Query 036943
Match_columns 77
No_of_seqs 110 out of 689
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 06:58:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036943.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036943hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00169 CETS family protein; 99.9 1.1E-25 2.3E-30 150.5 7.3 77 1-77 1-77 (175)
2 KOG3346 Phosphatidylethanolami 99.9 1.3E-23 2.7E-28 141.6 7.6 74 4-77 3-78 (185)
3 cd00866 PEBP_euk PhosphatidylE 99.4 2E-12 4.3E-17 83.5 5.8 51 27-77 2-54 (154)
4 PF01161 PBP: Phosphatidyletha 98.8 6.5E-09 1.4E-13 66.4 5.2 44 26-76 2-47 (146)
5 cd00457 PEBP PhosphatidylEthan 97.9 1.8E-05 3.8E-10 51.9 4.1 41 36-76 6-52 (159)
6 PRK10257 putative kinase inhib 96.8 0.0023 4.9E-08 42.3 4.2 26 51-76 31-57 (158)
7 PRK09818 putative kinase inhib 96.7 0.0035 7.7E-08 42.4 4.4 47 28-76 22-78 (183)
8 cd00865 PEBP_bact_arch Phospha 96.4 0.0036 7.8E-08 40.5 3.2 26 50-75 26-52 (150)
9 COG1881 Phospholipid-binding p 96.4 0.0041 8.9E-08 41.8 3.3 43 34-76 27-74 (174)
10 TIGR00481 Raf kinase inhibitor 96.3 0.0059 1.3E-07 39.5 3.8 26 51-76 15-41 (141)
11 PF07703 A2M_N_2: Alpha-2-macr 44.5 66 0.0014 19.4 4.4 17 54-71 114-130 (136)
12 PF00827 Ribosomal_L15e: Ribos 40.7 15 0.00034 25.2 1.1 14 62-75 126-139 (192)
13 PRK04243 50S ribosomal protein 38.9 38 0.00083 23.4 2.8 15 62-76 127-141 (196)
14 PTZ00026 60S ribosomal protein 35.2 48 0.001 23.0 2.8 15 62-76 127-141 (204)
15 TIGR00334 5S_RNA_mat_M5 ribonu 35.0 28 0.00061 23.5 1.7 14 62-75 46-59 (174)
16 KOG1678 60s ribosomal protein 34.7 26 0.00056 23.9 1.4 12 62-73 127-138 (204)
17 COG0335 RplS Ribosomal protein 33.5 45 0.00096 21.2 2.3 28 4-32 4-31 (115)
18 COG1658 Small primase-like pro 32.0 34 0.00074 21.9 1.6 12 64-75 56-67 (127)
19 PHA01814 hypothetical protein 26.6 42 0.0009 21.4 1.3 30 15-44 103-135 (137)
20 PRK04017 hypothetical protein; 25.8 51 0.0011 21.2 1.6 14 62-75 64-77 (132)
21 PHA02605 54 baseplate subunit; 24.7 32 0.0007 25.2 0.6 72 1-76 92-170 (305)
22 COG3565 Predicted dioxygenase 23.9 1.2E+02 0.0027 19.6 3.1 24 49-73 97-120 (138)
23 COG1632 RPL15A Ribosomal prote 21.7 72 0.0016 22.0 1.8 14 62-75 126-139 (195)
24 PF01781 Ribosomal_L38e: Ribos 20.9 30 0.00066 20.0 -0.1 20 54-73 32-51 (69)
25 PTZ00181 60S ribosomal protein 20.1 69 0.0015 19.1 1.3 13 61-73 39-51 (82)
No 1
>PLN00169 CETS family protein; Provisional
Probab=99.92 E-value=1.1e-25 Score=150.50 Aligned_cols=77 Identities=78% Similarity=1.290 Sum_probs=73.0
Q ss_pred CCCccccccccCCcccccCCCCCCCceEEEEECCeEeCCCceeCccccccCCeEEEecCCCCCeEEEEEeCCCCCCC
Q 036943 1 MSSRDRDPLILGRVVGDVLDNFTRTIPMRITYLNKDVNNGRELKPSEVLNQPRVEIGGDDLRTFYTLVMVDPDAPSP 77 (77)
Q Consensus 1 m~~~~~~~l~~~~Iipdvl~~f~P~~~L~V~y~~~~V~~G~~l~~~~~~~~P~i~~~~~~~~~~yTLvmvDPDaPsr 77 (77)
|+..++++|++++||||||+.|.|+..|+|+|++..|++|+.|++++++++|+|+|.+.+.+++|||+|+|||||+|
T Consensus 1 ~~~~~~~~l~~~~iipdvid~f~P~~~L~V~y~s~~V~~G~~l~p~~t~~~P~i~~~~~~~~~~ytlim~DpDaP~~ 77 (175)
T PLN00169 1 MSPRDRDPLVVGRVVGDVLDPFTRSISLRVTYGSREVNNGCELKPSQVVNQPRVDIGGEDLRTFYTLVMVDPDAPSP 77 (175)
T ss_pred CCcccccchhhCCcCCcccCCcCCceEEEEEECCcCcCCcCCCCHHHhccCCEEEEccCCCCceeEEEEECCCCCCC
Confidence 77799999999999999999999999999999988999999999999999999999876667999999999999985
No 2
>KOG3346 consensus Phosphatidylethanolamine binding protein [General function prediction only]
Probab=99.90 E-value=1.3e-23 Score=141.61 Aligned_cols=74 Identities=49% Similarity=0.735 Sum_probs=69.5
Q ss_pred ccccccccCCcccccCCCCCCCceEEEEECC-eEeCCCceeCccccccCCeEEEecC-CCCCeEEEEEeCCCCCCC
Q 036943 4 RDRDPLILGRVVGDVLDNFTRTIPMRITYLN-KDVNNGRELKPSEVLNQPRVEIGGD-DLRTFYTLVMVDPDAPSP 77 (77)
Q Consensus 4 ~~~~~l~~~~Iipdvl~~f~P~~~L~V~y~~-~~V~~G~~l~~~~~~~~P~i~~~~~-~~~~~yTLvmvDPDaPsr 77 (77)
.+++.+.+++||+|||+.+.|...|+|+|++ ..|++|+.|+|++++++|+|+|.+. +.+++|||+|+|||||||
T Consensus 3 ~~~~~~~~~~iv~Dvl~~~~p~~~l~V~y~~~~~v~~G~~l~pt~~~~~P~v~~~~~a~~~~~yTLvm~DPDaPsr 78 (185)
T KOG3346|consen 3 DIRDPLNKHRIVPDVLDDFEPSVKLNVTYNSDIVVENGNELTPTQVKNRPIVSWDGFADPGSLYTLVMTDPDAPSR 78 (185)
T ss_pred chhhhhhccCcchhhhccCCCceEEEEEeCCCeeecCCCEeCchhhccCCeEEEcCcCCCCCeEEEEEeCCCCCCC
Confidence 6789999999999999998999999999965 8899999999999999999999973 669999999999999997
No 3
>cd00866 PEBP_euk PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in eukaryotes. PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea). The members in this subgroup are present in eukaryotes. Members here include those in plants such as Arabidopsis thaliana FLOWERING LOCUS (FT) and TERMINAL FLOWER1 (FT1) which function as a promoter and a repressor of the floral transitions, respectively as well as the mammalian Raf kinase inhibitory protein (RKIP) which inhibits MAP kinase (Raf-MEK-ERK), G protein-coupled receptor (GPCR) kinase and NFkappaB signaling cascades. Although their overall structures are similar, the members of the PEBP family have very different substrates and oligomerization states (monomer/dimer/tetramer).
Probab=99.35 E-value=2e-12 Score=83.50 Aligned_cols=51 Identities=43% Similarity=0.679 Sum_probs=46.9
Q ss_pred eEEEEECC-eEeCCCceeCccccccCCeEEEecCC-CCCeEEEEEeCCCCCCC
Q 036943 27 PMRITYLN-KDVNNGRELKPSEVLNQPRVEIGGDD-LRTFYTLVMVDPDAPSP 77 (77)
Q Consensus 27 ~L~V~y~~-~~V~~G~~l~~~~~~~~P~i~~~~~~-~~~~yTLvmvDPDaPsr 77 (77)
.|.|+|++ ..+.+|+.+++++++..|+|+|.... .++.|||+|+|||+|++
T Consensus 2 ~l~v~y~~~~~v~~G~~l~~~~~~~~P~i~~~~~~~~~~~y~lvm~DpD~p~~ 54 (154)
T cd00866 2 DLTVSYGSSGVVTPGNLLTPSETQKAPTVSFSSEDPPDKLYTLVMVDPDAPSR 54 (154)
T ss_pred eEEEEECCCcCcCCCCCCCHHHhCcCCeEEEecCCCCCCeEEEEEECCCCCCC
Confidence 68999987 88999999999999999999999875 58999999999999974
No 4
>PF01161 PBP: Phosphatidylethanolamine-binding protein; InterPro: IPR008914 The PEBP (PhosphatidylEthanolamine-Binding Protein) family is a highly conserved group of proteins that have been identified in numerous tissues in a wide variety of organisms, including bacteria, yeast, nematodes, plants, drosophila and mammals. The various functions described for members of this family include lipid binding, neuronal development [], serine protease inhibition [], the control of the morphological switch between shoot growth and flower structures [], and the regulation of several signalling pathways such as the MAP kinase pathway [], and the NF-kappaB pathway []. The control of the latter two pathways involves the PEBP protein RKIP, which interacts with MEK and Raf-1 to inhibit the MAP kinase pathway, and with TAK1, NIK, IKKalpha and IKKbeta to inhibit the NF-kappaB pathway. Other PEBP-like proteins that show strong structural homology to PEBP include Escherichia coli YBHB and YBCL, the Rattus norvegicus (Rat) neuropeptide HCNP, and Antirrhinum majus (Garden snapdragon) protein centroradialis (CEN). Structures have been determined for several members of the PEBP-like family, all of which show extensive fold conservation. The structure consists of a large central beta-sheet flanked by a smaller beta-sheet on one side, and an alpha helix on the other. Sequence alignments show two conserved central regions, CR1 and CR2, that form a consensus signature for the PEBP family. These two regions form part of the ligand-binding site, which can accommodate various anionic groups. The N- and C-terminal regions are the least conserved, and may be involved in interactions with different protein partners. The N-terminal residues 2-12 form the natural cleavage peptide HCNP involved in neuronal development. The C-terminal region is deleted in plant and bacterial PEBP homologues, and may help control accessibility to the active site. ; PDB: 1BD9_A 1BEH_A 2QYQ_A 2L7W_A 3AXY_A 2IQX_C 2IQY_A 1KN3_A 1FUX_A 1B7A_A ....
Probab=98.84 E-value=6.5e-09 Score=66.45 Aligned_cols=44 Identities=41% Similarity=0.588 Sum_probs=38.7
Q ss_pred ceEEEEE-CCeEeCCCceeCccc-cccCCeEEEecCCCCCeEEEEEeCCCCCC
Q 036943 26 IPMRITY-LNKDVNNGRELKPSE-VLNQPRVEIGGDDLRTFYTLVMVDPDAPS 76 (77)
Q Consensus 26 ~~L~V~y-~~~~V~~G~~l~~~~-~~~~P~i~~~~~~~~~~yTLvmvDPDaPs 76 (77)
..|.|.| ++..+.+|+.++++. ++..|+ ..+.|||+|+|||+|+
T Consensus 2 ~~L~v~f~~~~~~~~G~~~sp~~~~~~~P~-------~~~~y~lim~D~D~P~ 47 (146)
T PF01161_consen 2 GKLPVKFTGNKSVCPGNNVSPPLSWQNAPT-------GTKSYTLIMVDPDAPS 47 (146)
T ss_dssp CEEEEEECTTEECSTTEEEEGGGECSS-TC-------TTSEEEEEEEETTSSB
T ss_pred cCcCceeEcccccCCCCCCCcCcccccCCC-------CCcEEEEEEECCCCCc
Confidence 4689999 788899999999999 888997 3789999999999987
No 5
>cd00457 PEBP PhosphatidylEthanolamine-Binding Protein (PEBP) domain. PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea). A number of biological roles for members of the PEBP family include serine protease inhibition, membrane biogenesis, regulation of flowering plant stem architecture, and Raf-1 kinase inhibition. Although their overall structures are similar, the members of the PEBP family bind very different substrates including phospholipids, opioids, and hydrophobic odorant molecules as well as having different oligomerization states (monomer/dimer/tetramer).
Probab=97.90 E-value=1.8e-05 Score=51.93 Aligned_cols=41 Identities=39% Similarity=0.511 Sum_probs=32.7
Q ss_pred EeCC-CceeCc----cccccCCeEEEecCC-CCCeEEEEEeCCCCCC
Q 036943 36 DVNN-GRELKP----SEVLNQPRVEIGGDD-LRTFYTLVMVDPDAPS 76 (77)
Q Consensus 36 ~V~~-G~~l~~----~~~~~~P~i~~~~~~-~~~~yTLvmvDPDaPs 76 (77)
.+.. |+.|+. ......|.++|...+ ..+.|+|+|+|||||.
T Consensus 6 ~~~~~g~~lp~~~~~~g~~~sP~l~w~~~p~~t~s~ali~~DpDap~ 52 (159)
T cd00457 6 EVGPSGSVLPPEYSFEGVGRFPSLSWDGPPPDVKEYVLVMEDPDAPL 52 (159)
T ss_pred CcCCCCCccChhhccCCCCcCCceEecCCCCCCeEEEEEEECCCCCC
Confidence 4555 777777 677778899998764 4689999999999984
No 6
>PRK10257 putative kinase inhibitor protein; Provisional
Probab=96.81 E-value=0.0023 Score=42.35 Aligned_cols=26 Identities=23% Similarity=0.441 Sum_probs=21.7
Q ss_pred CCeEEEecCCC-CCeEEEEEeCCCCCC
Q 036943 51 QPRVEIGGDDL-RTFYTLVMVDPDAPS 76 (77)
Q Consensus 51 ~P~i~~~~~~~-~~~yTLvmvDPDaPs 76 (77)
-|.++|...+. -+.|.|+|.|||||+
T Consensus 31 SP~L~w~~~P~~t~s~ali~~DpDap~ 57 (158)
T PRK10257 31 SPHLAWDDVPAGTKSFVVTCYDPDAPT 57 (158)
T ss_pred CceEEEcCCCCCceEEEEEEECCCCCC
Confidence 57789987653 489999999999996
No 7
>PRK09818 putative kinase inhibitor; Provisional
Probab=96.66 E-value=0.0035 Score=42.35 Aligned_cols=47 Identities=26% Similarity=0.591 Sum_probs=33.7
Q ss_pred EEEEECCeEeCCCceeCccccc---------cCCeEEEecCCC-CCeEEEEEeCCCCCC
Q 036943 28 MRITYLNKDVNNGRELKPSEVL---------NQPRVEIGGDDL-RTFYTLVMVDPDAPS 76 (77)
Q Consensus 28 L~V~y~~~~V~~G~~l~~~~~~---------~~P~i~~~~~~~-~~~yTLvmvDPDaPs 76 (77)
++|+ +..+..|..|....+. .-|.++|...+. -+.|.|+|.|||||.
T Consensus 22 ~~lt--S~~f~~G~~ip~~~~~~~~~~~G~n~SP~L~W~~~P~gtks~aLi~~DpDaP~ 78 (183)
T PRK09818 22 FQVT--SNEIKTGEQLTTSHVFSGFGCEGGNTSPSLTWSGAPEGTKSFAVTVYDPDAPT 78 (183)
T ss_pred EEEE--CcCccCcCCCCHHHcccccCCCCCCcceeEEEccCCCCcEEEEEEEECCCCCC
Confidence 5554 3355677777765432 368899987653 478999999999996
No 8
>cd00865 PEBP_bact_arch PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea. PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea). The members in this subgroup are present in bacterial and archaea. Members here include Escherichia coli YBHB and YBCL which are thought to regulate protein phosphorylation as well as Sulfolobus solfataricus SsCEI which inhibits serine proteases alpha-chymotrypsin and elastase. Although their overall structures are similar, the members of the PEBP family have very different substrates and oligomerization states (monomer/dimer/tetramer). In a few of the bacterial members present here the dimerization interface is proposed to form the ligand binding site, unlike in other PEBP members.
Probab=96.45 E-value=0.0036 Score=40.49 Aligned_cols=26 Identities=31% Similarity=0.455 Sum_probs=21.4
Q ss_pred cCCeEEEecCC-CCCeEEEEEeCCCCC
Q 036943 50 NQPRVEIGGDD-LRTFYTLVMVDPDAP 75 (77)
Q Consensus 50 ~~P~i~~~~~~-~~~~yTLvmvDPDaP 75 (77)
.-|.|+|...+ ..+.|+|+|+|||+|
T Consensus 26 ~SP~l~w~~~p~~t~s~al~m~D~Dap 52 (150)
T cd00865 26 VSPPLSWSGVPAGTKSLALIVEDPDAP 52 (150)
T ss_pred cCCCeEEcCCCCCCeEEEEEEEcCCCC
Confidence 35778998764 368999999999998
No 9
>COG1881 Phospholipid-binding protein [General function prediction only]
Probab=96.40 E-value=0.0041 Score=41.79 Aligned_cols=43 Identities=21% Similarity=0.329 Sum_probs=30.7
Q ss_pred CeEeCCCceeCcccc----ccCCeEEEecCC-CCCeEEEEEeCCCCCC
Q 036943 34 NKDVNNGRELKPSEV----LNQPRVEIGGDD-LRTFYTLVMVDPDAPS 76 (77)
Q Consensus 34 ~~~V~~G~~l~~~~~----~~~P~i~~~~~~-~~~~yTLvmvDPDaPs 76 (77)
+..+..|+.+....+ .--|.++|...+ ..+.|.|+|.|||||+
T Consensus 27 s~~f~~g~~ip~~~t~~g~~~sPpl~ws~~P~~tkS~AL~v~DpDAP~ 74 (174)
T COG1881 27 SNAFADGAPIPDEYTCGGPNISPPLSWSGVPEGTKSFALTVDDPDAPT 74 (174)
T ss_pred chhhhCCCccchhhhcCCCCcCCceeecCCCCCCeeEEEEEECCCCCC
Confidence 345677777765544 335668888653 3578999999999995
No 10
>TIGR00481 Raf kinase inhibitor-like protein, YbhB/YbcL family.
Probab=96.35 E-value=0.0059 Score=39.48 Aligned_cols=26 Identities=31% Similarity=0.506 Sum_probs=21.6
Q ss_pred CCeEEEecCCC-CCeEEEEEeCCCCCC
Q 036943 51 QPRVEIGGDDL-RTFYTLVMVDPDAPS 76 (77)
Q Consensus 51 ~P~i~~~~~~~-~~~yTLvmvDPDaPs 76 (77)
-|.++|...+. .+.|.|+|.|||||+
T Consensus 15 SP~l~w~~~P~~t~s~al~~~D~Dap~ 41 (141)
T TIGR00481 15 SPPLSWDGVPEGAKSLALTCIDPDAPT 41 (141)
T ss_pred CcEEEEcCCCCCceEEEEEEECCCCCC
Confidence 67799987643 479999999999996
No 11
>PF07703 A2M_N_2: Alpha-2-macroglobulin family N-terminal region; InterPro: IPR011625 This is a domain of the alpha-2-macroglobulin family. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; PDB: 2QKI_D 3L3O_D 3NMS_A 2ICF_A 2A73_A 2ICE_D 2HR0_A 2A74_A 2XWJ_G 3OHX_A ....
Probab=44.45 E-value=66 Score=19.39 Aligned_cols=17 Identities=24% Similarity=0.288 Sum_probs=10.8
Q ss_pred EEEecCCCCCeEEEEEeC
Q 036943 54 VEIGGDDLRTFYTLVMVD 71 (77)
Q Consensus 54 i~~~~~~~~~~yTLvmvD 71 (77)
+++... .+...+|.+||
T Consensus 114 ~~i~~~-~~s~v~l~~VD 130 (136)
T PF07703_consen 114 LRIKAP-PNSLVGLSAVD 130 (136)
T ss_dssp EEEEES-TTEEEEEEEEE
T ss_pred EEEEeC-CCCEEEEEEeE
Confidence 344443 37788888887
No 12
>PF00827 Ribosomal_L15e: Ribosomal L15; InterPro: IPR000439 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 archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities []. One of these families consists of: Mammalian L15. Insect L15. Plant L15. Yeast YL10 (L13) (Rp15r). Archaebacterial L15e. These proteins have about 200 amino acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_P 4A1E_L 4A17_L 4A1A_L 4A1C_L 2ZKR_m 3IZS_P 1S1I_L 3O58_O 3O5H_O ....
Probab=40.66 E-value=15 Score=25.19 Aligned_cols=14 Identities=29% Similarity=0.935 Sum_probs=10.9
Q ss_pred CCeEEEEEeCCCCC
Q 036943 62 RTFYTLVMVDPDAP 75 (77)
Q Consensus 62 ~~~yTLvmvDPDaP 75 (77)
-+.|-+|||||.-|
T Consensus 126 yK~fEVIlVDp~h~ 139 (192)
T PF00827_consen 126 YKWFEVILVDPNHP 139 (192)
T ss_dssp EEEEEEEEE-TTSH
T ss_pred ceeEEEEEecCCcH
Confidence 46899999999865
No 13
>PRK04243 50S ribosomal protein L15e; Validated
Probab=38.92 E-value=38 Score=23.36 Aligned_cols=15 Identities=33% Similarity=0.917 Sum_probs=12.6
Q ss_pred CCeEEEEEeCCCCCC
Q 036943 62 RTFYTLVMVDPDAPS 76 (77)
Q Consensus 62 ~~~yTLvmvDPDaPs 76 (77)
-+.|-+|||||.-|.
T Consensus 127 yK~fEVIlVDp~H~a 141 (196)
T PRK04243 127 YKWYEVILVDPHHPA 141 (196)
T ss_pred cccEEEEEecCCCcc
Confidence 478999999998764
No 14
>PTZ00026 60S ribosomal protein L15; Provisional
Probab=35.23 E-value=48 Score=23.03 Aligned_cols=15 Identities=33% Similarity=0.696 Sum_probs=12.6
Q ss_pred CCeEEEEEeCCCCCC
Q 036943 62 RTFYTLVMVDPDAPS 76 (77)
Q Consensus 62 ~~~yTLvmvDPDaPs 76 (77)
-+.|-+|||||.-|.
T Consensus 127 yK~yEVILvDp~H~a 141 (204)
T PTZ00026 127 YKFYEVILVDPFHNA 141 (204)
T ss_pred cccEEEEEecCCCcc
Confidence 478999999998764
No 15
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=35.02 E-value=28 Score=23.49 Aligned_cols=14 Identities=29% Similarity=0.648 Sum_probs=11.0
Q ss_pred CCeEEEEEeCCCCC
Q 036943 62 RTFYTLVMVDPDAP 75 (77)
Q Consensus 62 ~~~yTLvmvDPDaP 75 (77)
...=.+|++|||.+
T Consensus 46 ~~rgVIIfTDpD~~ 59 (174)
T TIGR00334 46 KKQGVIILTDPDFP 59 (174)
T ss_pred hcCCEEEEeCCCCc
Confidence 35567899999976
No 16
>KOG1678 consensus 60s ribosomal protein L15 [Translation, ribosomal structure and biogenesis]
Probab=34.65 E-value=26 Score=23.88 Aligned_cols=12 Identities=25% Similarity=0.758 Sum_probs=10.4
Q ss_pred CCeEEEEEeCCC
Q 036943 62 RTFYTLVMVDPD 73 (77)
Q Consensus 62 ~~~yTLvmvDPD 73 (77)
=++|-+|||||+
T Consensus 127 Yk~fEVIlvDp~ 138 (204)
T KOG1678|consen 127 YKYFEVILVDPF 138 (204)
T ss_pred eeeEEEEEECcH
Confidence 468999999996
No 17
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=33.47 E-value=45 Score=21.18 Aligned_cols=28 Identities=14% Similarity=0.134 Sum_probs=19.6
Q ss_pred ccccccccCCcccccCCCCCCCceEEEEE
Q 036943 4 RDRDPLILGRVVGDVLDNFTRTIPMRITY 32 (77)
Q Consensus 4 ~~~~~l~~~~Iipdvl~~f~P~~~L~V~y 32 (77)
...+.|++..+-.| +|+|.|--.++|.+
T Consensus 4 ~~i~~le~~q~~~~-iP~f~~GDtvrv~v 31 (115)
T COG0335 4 PIIQQLEQEQIKKD-IPSFRPGDTVRVHV 31 (115)
T ss_pred HHHHHHHHHHHHhh-CCCCCCCCEEEEEE
Confidence 34566666666666 89999987777665
No 18
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=32.03 E-value=34 Score=21.90 Aligned_cols=12 Identities=25% Similarity=0.479 Sum_probs=9.6
Q ss_pred eEEEEEeCCCCC
Q 036943 64 FYTLVMVDPDAP 75 (77)
Q Consensus 64 ~yTLvmvDPDaP 75 (77)
.=.++++|||.+
T Consensus 56 k~VIILTD~D~~ 67 (127)
T COG1658 56 KGVIILTDPDRK 67 (127)
T ss_pred CCEEEEeCCCcc
Confidence 347999999975
No 19
>PHA01814 hypothetical protein
Probab=26.65 E-value=42 Score=21.42 Aligned_cols=30 Identities=37% Similarity=0.640 Sum_probs=21.8
Q ss_pred ccccCCCCC-CC-ceEEEEECCeEe-CCCceeC
Q 036943 15 VGDVLDNFT-RT-IPMRITYLNKDV-NNGRELK 44 (77)
Q Consensus 15 ipdvl~~f~-P~-~~L~V~y~~~~V-~~G~~l~ 44 (77)
|-|||..|. |- -.+.+.|.++.+ +.|..++
T Consensus 103 iddvls~fekplesdi~iiyq~kviyd~gkvid 135 (137)
T PHA01814 103 IDDVLSNFEKPLESDITIIYQNKVIYDNGKVID 135 (137)
T ss_pred HHHHHhhccCccccceEEEEeccEEEeCceecc
Confidence 678888887 53 458888976665 7787764
No 20
>PRK04017 hypothetical protein; Provisional
Probab=25.83 E-value=51 Score=21.24 Aligned_cols=14 Identities=21% Similarity=0.256 Sum_probs=11.1
Q ss_pred CCeEEEEEeCCCCC
Q 036943 62 RTFYTLVMVDPDAP 75 (77)
Q Consensus 62 ~~~yTLvmvDPDaP 75 (77)
+..=.++++|||.+
T Consensus 64 ~~r~VIILTD~D~~ 77 (132)
T PRK04017 64 RGKEVIILTDFDRK 77 (132)
T ss_pred cCCeEEEEECCCcc
Confidence 45568999999975
No 21
>PHA02605 54 baseplate subunit; Provisional
Probab=24.68 E-value=32 Score=25.16 Aligned_cols=72 Identities=25% Similarity=0.246 Sum_probs=40.5
Q ss_pred CCCccccccccCCcccccCCCCC----CCceEEEEECCeEe-CCCceeCcc--ccccCCeEEEecCCCCCeEEEEEeCCC
Q 036943 1 MSSRDRDPLILGRVVGDVLDNFT----RTIPMRITYLNKDV-NNGRELKPS--EVLNQPRVEIGGDDLRTFYTLVMVDPD 73 (77)
Q Consensus 1 m~~~~~~~l~~~~Iipdvl~~f~----P~~~L~V~y~~~~V-~~G~~l~~~--~~~~~P~i~~~~~~~~~~yTLvmvDPD 73 (77)
|++++.+.|--.-.+...|.+|- ....|.| ..| -||+.|.-+ -....|.|++...+-+.+=.=+++|.|
T Consensus 92 ms~r~v~sl~g~~~~g~~l~~f~~~~~~~~gl~v----~sV~~P~~~l~ye~d~n~~~P~i~~t~rEFDPLtVtF~vDse 167 (305)
T PHA02605 92 MSSRTVQSLLGQFEVGTYLLDFFNMAYYNSGLLI----YSVKMPENRLGYEMDYNHNSPNIRITGREYDPLVLSFRMDSE 167 (305)
T ss_pred cCHHHHHHhcCchhHhHHHHHHHhccccccceEE----EEeecCCccccceeeccCCCCceEEeccccCCEEEEEEECHH
Confidence 45555555554444444444331 2222222 245 478886554 346799999988764555555778877
Q ss_pred CCC
Q 036943 74 APS 76 (77)
Q Consensus 74 aPs 76 (77)
+.+
T Consensus 168 ~~~ 170 (305)
T PHA02605 168 ASN 170 (305)
T ss_pred HHH
Confidence 654
No 22
>COG3565 Predicted dioxygenase of extradiol dioxygenase family [General function prediction only]
Probab=23.91 E-value=1.2e+02 Score=19.57 Aligned_cols=24 Identities=29% Similarity=0.480 Sum_probs=20.1
Q ss_pred ccCCeEEEecCCCCCeEEEEEeCCC
Q 036943 49 LNQPRVEIGGDDLRTFYTLVMVDPD 73 (77)
Q Consensus 49 ~~~P~i~~~~~~~~~~yTLvmvDPD 73 (77)
..+|.|+|.+.. +..-||.+-||-
T Consensus 97 ~i~P~vRF~Ge~-gEq~TlFl~DP~ 120 (138)
T COG3565 97 HIPPKVRFKGEP-GEQRTLFLFDPS 120 (138)
T ss_pred ccCceEEecCCc-cceEEEEEECCC
Confidence 458899999975 888999999984
No 23
>COG1632 RPL15A Ribosomal protein L15E [Translation, ribosomal structure and biogenesis]
Probab=21.75 E-value=72 Score=22.01 Aligned_cols=14 Identities=29% Similarity=0.911 Sum_probs=12.0
Q ss_pred CCeEEEEEeCCCCC
Q 036943 62 RTFYTLVMVDPDAP 75 (77)
Q Consensus 62 ~~~yTLvmvDPDaP 75 (77)
-+.|-+|||||+-|
T Consensus 126 yK~fEvIlvDp~H~ 139 (195)
T COG1632 126 YKYFEVILVDPRHP 139 (195)
T ss_pred eeeEEEEEecCCCh
Confidence 47899999999866
No 24
>PF01781 Ribosomal_L38e: Ribosomal L38e protein family; InterPro: IPR002675 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 L38e forms part of the 60S ribosomal subunit []. This family is found in eukaryotes.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_n 3IZR_n 4A1D_P 4A19_P 4A18_P 4A1B_P.
Probab=20.89 E-value=30 Score=19.99 Aligned_cols=20 Identities=30% Similarity=0.358 Sum_probs=11.4
Q ss_pred EEEecCCCCCeEEEEEeCCC
Q 036943 54 VEIGGDDLRTFYTLVMVDPD 73 (77)
Q Consensus 54 i~~~~~~~~~~yTLvmvDPD 73 (77)
+.|...-..-+|||++.|.+
T Consensus 32 tKFKvRcsryLYTLvv~d~~ 51 (69)
T PF01781_consen 32 TKFKVRCSRYLYTLVVKDKE 51 (69)
T ss_dssp EEEEEECSS-EEEESS-SHH
T ss_pred eEEEEEecceEEEEEEcCHH
Confidence 34443323689999998854
No 25
>PTZ00181 60S ribosomal protein L38; Provisional
Probab=20.06 E-value=69 Score=19.14 Aligned_cols=13 Identities=46% Similarity=0.685 Sum_probs=10.5
Q ss_pred CCCeEEEEEeCCC
Q 036943 61 LRTFYTLVMVDPD 73 (77)
Q Consensus 61 ~~~~yTLvmvDPD 73 (77)
..-+|||++.|.+
T Consensus 39 srYLYTLvv~D~~ 51 (82)
T PTZ00181 39 SRYLYTLVVADKK 51 (82)
T ss_pred cceEEEEEeCCHH
Confidence 3689999998853
Done!