Query 038679
Match_columns 101
No_of_seqs 133 out of 543
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 13:31:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038679.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038679hhsearch_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 1.7E-25 3.6E-30 136.0 3.0 38 1-38 1-38 (38)
3 PRK00465 rpmJ 50S ribosomal pr 99.9 4E-25 8.7E-30 133.3 4.0 37 1-38 1-37 (37)
4 COG0257 RpmJ Ribosomal protein 99.9 3.8E-25 8.2E-30 134.5 3.6 38 1-38 1-38 (38)
5 TIGR01022 rpmJ_bact ribosomal 99.9 1.7E-24 3.7E-29 130.7 4.0 37 1-38 1-37 (37)
6 PRK00831 rpmJ 50S ribosomal pr 99.9 7E-24 1.5E-28 130.4 3.8 38 1-38 1-41 (41)
7 CHL00029 rpl36 ribosomal prote 99.4 1.1E-13 2.3E-18 78.1 2.5 26 1-26 1-26 (26)
8 PF10984 DUF2794: Protein of u 49.0 11 0.00023 26.4 1.3 25 21-46 47-72 (85)
9 PF13806 Rieske_2: Rieske-like 42.1 25 0.00055 23.9 2.3 30 8-40 40-77 (104)
10 PF05258 DUF721: Protein of un 30.9 55 0.0012 20.0 2.4 23 12-35 39-62 (89)
11 PF03716 WCCH: WCCH motif ; I 28.3 36 0.00078 18.7 1.1 16 27-42 8-23 (25)
12 cd00472 Ribosomal_L24e_L24 Rib 22.8 64 0.0014 20.5 1.6 14 15-28 20-33 (54)
13 PRK00807 50S ribosomal protein 22.2 81 0.0018 19.6 2.0 14 15-28 18-31 (52)
14 COG2023 RPR2 RNase P subunit R 20.7 79 0.0017 22.9 1.9 19 10-28 58-86 (105)
15 PF01147 Crust_neurohorm: Crus 20.5 1.1 2.3E-05 30.4 -7.2 24 7-30 19-42 (73)
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=135.46 Aligned_cols=38 Identities=63% Similarity=1.176 Sum_probs=33.9
Q ss_pred CcccchhhhccCCceEEEeCCEEEEEcCCCCCcccccC
Q 038679 1 MKVRSSVKKLCQFCKIVKRRGHIFVICSANPKHKQRQG 38 (101)
Q Consensus 1 MKVrsSvKk~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=1.7e-25 Score=136.01 Aligned_cols=38 Identities=58% Similarity=1.142 Sum_probs=37.5
Q ss_pred CcccchhhhccCCceEEEeCCEEEEEcCCCCCcccccC
Q 038679 1 MKVRSSVKKLCQFCKIVKRRGHIFVICSANPKHKQRQG 38 (101)
Q Consensus 1 MKVrsSvKk~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=4e-25 Score=133.29 Aligned_cols=37 Identities=70% Similarity=1.231 Sum_probs=36.5
Q ss_pred CcccchhhhccCCceEEEeCCEEEEEcCCCCCcccccC
Q 038679 1 MKVRSSVKKLCQFCKIVKRRGHIFVICSANPKHKQRQG 38 (101)
Q Consensus 1 MKVrsSvKk~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=3.8e-25 Score=134.50 Aligned_cols=38 Identities=71% Similarity=1.241 Sum_probs=37.7
Q ss_pred CcccchhhhccCCceEEEeCCEEEEEcCCCCCcccccC
Q 038679 1 MKVRSSVKKLCQFCKIVKRRGHIFVICSANPKHKQRQG 38 (101)
Q Consensus 1 MKVrsSvKk~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=1.7e-24 Score=130.66 Aligned_cols=37 Identities=73% Similarity=1.240 Sum_probs=36.2
Q ss_pred CcccchhhhccCCceEEEeCCEEEEEcCCCCCcccccC
Q 038679 1 MKVRSSVKKLCQFCKIVKRRGHIFVICSANPKHKQRQG 38 (101)
Q Consensus 1 MKVrsSvKk~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=7e-24 Score=130.41 Aligned_cols=38 Identities=50% Similarity=0.919 Sum_probs=36.5
Q ss_pred Ccccchhhhc---cCCceEEEeCCEEEEEcCCCCCcccccC
Q 038679 1 MKVRSSVKKL---CQFCKIVKRRGHIFVICSANPKHKQRQG 38 (101)
Q Consensus 1 MKVrsSvKk~---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 9999999995 5999999999999999999999999998
No 7
>CHL00029 rpl36 ribosomal protein L36
Probab=99.41 E-value=1.1e-13 Score=78.12 Aligned_cols=26 Identities=58% Similarity=1.260 Sum_probs=25.5
Q ss_pred CcccchhhhccCCceEEEeCCEEEEE
Q 038679 1 MKVRSSVKKLCQFCKIVKRRGHIFVI 26 (101)
Q Consensus 1 MKVrsSvKk~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=48.99 E-value=11 Score=26.43 Aligned_cols=25 Identities=28% Similarity=0.484 Sum_probs=19.1
Q ss_pred CEEEEEcCCCCCcccccC-CCCCCCCC
Q 038679 21 GHIFVICSANPKHKQRQG-MSTFPNEG 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 45899997 999999999 55555455
No 9
>PF13806 Rieske_2: Rieske-like [2Fe-2S] domain; PDB: 2JO6_A 3C0D_A 3D89_A 2JZA_A.
Probab=42.08 E-value=25 Score=23.91 Aligned_cols=30 Identities=30% Similarity=0.482 Sum_probs=20.1
Q ss_pred hhccCCc--------eEEEeCCEEEEEcCCCCCcccccCCC
Q 038679 8 KKLCQFC--------KIVKRRGHIFVICSANPKHKQRQGMS 40 (101)
Q Consensus 8 Kk~C~~C--------~vVRRkGRlyViCK~nPRHKQRQG~~ 40 (101)
..+|++| .+-..+|..+|+| |-||++=-..
T Consensus 40 ~n~Cph~~~~~Ls~G~i~~~~g~~~V~C---PlH~~~f~L~ 77 (104)
T PF13806_consen 40 DNRCPHSQAGPLSDGLIGDGNGEPCVAC---PLHKWRFDLR 77 (104)
T ss_dssp ESBETTTTSSCGCGSEEEECTTEEEEEE---TTTTEEEETT
T ss_pred eccCCccCCcccceeEEccCCCCEEEEC---CCCCCeEECC
Confidence 3457666 3444578889999 7788775443
No 10
>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=30.90 E-value=55 Score=19.98 Aligned_cols=23 Identities=17% Similarity=0.300 Sum_probs=17.1
Q ss_pred CCceEEE-eCCEEEEEcCCCCCccc
Q 038679 12 QFCKIVK-RRGHIFVICSANPKHKQ 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 6788777 8999999996 654433
No 11
>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=28.33 E-value=36 Score=18.71 Aligned_cols=16 Identities=38% Similarity=0.798 Sum_probs=11.5
Q ss_pred cCCCCCcccccCCCCC
Q 038679 27 CSANPKHKQRQGMSTF 42 (101)
Q Consensus 27 CK~nPRHKQRQG~~t~ 42 (101)
|..=|||||..++...
T Consensus 8 cphCprHk~k~~m~~q 23 (25)
T PF03716_consen 8 CPHCPRHKQKKSMDQQ 23 (25)
T ss_pred CCCCcccccccccccc
Confidence 4556999998887543
No 12
>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=22.77 E-value=64 Score=20.49 Aligned_cols=14 Identities=36% Similarity=0.809 Sum_probs=12.5
Q ss_pred eEEEeCCEEEEEcC
Q 038679 15 KIVKRRGHIFVICS 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 13
>PRK00807 50S ribosomal protein L24e; Validated
Probab=22.17 E-value=81 Score=19.59 Aligned_cols=14 Identities=43% Similarity=0.781 Sum_probs=12.2
Q ss_pred eEEEeCCEEEEEcC
Q 038679 15 KIVKRRGHIFVICS 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 14
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=20.74 E-value=79 Score=22.89 Aligned_cols=19 Identities=37% Similarity=1.006 Sum_probs=14.4
Q ss_pred ccCCceE---------EE-eCCEEEEEcC
Q 038679 10 LCQFCKI---------VK-RRGHIFVICS 28 (101)
Q Consensus 10 ~C~~C~v---------VR-RkGRlyViCK 28 (101)
+|++|+- || ++++|.|.|.
T Consensus 58 ~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~ 86 (105)
T COG2023 58 ICKKCYTPLVPGKNARVRLRKGRVVVTCL 86 (105)
T ss_pred hccccCcccccCcceEEEEcCCeEEEEec
Confidence 4888875 33 7888999995
No 15
>PF01147 Crust_neurohorm: Crustacean CHH/MIH/GIH neurohormone family; InterPro: IPR001166 Arthropod express a family of neuropeptides [] which so far consist of the following types of neurohormones: Crustacean hyperglycemic hormone (CHH). CHH is primarily involved in blood sugar regulation, but also plays a role in the control of molting and reproduction. Molt-inhibiting hormone (MIH). MIH inhibits Y-organs where molting hormone (ecdysteroid) is secreted. A molting cycle is initiated when MIH secretion diminishes or stops. Gonad-inhibiting hormone (GIH), also known as vitellogenesis-inhibiting hormone (VIH) because of its role in inhibiting vitellogenesis in female animals. Mandibular organ-inhibiting hormone (MOIH). MOIH represses the synthesis of methyl farnesoate, the precursor of insect juvenile hormone III in the mandibular organ. Ion transport peptide (ITP) from locust. ITP stimulates salt and water reabsorption and inhibits acid secretion in the ileum of the locust. Caenorhabditis elegans hypothetical protein ZC168.2. These neurohormones are peptides of 70 to 80 residues which are processed from larger size precursors. They contain six conserved cysteines that are involved in disulphide bonds, as shown in the following schematic representation. ; GO: 0005184 neuropeptide hormone activity, 0005576 extracellular region; PDB: 1J0T_A.
Probab=20.54 E-value=1.1 Score=30.35 Aligned_cols=24 Identities=21% Similarity=0.526 Sum_probs=19.2
Q ss_pred hhhccCCceEEEeCCEEEEEcCCC
Q 038679 7 VKKLCQFCKIVKRRGHIFVICSAN 30 (101)
Q Consensus 7 vKk~C~~C~vVRRkGRlyViCK~n 30 (101)
|-.+|+||+-+=|+..|+..|++|
T Consensus 19 ldrVC~DCyNl~R~p~v~~~CR~n 42 (73)
T PF01147_consen 19 LDRVCDDCYNLFREPNVASECRSN 42 (73)
T ss_dssp HHHHHHHHHHHHT-TTTHHHHTSS
T ss_pred HHHHHHHHHHHHcCccHHHHHHHc
Confidence 456799999999998888888865
Done!