82 ~~~~~Lm~i~~p~gV~vei~~ 102 (104)
T COG0051 82 KTVDALMRLDLPAGVDVEIKL 102 (104)
T ss_pred HHHHHHHCCCCCCCCEEEEEE
T ss_conf 999998622589995599997
No 5
>PTZ00039 40S ribosomal protein S20; Provisional
Probab=100.00 E-value=3.4e-39 Score=249.55 Aligned_cols=103 Identities=24% Similarity=0.469 Sum_probs=98.6
Q ss_pred CCCCCEEEEEEEEEECHHHHHHHHHHHHHHHHHHCCEECCCCCCCCEEEEEEEECCCCCC-CCCHHHHHEEEEEEEEEEE
Q ss_conf 998864899999971688999999999999997188011564898213699873067898-6314235223344578797
Q gi|254780262|r 1 MTSRNIRICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVD-KKSRDQLEMRIYKRLLYII 79 (104)
Q Consensus 1 m~~~~~kirIkl~s~d~~~Ld~~~~~i~~~a~~~g~~v~GpipLPtk~~~~tvlrSPhv~-KksreqfE~r~hkRlI~i~ 79 (104)
++.+-|||||+|+|||+..||.+|..|+++|+.+|+.++||||||||+.+|||+||||++ ++||||||||+|||+|||+
T Consensus 12 ~~~~~qKIRIkL~s~d~~~Ld~~~~~Ii~~ak~tg~~v~GPIpLPTK~~~~tv~kSP~~~gk~s~e~fEmRiHKRlIDi~ 91 (115)
T PTZ00039 12 EKNRLHKIRITLTSRNLKSIEKVCADIITGAKEKNLKVSGPVRMPVKTLKITTRKSPCGEGTNTWDRFEMRIYKRVIDLY 91 (115)
T ss_pred CCCCEEEEEEEEEECCHHHHHHHHHHHHHHHHHCCCEEECCCCCCCEEEEEEEECCCCCCCCCHHHHHHHHHHHEEEEEC
T ss_conf 23540799999997576589999999999998769987778448835479998528977898468988775442455522
Q ss_pred CCCHHHHHHHHCCCCCCCCEEEEEC
Q ss_conf 6998999998647899984589989
Q gi|254780262|r 80 KPTPQTVDALMKLDIAAGVNVVIKL 104 (104)
Q Consensus 80 ~~~~~~~~~l~~~~lp~gV~i~i~~ 104 (104)
+ +++++++||+++||+||+|||+|
T Consensus 92 ~-~~~~v~~lm~l~lp~GV~IEIkl 115 (115)
T PTZ00039 92 S-SSEVVTQITSINIDPGVEVEVII 115 (115)
T ss_pred C-CHHHHHHHHCCCCCCCCEEEEEC
T ss_conf 8-89999998688899997799869
No 6
>PRK12271 rps10p 30S ribosomal protein S10P; Reviewed
Probab=100.00 E-value=1.1e-38 Score=246.71 Aligned_cols=98 Identities=28% Similarity=0.460 Sum_probs=95.6
Q ss_pred EEEEEEEEEECHHHHHHHHHHHHHHHHHHCCEECCCCCCCCEEEEEEEECCCCCC-CCCHHHHHEEEEEEEEEEECCCHH
Q ss_conf 4899999971688999999999999997188011564898213699873067898-631423522334457879769989
Q gi|254780262|r 6 IRICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVD-KKSRDQLEMRIYKRLLYIIKPTPQ 84 (104)
Q Consensus 6 ~kirIkl~s~d~~~Ld~~~~~i~~~a~~~g~~v~GpipLPtk~~~~tvlrSPhv~-KksreqfE~r~hkRlI~i~~~~~~ 84 (104)
|||||+|+|||+..||++|++|+++|+.+|++++||+||||++++|||+||||++ ++||||||||+|||+||| +++++
T Consensus 2 qkiRIkL~S~d~~~Ld~~~~~I~~~ak~tg~~v~GPipLPTk~~~~tv~rSPh~~~k~sre~fE~RiHKRlIdi-~~~~~ 80 (102)
T PRK12271 2 QKARIRLSGTNPEDLDGVCNQIKEIAEKTGVKMSGPIPLPTKRLVVPTRKSPDGEGTATWDHWEMRVHKRLIDI-DADER 80 (102)
T ss_pred CEEEEEEEECCHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCEEEEEEEECCCCCCCCCHHHEEEEEEEEEEEE-CCCHH
T ss_conf 43999999778889999999999999973997856526998358985442787589853555387877799983-19889
Q ss_pred HHHHHHCCCCCCCCEEEEEC
Q ss_conf 99998647899984589989
Q gi|254780262|r 85 TVDALMKLDIAAGVNVVIKL 104 (104)
Q Consensus 85 ~~~~l~~~~lp~gV~i~i~~ 104 (104)
++++||+++||+||+|||+|
T Consensus 81 ~v~~l~~l~lp~gV~ieik~ 100 (102)
T PRK12271 81 ALRQLMRIRVPDDVQIEIEL 100 (102)
T ss_pred HHHHHHCCCCCCCCEEEEEE
T ss_conf 99998678899996899999
No 7
>pfam00338 Ribosomal_S10 Ribosomal protein S10p/S20e. This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.
Probab=100.00 E-value=2.1e-35 Score=227.47 Aligned_cols=97 Identities=53% Similarity=0.808 Sum_probs=95.1
Q ss_pred EEEEEEEECHHHHHHHHHHHHHHHHHHCCEECCCCCCCCEEEEEEEECCCCCCCCCHHHHHEEEEEEEEEEECCCHHHHH
Q ss_conf 99999971688999999999999997188011564898213699873067898631423522334457879769989999
Q gi|254780262|r 8 ICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMRIYKRLLYIIKPTPQTVD 87 (104)
Q Consensus 8 irIkl~s~d~~~Ld~~~~~i~~~a~~~g~~v~GpipLPtk~~~~tvlrSPhv~KksreqfE~r~hkRlI~i~~~~~~~~~ 87 (104)
++|+|+|||+.+||++|++|.++|+++|++++||+||||++++||++||||+|||||||||+|+|+|+|+|+++++++++
T Consensus 1 i~I~l~s~d~~~L~~~~~~i~~~a~~~gi~v~gpi~lPtk~~~~tvlrSPhv~kksreqfE~rthkR~i~i~~~~~~~~~ 80 (97)
T pfam00338 1 IRIKLKSYDHKLLESYVKFIVEAAKRLGIKVSGPIPLPTKRLRVTVLRSPHVDKKSREQFEMRTHKRLIDIYDATPETVD 80 (97)
T ss_pred CEEEEEECCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHEEEEEEECCCHHHHH
T ss_conf 98999978889999999999999999599847875688136999998078777407999998542389999479989999
Q ss_pred HHHCCCCCCCCEEEEEC
Q ss_conf 98647899984589989
Q gi|254780262|r 88 ALMKLDIAAGVNVVIKL 104 (104)
Q Consensus 88 ~l~~~~lp~gV~i~i~~ 104 (104)
.||.+++|+||+|+|++
T Consensus 81 ~l~~i~lp~GV~i~v~~ 97 (97)
T pfam00338 81 ALLRIDLPEGVDVEIKL 97 (97)
T ss_pred HHHCCCCCCCCEEEEEC
T ss_conf 99718799995799979
No 8
>TIGR01046 S10_Arc_S20_Euk ribosomal protein S10; InterPro: IPR005729 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 of 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 model describes the archaeal ribosomal protein and its equivalents in eukaryotes.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=99.97 E-value=3.3e-31 Score=202.98 Aligned_cols=98 Identities=29% Similarity=0.501 Sum_probs=95.0
Q ss_pred EEEEEEEEEECHHHHHHHHHHHHHHHHHHCCEECCCCCCCCEEEEEEEECCCCCCC-CCHHHHHEEEEEEEEEEECCCHH
Q ss_conf 48999999716889999999999999971880115648982136998730678986-31423522334457879769989
Q gi|254780262|r 6 IRICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDK-KSRDQLEMRIYKRLLYIIKPTPQ 84 (104)
Q Consensus 6 ~kirIkl~s~d~~~Ld~~~~~i~~~a~~~g~~v~GpipLPtk~~~~tvlrSPhv~K-ksreqfE~r~hkRlI~i~~~~~~ 84 (104)
+|+||+|.|.|++.||..|.+|.++|+++|+.++||||||||+.+.++.|||||++ ++||+||||+||||||| ++++.
T Consensus 1 ~k~RI~L~s~n~~~L~~vc~qi~~iA~~tgv~~~GPvpLPtk~l~v~trk~P~GEGS~twd~w~mriHKRLiDi-~ader 79 (99)
T TIGR01046 1 HKARIKLTSTNVRSLEEVCEQIKEIAEKTGVRMSGPVPLPTKRLRVPTRKSPDGEGSKTWDRWEMRIHKRLIDI-EADER 79 (99)
T ss_pred CCEEEEECCCCHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCEEEEEEEECCCCCCCCCEEEEEEEEEEEEECC-CCCHH
T ss_conf 93568861589578899999998877745955558806985357886766789998672012345785677337-78067
Q ss_pred HHHHHHCCCCCCCCEEEEEC
Q ss_conf 99998647899984589989
Q gi|254780262|r 85 TVDALMKLDIAAGVNVVIKL 104 (104)
Q Consensus 85 ~~~~l~~~~lp~gV~i~i~~ 104 (104)
++.++|++++|++|+|||++
T Consensus 80 ~lrqim~i~vp~~V~iEi~~ 99 (99)
T TIGR01046 80 ALRQIMRIRVPEDVEIEIEL 99 (99)
T ss_pred HHHCEEEEECCCCCEEEEEC
T ss_conf 63001255518995798868
No 9
>KOG3321 consensus
Probab=99.94 E-value=4.4e-28 Score=184.79 Aligned_cols=97 Identities=33% Similarity=0.503 Sum_probs=93.9
Q ss_pred EEEEEEEEECHHHHHHHHHHHHHHHHHHCCEECCCCCCCCEEEEEEEECCCCCCCCCHHHHHEEEEEEEEEEECCCHHHH
Q ss_conf 89999997168899999999999999718801156489821369987306789863142352233445787976998999
Q gi|254780262|r 7 RICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMRIYKRLLYIIKPTPQTV 86 (104)
Q Consensus 7 kirIkl~s~d~~~Ld~~~~~i~~~a~~~g~~v~GpipLPtk~~~~tvlrSPhv~KksreqfE~r~hkRlI~i~~~~~~~~ 86 (104)
++.|.++|||.++||+|..||+.+|+++||++.||-|||+++.+||+|||||+||||+||||+|||.|+|++++.|+.|+
T Consensus 48 ~~ai~lrg~D~avLdsYt~Fi~~ta~~LgIp~~~~~plp~~~Er~TlLrS~fIhKK~k~~yE~rTH~R~i~l~~~tgsTl 127 (175)
T KOG3321 48 LVAIELRGHDKAVLDSYTDFICRTAYYLGIPIKGPEPLPKKRERWTLLRSPFIHKKSKENYERRTHSRLIELYSVTGSTL 127 (175)
T ss_pred EEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH
T ss_conf 35677415765777889999999999857865788899504556666524545657765588998988888760684689
Q ss_pred HHHHCC---CCCCCCEEEEE
Q ss_conf 998647---89998458998
Q gi|254780262|r 87 DALMKL---DIAAGVNVVIK 103 (104)
Q Consensus 87 ~~l~~~---~lp~gV~i~i~ 103 (104)
|.|++| ++|+||.++++
T Consensus 128 ~tfleYI~rn~pegV~mq~~ 147 (175)
T KOG3321 128 DTFLEYIQRNLPEGVGMQAK 147 (175)
T ss_pred HHHHHHHHHHCHHHHCCEEC
T ss_conf 99999999628232211002
No 10
>KOG0900 consensus
Probab=99.79 E-value=8.4e-20 Score=136.47 Aligned_cols=100 Identities=25% Similarity=0.486 Sum_probs=92.2
Q ss_pred CCEEEEEEEEEECHHHHHHHHHHHHHHHHHHCCEECCCCCCCCEEEEEEEECCCCCC-CCCHHHHHEEEEEEEEEEECCC
Q ss_conf 864899999971688999999999999997188011564898213699873067898-6314235223344578797699
Q gi|254780262|r 4 RNIRICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVD-KKSRDQLEMRIYKRLLYIIKPT 82 (104)
Q Consensus 4 ~~~kirIkl~s~d~~~Ld~~~~~i~~~a~~~g~~v~GpipLPtk~~~~tvlrSPhv~-KksreqfE~r~hkRlI~i~~~~ 82 (104)
...+++|.+.|...+.|+..|..+.++|+..++++.||++||||.+++|++++||+. ++.|+.|+||+|+|+||+..++
T Consensus 18 ~~~~~~it~~~~~~kslekvC~dl~~~ak~~nl~~kg~vr~Ptk~~~itt~k~p~g~g~k~w~~f~mRiH~R~idl~s~s 97 (121)
T KOG0900 18 EIHKIRITLTSQKVKSLEKVCADLVRGAKEKNLKVKGPVRLPTKVLKITTRKTPCGEGSKTWDRFEMRVHKRLIDLHSPS 97 (121)
T ss_pred HHHCCCEEEEHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCHH
T ss_conf 53135455327778789999999998876427741576458830588998405776774078888999998884347869
Q ss_pred HHHHHHHHCCCCCCCCEEEEEC
Q ss_conf 8999998647899984589989
Q gi|254780262|r 83 PQTVDALMKLDIAAGVNVVIKL 104 (104)
Q Consensus 83 ~~~~~~l~~~~lp~gV~i~i~~ 104 (104)
+.+++++.+.+++||++++.+
T Consensus 98 -e~vkqitsi~~epgVevev~i 118 (121)
T KOG0900 98 -EIVKQITSISIEPGVEVEVTI 118 (121)
T ss_pred -HHHHHHHHHCCCCCCEEEEEE
T ss_conf -998776641268885689996
No 11
>KOG4060 consensus
Probab=98.47 E-value=7.2e-07 Score=61.04 Aligned_cols=94 Identities=11% Similarity=0.258 Sum_probs=79.4
Q ss_pred EEEEEEEECHHHHHHHHHHHHHHHHHHCCEECCCCCCCCEEEEEEEECCCCCCCCCHHHHHEEEEEEEEEEECCCHHHHH
Q ss_conf 99999971688999999999999997188011564898213699873067898631423522334457879769989999
Q gi|254780262|r 8 ICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMRIYKRLLYIIKPTPQTVD 87 (104)
Q Consensus 8 irIkl~s~d~~~Ld~~~~~i~~~a~~~g~~v~GpipLPtk~~~~tvlrSPhv~KksreqfE~r~hkRlI~i~~~~~~~~~ 87 (104)
+-+.++|||-..|++|.+++.+.|+.+++.+..-..+|++....--++ |-. -.+--.+-+.||-|.+++.+.++-...
T Consensus 55 lNV~i~gyD~~~lEsYq~yvH~la~~l~~~V~dsYA~p~qt~~v~~l~-p~s-tv~ese~~ltTyeRvvqls~v~Ap~~~ 132 (176)
T KOG4060 55 LNVHITGYDMTLLESYQQYVHNLANSLSIKVEDSYAMPTQTIEVLQLQ-PQS-TVMESESVLTTYERVVQLSGVSAPFAE 132 (176)
T ss_pred EEEEEEECCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCCCEEEEEEC-CCC-EEEEHHHHHHHHHHEEEECCCCCHHHH
T ss_conf 889987135306899999999788773723676202676425678944-786-132013211314221454466751389
Q ss_pred HHHCC---CCCCCCEEEEE
Q ss_conf 98647---89998458998
Q gi|254780262|r 88 ALMKL---DIAAGVNVVIK 103 (104)
Q Consensus 88 ~l~~~---~lp~gV~i~i~ 103 (104)
.|+++ .||+||.+.|+
T Consensus 133 ~Fl~iiqa~lPeGV~l~Vk 151 (176)
T KOG4060 133 IFLEIIQASLPEGVRLSVK 151 (176)
T ss_pred HHHHHHHHHCCCCEEEEEE
T ss_conf 9999999748766188755
No 12
>PRK05580 primosome assembly protein PriA; Validated
Probab=56.29 E-value=18 Score=17.84 Aligned_cols=78 Identities=17% Similarity=0.256 Sum_probs=49.4
Q ss_pred EEEEEEEECHHHHHHHHHHHHHHHHHH---CCEECCCCCCCCEEEEEEEECCCCCCCCCHHHHHEEEEEEEEEEECCCHH
Q ss_conf 999999716889999999999999971---88011564898213699873067898631423522334457879769989
Q gi|254780262|r 8 ICICLKAFDSRILDSSMREIVLTTKKS---GSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMRIYKRLLYIIKPTPQ 84 (104)
Q Consensus 8 irIkl~s~d~~~Ld~~~~~i~~~a~~~---g~~v~GpipLPtk~~~~tvlrSPhv~KksreqfE~r~hkRlI~i~~~~~~ 84 (104)
++|.+.|-+...+.+++..+....+.. ++.+-||.|.|-.+ -++.| .-.|-|...+..
T Consensus 608 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlGP~~~~i~k--------------~~~~y-----r~~ilik~~~~~ 668 (699)
T PRK05580 608 ALVRGSAKAVAKALKFAQQLALLLKPPLGEGVEVLGPVPAPIAR--------------IAGRY-----RWQILLRSPRRA 668 (699)
T ss_pred HEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHH--------------HCCEE-----EEEEEEECCCHH
T ss_conf 17899539999999999999998763147990998986765378--------------78906-----999999879779
Q ss_pred HHHHHH-----CC-CCCCCCEEEEEC
Q ss_conf 999986-----47-899984589989
Q gi|254780262|r 85 TVDALM-----KL-DIAAGVNVVIKL 104 (104)
Q Consensus 85 ~~~~l~-----~~-~lp~gV~i~i~~ 104 (104)
.+..++ .+ ..+.||.+.|.+
T Consensus 669 ~l~~~l~~~~~~~~~~~~~v~~~idv 694 (699)
T PRK05580 669 ALQAALRAWLALLSALRRKVRLSIDI 694 (699)
T ss_pred HHHHHHHHHHHHHHCCCCCCEEEEEC
T ss_conf 99999999999874278886699971
No 13
>pfam05435 Phi-29_GP3 Phi-29 DNA terminal protein GP3. This family consists of DNA terminal protein GP3 sequences from Phi-29 like bacteriophages. DNA terminal protein GP3 is linked to the 5' ends of both strands of the genome through a phosphodiester bond between the beta-hydroxyl group of a serine residue and the 5'-phosphate of the terminal deoxyadenylate. This protein is essential for DNA replication and is involved in the priming of DNA elongation.
Probab=49.42 E-value=20 Score=17.56 Aligned_cols=38 Identities=26% Similarity=0.402 Sum_probs=28.7
Q ss_pred EEEEEEECH----HHHHHHHHHHHHHHHHHCCEECCCCCCCC
Q ss_conf 999997168----89999999999999971880115648982
Q gi|254780262|r 9 CICLKAFDS----RILDSSMREIVLTTKKSGSQIVGPIPFPR 46 (104)
Q Consensus 9 rIkl~s~d~----~~Ld~~~~~i~~~a~~~g~~v~GpipLPt 46 (104)
||+++-.|. +++...-..|.++.++.|+..+|-|.+|.
T Consensus 6 riRit~ndkaeyakLvkntKAKitRtkKkYG~Dls~eI~~p~ 47 (266)
T pfam05435 6 RIRITKNDKAEYAKLVKNTKAKITRTKKKYGQDLSGEISPPS 47 (266)
T ss_pred CEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
T ss_conf 501033648999999876489999899983666655338998
No 14
>PHA00490 terminal protein
Probab=41.93 E-value=31 Score=16.49 Aligned_cols=38 Identities=26% Similarity=0.411 Sum_probs=28.7
Q ss_pred EEEEEEECH----HHHHHHHHHHHHHHHHHCCEECCCCCCCC
Q ss_conf 999997168----89999999999999971880115648982
Q gi|254780262|r 9 CICLKAFDS----RILDSSMREIVLTTKKSGSQIVGPIPFPR 46 (104)
Q Consensus 9 rIkl~s~d~----~~Ld~~~~~i~~~a~~~g~~v~GpipLPt 46 (104)
||+++-.|. +++...-..|.++.++.|+..+|-|.+|.
T Consensus 6 riRit~ndkaeyakLvkntKAKitRtkKkYG~Dlt~eI~~p~ 47 (266)
T PHA00490 6 RIRITKNDKAEYAKLVKNTKAKITRTKKKYGQDLTGEISPPS 47 (266)
T ss_pred CEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
T ss_conf 501033648999999876489999899983666644248998
No 15
>pfam04743 consensus
Probab=33.31 E-value=18 Score=17.82 Aligned_cols=31 Identities=32% Similarity=0.557 Sum_probs=20.2
Q ss_pred EEEEEEEEEECCC-HHHHHHHHCCCCCCCCEE
Q ss_conf 3344578797699-899999864789998458
Q gi|254780262|r 70 RIYKRLLYIIKPT-PQTVDALMKLDIAAGVNV 100 (104)
Q Consensus 70 r~hkRlI~i~~~~-~~~~~~l~~~~lp~gV~i 100 (104)
+.|+|+.+-.... ++-..+=..+-+|+||.+
T Consensus 14 ~~Y~~l~d~~~~~~peRwr~EI~lglPPGV~v 45 (160)
T pfam04743 14 KRYKRLPDVVEDCEPERWRAEIDLGLPPGVSV 45 (160)
T ss_pred CCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCH
T ss_conf 74223787511116199999997379998648
No 16
>PRK00140 rplK 50S ribosomal protein L11; Validated
Probab=32.99 E-value=6.9 Score=20.31 Aligned_cols=28 Identities=14% Similarity=0.246 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHCCEECCCCCCCCEEEEE
Q ss_conf 99999999999997188011564898213699
Q gi|254780262|r 20 LDSSMREIVLTTKKSGSQIVGPIPFPRSIRRF 51 (104)
Q Consensus 20 Ld~~~~~i~~~a~~~g~~v~GpipLPtk~~~~ 51 (104)
+-.||+.+-+..+... .-+|+|++...|
T Consensus 35 i~~F~k~fN~~T~~~~----~g~~vpV~Itv~ 62 (142)
T PRK00140 35 IMEFCKAFNARTQDQE----KGLPIPVVITVY 62 (142)
T ss_pred HHHHHHHHHHHHHHCC----CCCEEEEEEEEC
T ss_conf 9999999999886157----998075899993
No 17
>KOG3473 consensus
Probab=31.13 E-value=42 Score=15.74 Aligned_cols=44 Identities=11% Similarity=0.193 Sum_probs=32.5
Q ss_pred CCEEEEEEEEEECHHHHHHHHHHHHHHHHHHCC-EECCCCCCCCE
Q ss_conf 864899999971688999999999999997188-01156489821
Q gi|254780262|r 4 RNIRICICLKAFDSRILDSSMREIVLTTKKSGS-QIVGPIPFPRS 47 (104)
Q Consensus 4 ~~~kirIkl~s~d~~~Ld~~~~~i~~~a~~~g~-~v~GpipLPtk 47 (104)
++++=.+.++-++..+|+++|.++.-..++++. ...-+++.|+.
T Consensus 54 e~~~n~v~f~di~shiLeKvc~Yl~Yk~rY~~~s~eiPeF~Ippe 98 (112)
T KOG3473 54 EAEKNEVYFRDIPSHILEKVCEYLAYKVRYTNSSTEIPEFDIPPE 98 (112)
T ss_pred CCCCCEEEECCCHHHHHHHHHHHHHHHEEECCCCCCCCCCCCCHH
T ss_conf 033665785355589999999985522154156465888989878
No 18
>COG2121 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.44 E-value=48 Score=15.39 Aligned_cols=20 Identities=20% Similarity=0.111 Sum_probs=14.2
Q ss_pred EEECCCCCCCCCHHHHHEEE
Q ss_conf 87306789863142352233
Q gi|254780262|r 52 TVNRSPHVDKKSRDQLEMRI 71 (104)
Q Consensus 52 tvlrSPhv~KksreqfE~r~ 71 (104)
-+--|+|.-.||||+||+-.
T Consensus 153 ~~~~sr~~~lKsWDk~~IP~ 172 (214)
T COG2121 153 GVATSRCWRLKTWDKTIIPL 172 (214)
T ss_pred EEEEEEEEEECCCCCCCCCC
T ss_conf 87531034424432223357
No 19
>TIGR01348 PDHac_trf_long pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase; InterPro: IPR006256 This group of sequences are a subset of pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase specifically close by both phylogenetic and percent identity (UPGMA) trees. Members contain two or three copies of the lipoyl-binding domain. Escherichia coli AceF is included in this set while mitochondrial and some other bacterial forms are excluded. dihydrolipoyllysine-residue acetyltransferase E2 component of pyruvate dehydrogenase complex; GO: 0004742 dihydrolipoyllysine-residue acetyltransferase activity, 0006096 glycolysis, 0045254 pyruvate dehydrogenase complex.
Probab=26.25 E-value=41 Score=15.78 Aligned_cols=20 Identities=20% Similarity=0.439 Sum_probs=12.6
Q ss_pred EECHHHHHHH--HHHHHHHHHH
Q ss_conf 7168899999--9999999997
Q gi|254780262|r 14 AFDSRILDSS--MREIVLTTKK 33 (104)
Q Consensus 14 s~d~~~Ld~~--~~~i~~~a~~ 33 (104)
||||+++|-+ ++|+..+...
T Consensus 625 sYDHRvIdGA~AArF~~~l~~~ 646 (655)
T TIGR01348 625 SYDHRVIDGADAARFTTYLSEL 646 (655)
T ss_pred HHCCHHHHHHHHHHHHHHHHHH
T ss_conf 0010022354688999998755
No 20
>TIGR01632 L11_bact ribosomal protein L11; InterPro: IPR006519 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 of 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 L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities , groups bacterial, chloroplast, cyanelle, and most mitochondrial forms of ribosomal protein L11. L11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of L11 has been shown to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure. This entry represents the bacterial, chloroplast and mitochondrial forms. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=25.06 E-value=15 Score=18.42 Aligned_cols=31 Identities=29% Similarity=0.494 Sum_probs=19.4
Q ss_pred EEEEE--ECHHHHHHHHHHHHHHHHHHCCEECC
Q ss_conf 99997--16889999999999999971880115
Q gi|254780262|r 10 ICLKA--FDSRILDSSMREIVLTTKKSGSQIVG 40 (104)
Q Consensus 10 Ikl~s--~d~~~Ld~~~~~i~~~a~~~g~~v~G 40 (104)
+|+.= -++..+|.+++-|.-+|+.+|+.|.|
T Consensus 112 ~K~~D~~ln~~~~EaA~k~I~GtAkSMGi~v~~ 144 (144)
T TIGR01632 112 IKMSDERLNTKDLEAAMKIIAGTAKSMGIEVVG 144 (144)
T ss_pred HHCCCCCCCHHCHHHHHHHHCCCCCCCCEEECC
T ss_conf 616898888102553154300000218615259
No 21
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=24.70 E-value=61 Score=14.78 Aligned_cols=68 Identities=18% Similarity=0.222 Sum_probs=44.2
Q ss_pred ECHHHHHHHHHHHHHHHHHHCCEECCCCCCCCEEEEEEEECCCCCCCCCHHHHHEEEEEEEEEEECCCHHHHHHH
Q ss_conf 168899999999999999718801156489821369987306789863142352233445787976998999998
Q gi|254780262|r 15 FDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMRIYKRLLYIIKPTPQTVDAL 89 (104)
Q Consensus 15 ~d~~~Ld~~~~~i~~~a~~~g~~v~GpipLPtk~~~~tvlrSPhv~KksreqfE~r~hkRlI~i~~~~~~~~~~l 89 (104)
|....|+.++..|....-... .-|....++|++-||.+|.=.---=-+-+|.-||-+.+..++.+-.|
T Consensus 61 Y~D~Kler~Vari~g~lt~~S-------~~p~q~YriTilnSP~INAFALPGGYlYitRGLlAland~sEvAAVl 128 (479)
T COG4784 61 YRDPKLERMVARIVGALTAVS-------ENPQQTYRITILNSPNINAFALPGGYLYITRGLLALANDSSEVAAVL 128 (479)
T ss_pred CCCHHHHHHHHHHHHHHHHHC-------CCCCCEEEEEEECCCCCCCCCCCCCEEEEEHHHHHHCCCHHHHHHHH
T ss_conf 587889999999976763202-------58774389998358775431158744887522888747778899998
No 22
>KOG2934 consensus
Probab=22.67 E-value=14 Score=18.52 Aligned_cols=21 Identities=29% Similarity=0.411 Sum_probs=18.6
Q ss_pred CCCCCCCCEEEEEEEECCCCC
Q ss_conf 156489821369987306789
Q gi|254780262|r 39 VGPIPFPRSIRRFTVNRSPHV 59 (104)
Q Consensus 39 ~GpipLPtk~~~~tvlrSPhv 59 (104)
-|+++||-+++.|--+|||-+
T Consensus 127 lG~L~Lp~~rrhw~alR~~~g 147 (204)
T KOG2934 127 LGYLRLPVMRRHWLALRSPPG 147 (204)
T ss_pred CCCCCCHHHHHHHHHHHCCCC
T ss_conf 252110667766675307997
No 23
>pfam04533 Herpes_U44 Herpes virus U44 protein. This is a family of proteins from dsDNA beta-herpesvirinae and gamma-herpesvirinae viruses. The function is not known, and the proteins are named variously as U44, BSRF1, UL71, and M71. The family BSRF1 has been merged into this.
Probab=22.43 E-value=41 Score=15.80 Aligned_cols=39 Identities=26% Similarity=0.298 Sum_probs=25.7
Q ss_pred CCCCCCCCCHHHHHEEEEEEEEEEECCCHHHHHHHHCCCCCCCCEE
Q ss_conf 0678986314235223344578797699899999864789998458
Q gi|254780262|r 55 RSPHVDKKSRDQLEMRIYKRLLYIIKPTPQTVDALMKLDIAAGVNV 100 (104)
Q Consensus 55 rSPhv~KksreqfE~r~hkRlI~i~~~~~~~~~~l~~~~lp~gV~i 100 (104)
.+||+.... -|.|+.+-....++-......+-+|+||.+
T Consensus 13 ~w~FGr~~~-------~Y~~L~d~~~~c~er~~~EIdlglPPGV~~ 51 (211)
T pfam04533 13 LWPFGRPGN-------NYERLPDEVEECPERWRAEIDLGLPPGVLV 51 (211)
T ss_pred CCCCCCCCC-------CCCCCCCCCCCCCHHHHHHHHCCCCCCCCH
T ss_conf 034689886-------521168863348599999985469997456
No 24
>PRK01143 rpl11p 50S ribosomal protein L11P; Validated
Probab=20.48 E-value=25 Score=17.10 Aligned_cols=26 Identities=27% Similarity=0.328 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHHCCEECCCCCCCCEEEE
Q ss_conf 9999999999999718801156489821369
Q gi|254780262|r 20 LDSSMREIVLTTKKSGSQIVGPIPFPRSIRR 50 (104)
Q Consensus 20 Ld~~~~~i~~~a~~~g~~v~GpipLPtk~~~ 50 (104)
+-.||+.+-+..+... | +++|.+...
T Consensus 31 i~~f~k~fN~~T~~~~----G-~~Vpv~Itv 56 (163)
T PRK01143 31 VQQVVKEINEKTKDFK----G-MQVPVKIIV 56 (163)
T ss_pred HHHHHHHHHHHHHHCC----C-CCCCEEEEE
T ss_conf 8999999999987536----9-844259999
No 25
>TIGR00004 TIGR00004 endoribonuclease L-PSP, putative; InterPro: IPR006056 This family includes proteins encoded by the yabJ gene from Bacillus subtilis that is required for adenine-mediated repression of purine biosynthetic genes in vivo and codes for an acid-soluble, 14-kDa protein. The structure of this protein has been solved and the protein is found to form a homotrimer. The trimer has a deep cleft that is a probably ligand binding site and possibly forms an enzymatic active site. However the ligand and reaction are unknown..
Probab=20.35 E-value=57 Score=14.98 Aligned_cols=34 Identities=15% Similarity=0.225 Sum_probs=19.4
Q ss_pred EEEEEEEEECCCHHHHHHHHCC-CCCCCCEEEEEC
Q ss_conf 3445787976998999998647-899984589989
Q gi|254780262|r 71 IYKRLLYIIKPTPQTVDALMKL-DIAAGVNVVIKL 104 (104)
Q Consensus 71 ~hkRlI~i~~~~~~~~~~l~~~-~lp~gV~i~i~~ 104 (104)
+|.+..+=++.++.-+++..+. .||-||.||||.
T Consensus 91 vY~~YF~~~~V~~~PARs~V~VA~LPk~v~vEIEa 125 (129)
T TIGR00004 91 VYGQYFDEHSVEPYPARSAVQVAALPKDVLVEIEA 125 (129)
T ss_pred HHHHHCCCCCCCCCCCHHHHHHHHCCCCCEEEEEE
T ss_conf 98875487777877731113112079998067888
No 26
>COG0080 RplK Ribosomal protein L11 [Translation, ribosomal structure and biogenesis]
Probab=20.30 E-value=36 Score=16.15 Aligned_cols=27 Identities=22% Similarity=0.329 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHHHCCEECCCCCCCCEEEEE
Q ss_conf 99999999999997188011564898213699
Q gi|254780262|r 20 LDSSMREIVLTTKKSGSQIVGPIPFPRSIRRF 51 (104)
Q Consensus 20 Ld~~~~~i~~~a~~~g~~v~GpipLPtk~~~~ 51 (104)
+-.+|+.+-+..+.. .-.+.|.....|
T Consensus 34 i~~f~k~fN~~T~~~-----~G~~vPV~Itv~ 60 (141)
T COG0080 34 IMEFCKEFNAATKDE-----KGLPVPVVITVY 60 (141)
T ss_pred HHHHHHHHHHHHHCC-----CCCEEEEEEEEE
T ss_conf 899999999984136-----998441799997
No 27
>pfam02399 Herpes_ori_bp Origin of replication binding protein. This Pfam family represents the herpesvirus origin of replication binding protein, probably involved in DNA replication.
Probab=20.09 E-value=68 Score=14.51 Aligned_cols=31 Identities=32% Similarity=0.458 Sum_probs=21.7
Q ss_pred CEECCCCCCC----CEEEEEEEECCCCCCCCCHHH
Q ss_conf 8011564898----213699873067898631423
Q gi|254780262|r 36 SQIVGPIPFP----RSIRRFTVNRSPHVDKKSRDQ 66 (104)
Q Consensus 36 ~~v~GpipLP----tk~~~~tvlrSPhv~Kksreq 66 (104)
.+--||+.+| +..+.+||-|.|-+-+|+---
T Consensus 32 ~Q~~~pV~fp~P~~~~~r~V~VVRAPMGSGKTTAL 66 (829)
T pfam02399 32 RQSDGPVTFPSPLAPRARPVLVVRAPMGSGKTTAL 66 (829)
T ss_pred EECCCCEECCCCCCCCCCEEEEEECCCCCCHHHHH
T ss_conf 30699740599999877446899768888718999
Done!