Query 034201
Match_columns 101
No_of_seqs 135 out of 542
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 10:54:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034201.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034201hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00444 Ribosomal_L36: Riboso 99.9 1.4E-25 3E-30 135.5 3.2 38 1-38 1-38 (38)
2 KOG4122 Mitochondrial/chloropl 99.9 1.3E-25 2.8E-30 136.5 3.0 38 1-38 1-38 (38)
3 PRK00465 rpmJ 50S ribosomal pr 99.9 3.8E-25 8.2E-30 133.4 4.0 37 1-38 1-37 (37)
4 COG0257 RpmJ Ribosomal protein 99.9 4.1E-25 8.8E-30 134.4 3.6 38 1-38 1-38 (38)
5 TIGR01022 rpmJ_bact ribosomal 99.9 1.6E-24 3.5E-29 130.8 4.0 37 1-38 1-37 (37)
6 PRK00831 rpmJ 50S ribosomal pr 99.9 4.5E-24 9.9E-29 131.3 4.0 38 1-38 1-41 (41)
7 CHL00029 rpl36 ribosomal prote 99.4 8.2E-14 1.8E-18 78.6 2.5 26 1-26 1-26 (26)
8 PF10984 DUF2794: Protein of u 45.6 13 0.00029 25.9 1.4 25 21-46 47-72 (85)
9 PF11137 DUF2909: Protein of u 39.3 14 0.00031 24.2 0.7 16 82-97 33-48 (63)
10 PF13806 Rieske_2: Rieske-like 37.3 32 0.00068 23.4 2.2 32 8-42 40-79 (104)
11 PF10893 DUF2724: Protein of u 35.2 9.4 0.0002 26.0 -0.6 17 69-87 6-22 (68)
12 PF03716 WCCH: WCCH motif ; I 33.6 23 0.0005 19.5 0.9 17 27-43 8-24 (25)
13 PF05258 DUF721: Protein of un 30.4 57 0.0012 19.9 2.4 23 12-35 39-62 (89)
14 PHA03343 US22 family homolog; 23.5 27 0.00059 31.6 0.0 73 15-92 311-389 (578)
15 cd00472 Ribosomal_L24e_L24 Rib 23.2 61 0.0013 20.6 1.6 14 15-28 20-33 (54)
16 PRK00807 50S ribosomal protein 22.5 92 0.002 19.3 2.3 14 15-28 18-31 (52)
17 COG2023 RPR2 RNase P subunit R 21.6 65 0.0014 23.3 1.7 20 9-28 57-86 (105)
18 PF08394 Arc_trans_TRASH: Arch 20.4 1.2E+02 0.0026 18.1 2.4 14 15-28 13-26 (37)
No 1
>PF00444 Ribosomal_L36: Ribosomal protein L36; InterPro: IPR000473 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 L36 is the smallest protein from the large subunit of the prokaryotic ribosome. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [] can be grouped into: bacterial L36; algal and plant chloroplast L36; Cyanelle L36. L36 is a small basic and cysteine-rich protein of 37 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBO_6 2HGU_8 2HGJ_8 1DGZ_A 1DFE_A 2HGQ_8 1VSP_b 1VSA_b 3PIP_4 1VOU_6 ....
Probab=99.91 E-value=1.4e-25 Score=135.50 Aligned_cols=38 Identities=63% Similarity=1.139 Sum_probs=33.9
Q ss_pred CcccchhhhcCCCceEEEeCCEEEEEcCCCCCcccccC
Q 034201 1 MKVRSSVKKMCEFCKIIKRRGRVYVICSANLKHKQRQG 38 (101)
Q Consensus 1 MKVRsSlKk~C~~C~vVRRkGRlyViCk~NPRHKQRQG 38 (101)
|||++|||++|++|++|+|+|||||||++|||||||||
T Consensus 1 MKVr~slk~~c~~C~~vrR~gr~~Vick~nprhKqrQg 38 (38)
T PF00444_consen 1 MKVRSSLKKRCKDCYVVRRKGRLYVICKKNPRHKQRQG 38 (38)
T ss_dssp -BESSS-S-SSSTSEEEEETTEEEEEESSSGGGCEEE-
T ss_pred CcchhhhhhcCCCCceEEECCEEEEECCCCCchhccCC
Confidence 99999999999999999999999999999999999998
No 2
>KOG4122 consensus Mitochondrial/chloroplast ribosomal protein L36 [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=1.3e-25 Score=136.53 Aligned_cols=38 Identities=61% Similarity=1.117 Sum_probs=37.5
Q ss_pred CcccchhhhcCCCceEEEeCCEEEEEcCCCCCcccccC
Q 034201 1 MKVRSSVKKMCEFCKIIKRRGRVYVICSANLKHKQRQG 38 (101)
Q Consensus 1 MKVRsSlKk~C~~C~vVRRkGRlyViCk~NPRHKQRQG 38 (101)
|||++|||++|++||+|+|+||+||||++|||||||||
T Consensus 1 fKvk~svkk~C~~Cy~VrRrgR~yViC~~~prHKqrqg 38 (38)
T KOG4122|consen 1 FKVKASVKKRCKDCYLVRRRGRVYVICKTHPRHKQRQG 38 (38)
T ss_pred CchhHHHHHhhhhceEEEEcccEEEEcCCCcchhhhcC
Confidence 89999999999999999999999999999999999997
No 3
>PRK00465 rpmJ 50S ribosomal protein L36; Reviewed
Probab=99.91 E-value=3.8e-25 Score=133.44 Aligned_cols=37 Identities=76% Similarity=1.180 Sum_probs=36.5
Q ss_pred CcccchhhhcCCCceEEEeCCEEEEEcCCCCCcccccC
Q 034201 1 MKVRSSVKKMCEFCKIIKRRGRVYVICSANLKHKQRQG 38 (101)
Q Consensus 1 MKVRsSlKk~C~~C~vVRRkGRlyViCk~NPRHKQRQG 38 (101)
|||++|||++|++|++|||+|+||||| +|||||||||
T Consensus 1 MKVr~SvKk~c~~C~vvrR~gr~~Vic-~nprhKqRQg 37 (37)
T PRK00465 1 MKVRASVKKICEKCKVIKRKGVVRVIC-ENPKHKQRQG 37 (37)
T ss_pred CcchhhhhhcCCCCEEEEECCEEEEEc-CCCCcccccC
Confidence 999999999999999999999999999 7999999998
No 4
>COG0257 RpmJ Ribosomal protein L36 [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=4.1e-25 Score=134.41 Aligned_cols=38 Identities=74% Similarity=1.209 Sum_probs=37.7
Q ss_pred CcccchhhhcCCCceEEEeCCEEEEEcCCCCCcccccC
Q 034201 1 MKVRSSVKKMCEFCKIIKRRGRVYVICSANLKHKQRQG 38 (101)
Q Consensus 1 MKVRsSlKk~C~~C~vVRRkGRlyViCk~NPRHKQRQG 38 (101)
|||++|+|++|++|++|||+|++||||++|||||||||
T Consensus 1 MKV~~SvK~~c~~CkivrRkGrv~VIck~~prhKqrQg 38 (38)
T COG0257 1 MKVRASVKKRCRDCKIVRRKGRVYVICKKNPKHKQRQG 38 (38)
T ss_pred CccccccccccCCceEEEecCEEEEEeCCCcchhhhcC
Confidence 99999999999999999999999999999999999998
No 5
>TIGR01022 rpmJ_bact ribosomal protein L36, bacterial type. Proteins found by this model occur exclusively in bacteria and organelles.
Probab=99.90 E-value=1.6e-24 Score=130.78 Aligned_cols=37 Identities=78% Similarity=1.189 Sum_probs=36.2
Q ss_pred CcccchhhhcCCCceEEEeCCEEEEEcCCCCCcccccC
Q 034201 1 MKVRSSVKKMCEFCKIIKRRGRVYVICSANLKHKQRQG 38 (101)
Q Consensus 1 MKVRsSlKk~C~~C~vVRRkGRlyViCk~NPRHKQRQG 38 (101)
||||+|||++|++|++|||+|+|||||+ |||||||||
T Consensus 1 MKVr~SvKk~c~~C~vvrR~grv~Vick-~prhKqRQG 37 (37)
T TIGR01022 1 MKVRASVKKICEKCKIIKRKGVVRVICK-NPKHKQRQG 37 (37)
T ss_pred CcchhhhhhhCcCCeEEEECCEEEEEeC-CCCccccCC
Confidence 9999999999999999999999999997 799999998
No 6
>PRK00831 rpmJ 50S ribosomal protein L36; Validated
Probab=99.89 E-value=4.5e-24 Score=131.26 Aligned_cols=38 Identities=50% Similarity=0.871 Sum_probs=36.5
Q ss_pred Ccccchhhhc---CCCceEEEeCCEEEEEcCCCCCcccccC
Q 034201 1 MKVRSSVKKM---CEFCKIIKRRGRVYVICSANLKHKQRQG 38 (101)
Q Consensus 1 MKVRsSlKk~---C~~C~vVRRkGRlyViCk~NPRHKQRQG 38 (101)
|||++|||++ |++|++|||+|++||||++|||||||||
T Consensus 1 MKVr~SvKk~~~~~~~c~vvrR~grv~Vick~nprhKqRQG 41 (41)
T PRK00831 1 MKVRNSLKSLKNRHRDCQVVRRKGRVYVINKKNPRFKARQG 41 (41)
T ss_pred CchhhhhhhhhccCCCCEEEEeCCEEEEEcCCCCcccccCC
Confidence 9999999994 5999999999999999999999999998
No 7
>CHL00029 rpl36 ribosomal protein L36
Probab=99.42 E-value=8.2e-14 Score=78.62 Aligned_cols=26 Identities=62% Similarity=1.308 Sum_probs=25.5
Q ss_pred CcccchhhhcCCCceEEEeCCEEEEE
Q 034201 1 MKVRSSVKKMCEFCKIIKRRGRVYVI 26 (101)
Q Consensus 1 MKVRsSlKk~C~~C~vVRRkGRlyVi 26 (101)
||||+|||++|++|++|||+|++|||
T Consensus 1 MKVr~Svkk~c~~c~ivrR~g~v~Vi 26 (26)
T CHL00029 1 MKIRASVRKICEKCRLIRRRGRIFVI 26 (26)
T ss_pred CcccccccccCCCCEEEeecCEEEEC
Confidence 99999999999999999999999996
No 8
>PF10984 DUF2794: Protein of unknown function (DUF2794); InterPro: IPR021252 This is a bacterial family of proteins with unknown function.
Probab=45.58 E-value=13 Score=25.92 Aligned_cols=25 Identities=28% Similarity=0.405 Sum_probs=18.7
Q ss_pred CEEEEEcCCCCCcccccC-cccccccC
Q 034201 21 GRVYVICSANLKHKQRQG-MSTFANEG 46 (101)
Q Consensus 21 GRlyViCk~NPRHKQRQG-~~t~a~~~ 46 (101)
--+|-|.| ||+...||| |...+..|
T Consensus 47 ~PlYrIeK-~p~l~~~qg~y~v~~~~G 72 (85)
T PF10984_consen 47 RPLYRIEK-RPKLARRQGAYAVIGEGG 72 (85)
T ss_pred CccEEEEe-CccchhhCCceeeecCCC
Confidence 35899997 999999999 44445444
No 9
>PF11137 DUF2909: Protein of unknown function (DUF2909); InterPro: IPR021313 This is a family of proteins conserved in Proteobacteria of unknown function.
Probab=39.32 E-value=14 Score=24.24 Aligned_cols=16 Identities=38% Similarity=0.553 Sum_probs=13.2
Q ss_pred chhhcchhhhhhhhhh
Q 034201 82 WSIIYGWRASLASLLF 97 (101)
Q Consensus 82 ~s~~~~wr~glas~l~ 97 (101)
++-..|||+|||.+||
T Consensus 33 m~~~L~~RV~lS~~l~ 48 (63)
T PF11137_consen 33 MVKALGRRVGLSALLF 48 (63)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4556799999999886
No 10
>PF13806 Rieske_2: Rieske-like [2Fe-2S] domain; PDB: 2JO6_A 3C0D_A 3D89_A 2JZA_A.
Probab=37.26 E-value=32 Score=23.43 Aligned_cols=32 Identities=28% Similarity=0.322 Sum_probs=21.2
Q ss_pred hhcCCCc--------eEEEeCCEEEEEcCCCCCcccccCcccc
Q 034201 8 KKMCEFC--------KIIKRRGRVYVICSANLKHKQRQGMSTF 42 (101)
Q Consensus 8 Kk~C~~C--------~vVRRkGRlyViCk~NPRHKQRQG~~t~ 42 (101)
..+|++| .+-...|..+|+| |-||++=-..|-
T Consensus 40 ~n~Cph~~~~~Ls~G~i~~~~g~~~V~C---PlH~~~f~L~tG 79 (104)
T PF13806_consen 40 DNRCPHSQAGPLSDGLIGDGNGEPCVAC---PLHKWRFDLRTG 79 (104)
T ss_dssp ESBETTTTSSCGCGSEEEECTTEEEEEE---TTTTEEEETTTT
T ss_pred eccCCccCCcccceeEEccCCCCEEEEC---CCCCCeEECCCc
Confidence 3456666 3444578889999 778887655543
No 11
>PF10893 DUF2724: Protein of unknown function (DUF2724); InterPro: IPR021221 This entry is represented by Bacteriophage 186, Fil. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=35.21 E-value=9.4 Score=25.96 Aligned_cols=17 Identities=41% Similarity=0.641 Sum_probs=13.9
Q ss_pred ccccccccCCCCcchhhcc
Q 034201 69 AGLASLIPKKHESWSIIYG 87 (101)
Q Consensus 69 ~g~as~~~~~~~~~s~~~~ 87 (101)
+..|+++ ++++ |+|-||
T Consensus 6 psfa~lL-kkQS-PamhyG 22 (68)
T PF10893_consen 6 PSFASLL-KKQS-PAMHYG 22 (68)
T ss_pred chHHHHH-HhcC-cccccC
Confidence 4678888 8888 999996
No 12
>PF03716 WCCH: WCCH motif ; InterPro: IPR005159 The WCCH motif is found in a retrotransposons and Gemini viruses. A specific function has not been associated to this motif [].
Probab=33.64 E-value=23 Score=19.47 Aligned_cols=17 Identities=35% Similarity=0.604 Sum_probs=12.4
Q ss_pred cCCCCCcccccCccccc
Q 034201 27 CSANLKHKQRQGMSTFA 43 (101)
Q Consensus 27 Ck~NPRHKQRQG~~t~a 43 (101)
|..=|||||..++..-|
T Consensus 8 cphCprHk~k~~m~~qa 24 (25)
T PF03716_consen 8 CPHCPRHKQKKSMDQQA 24 (25)
T ss_pred CCCCccccccccccccC
Confidence 45569999988876544
No 13
>PF05258 DUF721: Protein of unknown function (DUF721); InterPro: IPR007922 This family contains several actinomycete proteins of unknown function, and related sequences from other species.
Probab=30.44 E-value=57 Score=19.93 Aligned_cols=23 Identities=9% Similarity=0.215 Sum_probs=17.3
Q ss_pred CCceEEE-eCCEEEEEcCCCCCccc
Q 034201 12 EFCKIIK-RRGRVYVICSANLKHKQ 35 (101)
Q Consensus 12 ~~C~vVR-RkGRlyViCk~NPRHKQ 35 (101)
.+|+++. ++|.++|.|. ||-..+
T Consensus 39 ~~~~~~~i~~g~L~i~v~-~~~~~~ 62 (89)
T PF05258_consen 39 QHTRPVSIKDGTLVIEVD-SSAWAQ 62 (89)
T ss_pred ccEEEEEEECCEEEEEEC-CHHHHH
Confidence 5777777 8999999996 665443
No 14
>PHA03343 US22 family homolog; Provisional
Probab=23.46 E-value=27 Score=31.61 Aligned_cols=73 Identities=19% Similarity=0.269 Sum_probs=44.2
Q ss_pred eEEEeCCEEEEEcC----CCCCcccccCcccccccCCCC--CccccccccccccccccccccccccccCCCCcchhhcch
Q 034201 15 KIIKRRGRVYVICS----ANLKHKQRQGMSTFANEGLIP--FTSVETNVKQEIAPNHNIRAGLASLIPKKHESWSIIYGW 88 (101)
Q Consensus 15 ~vVRRkGRlyViCk----~NPRHKQRQG~~t~a~~~~~~--p~~~e~~~~~~i~~~~~~~~g~as~~~~~~~~~s~~~~w 88 (101)
.++-++|+|||+.+ .---+=.|-||+++.+.|.-- +.-.|.. -.|-...+--.+|++--+++ ++-+.||
T Consensus 311 ILiGe~GrVYVYdpG~v~~SLyLvSrsGF~dF~~rGLRE~~~~~~D~g----~tp~dyggDp~~silE~~~S-~dDLvga 385 (578)
T PHA03343 311 ILLGDDGFVYLYDDGGVGPVLHLLTKCGFADFCRRGLRERAGIDLDAG----STPIDYGEDPFKSILECRHS-IDDLVGA 385 (578)
T ss_pred EEEcCCceEEEEcCCCccceEEEeecccHHHHHHHHHHHhcCcccccc----cccccccCchhhhHHhhccC-HHHHHHH
Confidence 45679999999986 223455678999999988621 1111111 11111122225677766666 8888999
Q ss_pred hhhh
Q 034201 89 RASL 92 (101)
Q Consensus 89 r~gl 92 (101)
|==+
T Consensus 386 RDrl 389 (578)
T PHA03343 386 RDRL 389 (578)
T ss_pred HHHh
Confidence 8543
No 15
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=23.22 E-value=61 Score=20.57 Aligned_cols=14 Identities=29% Similarity=0.814 Sum_probs=12.5
Q ss_pred eEEEeCCEEEEEcC
Q 034201 15 KIIKRRGRVYVICS 28 (101)
Q Consensus 15 ~vVRRkGRlyViCk 28 (101)
.+||++|++|..|.
T Consensus 20 ~~Vr~Dgkv~~F~s 33 (54)
T cd00472 20 MYVRNDGKVFRFCS 33 (54)
T ss_pred EEEecCCCEEEEEC
Confidence 68999999999995
No 16
>PRK00807 50S ribosomal protein L24e; Validated
Probab=22.53 E-value=92 Score=19.34 Aligned_cols=14 Identities=29% Similarity=0.707 Sum_probs=12.2
Q ss_pred eEEEeCCEEEEEcC
Q 034201 15 KIIKRRGRVYVICS 28 (101)
Q Consensus 15 ~vVRRkGRlyViCk 28 (101)
.+|+.+|++|..|.
T Consensus 18 ~~vr~Dgkv~~Fcs 31 (52)
T PRK00807 18 MYVKKDGTILYFCS 31 (52)
T ss_pred EEEEeCCcEEEEeC
Confidence 46899999999996
No 17
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=21.58 E-value=65 Score=23.31 Aligned_cols=20 Identities=40% Similarity=0.916 Sum_probs=14.6
Q ss_pred hcCCCceE---------E-EeCCEEEEEcC
Q 034201 9 KMCEFCKI---------I-KRRGRVYVICS 28 (101)
Q Consensus 9 k~C~~C~v---------V-RRkGRlyViCk 28 (101)
.+|++|+- | -|+++|.|.|.
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~ 86 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCL 86 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEec
Confidence 34887765 2 37888999995
No 18
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=20.35 E-value=1.2e+02 Score=18.14 Aligned_cols=14 Identities=29% Similarity=0.707 Sum_probs=12.4
Q ss_pred eEEEeCCEEEEEcC
Q 034201 15 KIIKRRGRVYVICS 28 (101)
Q Consensus 15 ~vVRRkGRlyViCk 28 (101)
.++|.++++|..|-
T Consensus 13 ~~~k~~~~~y~fCC 26 (37)
T PF08394_consen 13 IVVKIGNKVYYFCC 26 (37)
T ss_pred EEEEECCeEEEEEC
Confidence 57899999999995
Done!