Query 031725
Match_columns 154
No_of_seqs 143 out of 968
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 04:29:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031725.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031725hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00359 rpmB 50S ribosomal pr 100.0 5.6E-33 1.2E-37 197.8 6.1 75 77-151 1-75 (76)
2 COG0227 RpmB Ribosomal protein 100.0 2.6E-31 5.7E-36 190.7 5.6 75 77-151 1-76 (77)
3 CHL00112 rpl28 ribosomal prote 100.0 3.1E-29 6.8E-34 173.7 4.9 62 77-138 1-62 (63)
4 PF00830 Ribosomal_L28: Riboso 99.9 1.8E-27 3.9E-32 162.8 3.4 61 79-139 1-61 (61)
5 TIGR00009 L28 ribosomal protei 99.9 1.3E-26 2.8E-31 156.7 4.9 56 77-134 1-56 (56)
6 KOG3278 Mitochondrial/chloropl 99.7 5.1E-18 1.1E-22 139.8 -0.3 77 72-148 37-115 (215)
7 KOG3279 Uncharacterized conser 96.3 0.00013 2.8E-09 62.6 -5.4 75 77-151 81-158 (283)
8 PF02575 YbaB_DNA_bd: YbaB/Ebf 30.4 84 0.0018 21.9 3.6 35 112-146 32-66 (93)
9 PF13348 Y_phosphatase3C: Tyro 18.9 61 0.0013 21.3 1.0 21 130-150 33-56 (68)
10 COG1813 Predicted transcriptio 18.8 51 0.0011 27.1 0.7 17 80-96 5-21 (165)
No 1
>PRK00359 rpmB 50S ribosomal protein L28; Reviewed
Probab=99.98 E-value=5.6e-33 Score=197.77 Aligned_cols=75 Identities=49% Similarity=0.688 Sum_probs=73.0
Q ss_pred ccccccccCcccccccccccccCcccccccCceeEEEEEEcCCCeEEEEEeeehhhhcccccCHHHHHHHccccc
Q 031725 77 ARRVCPFTGKKSNKANKVSFSNHKTTKRQFVNLQYKKVWWEAGKRYVKLRLSTKALKTIEKNGLDAVAKKAGIDL 151 (154)
Q Consensus 77 MSR~C~ltGKk~~~GNnVShS~~KTKR~wkPNLQkkri~~~~lgr~vkLrVSTkaLRTI~K~Gld~yl~k~~~~l 151 (154)
||++|++|||++.+||+||||+++|+|+|+||||++++|++++|++++|+|||+|||+|+|.|+|+|+++++++.
T Consensus 1 Msr~C~i~GK~~~~Gn~vShs~~kTkR~~~pNlq~~~~~~~~~g~~v~~~vst~~Lrti~k~Gl~~~~~~~~~~~ 75 (76)
T PRK00359 1 MSRVCEITGKGPMVGNNVSHSNNKTKRRFLPNLQKVRFWVEEEGRFVRLRVSARALRTIDKKGLDAVLKKARARG 75 (76)
T ss_pred CCCccccCCCCCccCCeeeecCCccCceecccceEEEEEEccCCEEEEEEEEchheeeehhhhHHHHHHhhhhcc
Confidence 899999999999999999999999999999999999999999999999999999999999999999999998764
No 2
>COG0227 RpmB Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=2.6e-31 Score=190.73 Aligned_cols=75 Identities=43% Similarity=0.602 Sum_probs=72.1
Q ss_pred ccccccccCcccccccccccccCcccccccCceeEEEEEEcCCCeEEEEEeeehhhhcccccC-HHHHHHHccccc
Q 031725 77 ARRVCPFTGKKSNKANKVSFSNHKTTKRQFVNLQYKKVWWEAGKRYVKLRLSTKALKTIEKNG-LDAVAKKAGIDL 151 (154)
Q Consensus 77 MSR~C~ltGKk~~~GNnVShS~~KTKR~wkPNLQkkri~~~~lgr~vkLrVSTkaLRTI~K~G-ld~yl~k~~~~l 151 (154)
|||+|+||||++++||+||||+++|||+|.||||++++|++++|++++|+|||+|||+|||.| +|+|+.+++..+
T Consensus 1 Msr~C~lTGk~~~~GnnvShs~~kTkRr~~pNlq~~~~~~~~~g~~~~l~Vsa~~Lrtidk~G~~~~~~~~~~~~~ 76 (77)
T COG0227 1 MSRRCQLTGKGPMSGNNVSHSHNKTKRRFLPNLQKVRFWSLSDGRFKRLRVSAKALRTIDKKGKIDAVLAKARARG 76 (77)
T ss_pred CCceeeeccccccccccccccccccceeecCccEEEEEEEccCCcEEEEEEEhHHhhccccccchhhhhhhhcccc
Confidence 899999999999999999999999999999999999999999999999999999999999996 999999987544
No 3
>CHL00112 rpl28 ribosomal protein L28; Provisional
Probab=99.95 E-value=3.1e-29 Score=173.66 Aligned_cols=62 Identities=48% Similarity=0.723 Sum_probs=60.6
Q ss_pred ccccccccCcccccccccccccCcccccccCceeEEEEEEcCCCeEEEEEeeehhhhccccc
Q 031725 77 ARRVCPFTGKKSNKANKVSFSNHKTTKRQFVNLQYKKVWWEAGKRYVKLRLSTKALKTIEKN 138 (154)
Q Consensus 77 MSR~C~ltGKk~~~GNnVShS~~KTKR~wkPNLQkkri~~~~lgr~vkLrVSTkaLRTI~K~ 138 (154)
|||+|++|||++.+||+||||+++|+|+|+||||++++|+++++++++|+|||+|||+|+|.
T Consensus 1 Msr~C~i~GK~~~~Gn~vSHs~~kTkR~f~pNLq~vr~~~~~~~~~~kl~Vstr~Lrt~~k~ 62 (63)
T CHL00112 1 MSKKCQLTGKKANNGYTVSHSHKRTKKLQKVNLQTKKIWSNTQNRWVKLKISTKAIKTLKKK 62 (63)
T ss_pred CCCeeccCCCcCccCceeEccCcccCceecccccEEEEEECCCCeEEEEEEEHHHhhhcccc
Confidence 89999999999999999999999999999999999999999999999999999999999985
No 4
>PF00830 Ribosomal_L28: Ribosomal L28 family; InterPro: IPR001383 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 ribosomal L28 protein family include proteins from bacteria and chloroplasts. The L24 protein from yeast, found in the large subunit of the mitochodrial ribosome, contains a region similar to the bacterial L28 protein.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZJP_U 3CF5_U 2ZJR_U 3PIP_U 3PIO_U 2ZJQ_U 3DLL_U 2Y15_1 3KIY_1 3V2D_1 ....
Probab=99.94 E-value=1.8e-27 Score=162.84 Aligned_cols=61 Identities=48% Similarity=0.666 Sum_probs=57.1
Q ss_pred ccccccCcccccccccccccCcccccccCceeEEEEEEcCCCeEEEEEeeehhhhcccccC
Q 031725 79 RVCPFTGKKSNKANKVSFSNHKTTKRQFVNLQYKKVWWEAGKRYVKLRLSTKALKTIEKNG 139 (154)
Q Consensus 79 R~C~ltGKk~~~GNnVShS~~KTKR~wkPNLQkkri~~~~lgr~vkLrVSTkaLRTI~K~G 139 (154)
|+|+||||++++||+||||+++|+|+|+||||++++|++++|++++|+|||+|||+|+|.|
T Consensus 1 r~c~~~GK~~~~Gn~vshs~~ktkR~~~pNlq~~~~~~~~lg~~~~v~vst~~Lrti~k~G 61 (61)
T PF00830_consen 1 RRCLITGKKPMFGNNVSHSNNKTKRRWKPNLQKKRLWSEILGKKIRVRVSTRALRTIDKKG 61 (61)
T ss_dssp -S-TTT-CTTCEECEEEEECEEEEEEEBTTEEEEEEEESTTSSEEEEEEEHCHHHHHHCHT
T ss_pred CEeecCCCeecccceEeecCCcCCcEEcCcCEEEEEEEcCCCeEEEEEEEhHHeeeeccCC
Confidence 5899999999999999999999999999999999999999999999999999999999987
No 5
>TIGR00009 L28 ribosomal protein L28. This model describes bacterial and chloroplast forms of the 50S ribosomal protein L28, a polypeptide about 60 amino acids in length. Mitochondrial homologs differ substantially in architecture and are not included.
Probab=99.93 E-value=1.3e-26 Score=156.73 Aligned_cols=56 Identities=45% Similarity=0.668 Sum_probs=54.3
Q ss_pred ccccccccCcccccccccccccCcccccccCceeEEEEEEcCCCeEEEEEeeehhhhc
Q 031725 77 ARRVCPFTGKKSNKANKVSFSNHKTTKRQFVNLQYKKVWWEAGKRYVKLRLSTKALKT 134 (154)
Q Consensus 77 MSR~C~ltGKk~~~GNnVShS~~KTKR~wkPNLQkkri~~~~lgr~vkLrVSTkaLRT 134 (154)
||++|++|||++++||+||||+++|+|+|+||||+++||++ |++++|+|||+|||+
T Consensus 1 Ms~~C~i~GK~~~~Gn~vshs~~ktkR~~~pNlq~~ri~~~--~~~~~~~vst~~Lkt 56 (56)
T TIGR00009 1 MSRKCQLTGKGPLSGNNVSHSHRKTKRRFKPNLQKKRVWVD--GRFKRLRVSAKCLRT 56 (56)
T ss_pred CCCEeeeCCCcCccCCeeeecCCccCceecccceEEEEEEC--CEEEEEEEEcHHhcC
Confidence 89999999999999999999999999999999999999997 499999999999996
No 6
>KOG3278 consensus Mitochondrial/chloroplast ribosomal protein L28 [Translation, ribosomal structure and biogenesis]
Probab=99.67 E-value=5.1e-18 Score=139.77 Aligned_cols=77 Identities=21% Similarity=0.232 Sum_probs=71.9
Q ss_pred CCcccccccccccCcccccccc-cccccCcccccccCceeEEEEEEcCCCeEEEEEeeehhhhccccc-CHHHHHHHcc
Q 031725 72 LQPIVARRVCPFTGKKSNKANK-VSFSNHKTTKRQFVNLQYKKVWWEAGKRYVKLRLSTKALKTIEKN-GLDAVAKKAG 148 (154)
Q Consensus 72 ~~~~~MSR~C~ltGKk~~~GNn-VShS~~KTKR~wkPNLQkkri~~~~lgr~vkLrVSTkaLRTI~K~-Gld~yl~k~~ 148 (154)
..-|..+++++|.|..++|||| ++.+.+||||.|.||+|.+++|++.+++.|+|+|+|++||||+|. |||+||.+..
T Consensus 37 ~~vf~q~~~gLYgGs~iq~GNn~i~~~g~KTRr~W~PNv~~K~L~S~il~~ki~vkvTt~vLrtIdKeGGiDeYL~K~~ 115 (215)
T KOG3278|consen 37 KVVFGQAKRGLYGGSHIQYGNNVIEDGGNKTRRCWKPNVQEKRLFSYILDSKIKVKVTTHVLRTIDKEGGIDEYLLKTP 115 (215)
T ss_pred HHHHhhcccccccccceecCcccccccCcccceeecCcchhhHHHHHHHhhheeeeeehHHHhhhccccChhHHHhcCc
Confidence 4455688899999999999999 788899999999999999999999999999999999999999999 8999999875
No 7
>KOG3279 consensus Uncharacterized conserved protein (melanoma antigen P15) [Function unknown]
Probab=96.30 E-value=0.00013 Score=62.61 Aligned_cols=75 Identities=19% Similarity=0.175 Sum_probs=63.5
Q ss_pred ccccccccCcccccccccccc-cCcccccccCceeEEEEEEcCCCeEEEEEeeehhhhccccc-CHHHHHHHcc-ccc
Q 031725 77 ARRVCPFTGKKSNKANKVSFS-NHKTTKRQFVNLQYKKVWWEAGKRYVKLRLSTKALKTIEKN-GLDAVAKKAG-IDL 151 (154)
Q Consensus 77 MSR~C~ltGKk~~~GNnVShS-~~KTKR~wkPNLQkkri~~~~lgr~vkLrVSTkaLRTI~K~-Gld~yl~k~~-~~l 151 (154)
-+..+...|-....|-.-+.- .+|--|-|-|||.+.-++++.++.++++-|+-++|+.||.. |+|-|+++.. +||
T Consensus 81 e~~~g~wgge~vikg~~~~~~tk~~~p~~wvp~l~~~v~~s~ild~y~~v~vteRtl~LIDE~~GLD~YILk~~~~DL 158 (283)
T KOG3279|consen 81 ESHRGIWGGEAVIKGFQKREQTKRRVPHFWVPNLRRSVVHSHVLDCYMSVVVTERTLELIDECHGLDHYILKNRACDL 158 (283)
T ss_pred cccccccccHHHHHHHHHHHHHhhcCCcccccchhhHHHHHHHHhhhheeeehHHHHHHHHHhcCcceeeecCcchhH
Confidence 455688888888777664442 45778899999999999999999999999999999999999 9999998876 555
No 8
>PF02575 YbaB_DNA_bd: YbaB/EbfC DNA-binding family; InterPro: IPR004401 The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta []. YbaB is co-transcribed with RecR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain.; PDB: 1PUG_B 3F42_B 1YBX_B 1J8B_A.
Probab=30.39 E-value=84 Score=21.89 Aligned_cols=35 Identities=14% Similarity=0.263 Sum_probs=25.5
Q ss_pred EEEEEcCCCeEEEEEeeehhhhcccccCHHHHHHH
Q 031725 112 KKVWWEAGKRYVKLRLSTKALKTIEKNGLDAVAKK 146 (154)
Q Consensus 112 kri~~~~lgr~vkLrVSTkaLRTI~K~Gld~yl~k 146 (154)
++++++..|+.+.|+|...+++..+..-|...+..
T Consensus 32 V~V~v~g~g~v~~i~i~~~~~~~~~~~~L~~~I~~ 66 (93)
T PF02575_consen 32 VTVTVNGNGEVVDIEIDPSALRPLDPEELEDLIVE 66 (93)
T ss_dssp EEEEEETTS-EEEEEE-GGGGCTS-HHHHHHHHHH
T ss_pred EEEEEecCceEEEEEEehHhhccCCHHHHHHHHHH
Confidence 78889999999999999999987776655555543
No 9
>PF13348 Y_phosphatase3C: Tyrosine phosphatase family C-terminal region; PDB: 1YWF_A 2OZ5_B.
Probab=18.85 E-value=61 Score=21.35 Aligned_cols=21 Identities=19% Similarity=0.499 Sum_probs=14.8
Q ss_pred hhhhccccc--CHHHHHHHc-ccc
Q 031725 130 KALKTIEKN--GLDAVAKKA-GID 150 (154)
Q Consensus 130 kaLRTI~K~--Gld~yl~k~-~~~ 150 (154)
.++.+|+.. |+++||.+. |++
T Consensus 33 ~~l~~i~~~yGs~e~Yl~~~lgl~ 56 (68)
T PF13348_consen 33 AALDAIDERYGSVENYLREELGLS 56 (68)
T ss_dssp HHHHHHHHHHSSHHHHHHHT-T--
T ss_pred HHHHHHHHHcCCHHHHHHHcCCCC
Confidence 457788877 799999665 764
No 10
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=18.75 E-value=51 Score=27.06 Aligned_cols=17 Identities=29% Similarity=0.542 Sum_probs=12.4
Q ss_pred cccccCccccccccccc
Q 031725 80 VCPFTGKKSNKANKVSF 96 (154)
Q Consensus 80 ~C~ltGKk~~~GNnVSh 96 (154)
.|++||+....+..|.-
T Consensus 5 ~CEiCG~~i~~~~~v~v 21 (165)
T COG1813 5 GCELCGREIDKPIKVKV 21 (165)
T ss_pred ceeccccccCCCeeEEe
Confidence 39999998876665544
Done!