Query 038355
Match_columns 93
No_of_seqs 102 out of 225
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 10:09:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038355.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038355hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01158 Ribosomal_L36e: Ribos 100.0 1.3E-47 2.9E-52 263.8 7.6 86 1-86 13-98 (98)
2 PTZ00196 60S ribosomal protein 100.0 4.1E-47 8.8E-52 261.6 9.4 85 1-85 13-97 (98)
3 KOG3452 60S ribosomal protein 100.0 5.5E-45 1.2E-49 252.2 9.2 88 1-88 15-102 (102)
4 COG5051 RPL36A Ribosomal prote 100.0 1.3E-30 2.9E-35 178.6 7.8 81 2-82 16-96 (97)
5 KOG2659 LisH motif-containing 45.1 38 0.00083 26.6 4.1 64 19-82 80-150 (228)
6 PF08068 DKCLD: DKCLD (NUC011) 44.9 12 0.00026 24.0 1.0 19 32-50 25-43 (59)
7 PRK14132 riboflavin kinase; Pr 42.7 14 0.00031 26.6 1.2 17 25-41 22-38 (126)
8 PF10607 CLTH: CTLH/CRA C-term 42.2 83 0.0018 21.1 4.9 28 36-63 40-67 (145)
9 PF12169 DNA_pol3_gamma3: DNA 34.9 1.4E+02 0.003 19.9 6.1 54 28-81 4-59 (143)
10 PF01982 CTP-dep_RFKase: Domai 32.6 31 0.00068 24.6 1.7 16 25-40 16-31 (121)
11 PRK14165 winged helix-turn-hel 32.0 26 0.00055 27.0 1.2 17 25-41 110-126 (217)
12 PF13058 DUF3920: Protein of u 26.7 71 0.0015 23.3 2.6 28 34-68 97-124 (126)
13 cd01433 Ribosomal_L16_L10e Rib 25.9 12 0.00026 25.4 -1.3 47 1-48 51-99 (112)
14 COG1339 Transcriptional regula 25.6 39 0.00086 26.6 1.3 15 27-41 110-124 (214)
15 PF01978 TrmB: Sugar-specific 24.4 47 0.001 19.9 1.2 17 32-48 2-18 (68)
16 COG1094 Predicted RNA-binding 23.7 95 0.0021 23.9 3.0 52 26-79 67-133 (194)
17 PF04328 DUF466: Protein of un 22.5 72 0.0016 20.2 1.8 22 22-43 8-29 (65)
18 PF04836 IFRD_C: Interferon-re 22.3 47 0.001 20.7 0.9 12 28-39 2-13 (54)
19 KOG0396 Uncharacterized conser 21.7 94 0.002 26.5 2.8 25 42-66 197-221 (389)
No 1
>PF01158 Ribosomal_L36e: Ribosomal protein L36e; InterPro: IPR000509 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 ribosomal proteins can be grouped on the basis of sequence similarities. The L36E ribosomal family consists of mammalian, Caenorhabditis elegans and Drosophila L36, Candida albicans L39, and yeast YL39 ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1B_Q 4A1D_Q 4A19_Q 4A18_Q 3IZS_k 3IZR_k.
Probab=100.00 E-value=1.3e-47 Score=263.77 Aligned_cols=86 Identities=59% Similarity=0.805 Sum_probs=75.7
Q ss_pred CccccCCCCCCCCCCCCCCcchhHHHHHHHHHhhccchhHHhHHHHhhhcchhhHHHHHHHhhhhhHHHHHHHHHHHHHH
Q 038355 1 HIVTNKELLPRPVDPKGKTSKRIHFERNVIREVAGFAPYEKRIDALLKVGKDKRALKLAKRKLCTYERAKMKHGEMSNVL 80 (93)
Q Consensus 1 h~vtk~~~~~r~s~~kg~~tkr~kfvr~~IrEv~GfaPYEkr~~eLlk~~kdKrAlKf~KKrlGth~RAKrK~eel~~vl 80 (93)
|+||+|+++||||+++|.+|+|++||||||+|||||||||+++||||++|+||+||||+|+|||||+|||+|+|||+|||
T Consensus 13 h~vtk~~~~~r~s~~kg~~tk~~kfvr~vIrEv~GfaPYEkr~mELlkv~kdKrAlKf~KKRlGth~RAKrKrEel~~vl 92 (98)
T PF01158_consen 13 HKVTKNVSKPRPSRRKGRLTKRTKFVRDVIREVCGFAPYEKRAMELLKVSKDKRALKFAKKRLGTHIRAKRKREELSNVL 92 (98)
T ss_dssp -----TTS---STTS-SHHCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCCHHHHHHHHHHHHCHHHHHHHHHHHHHHHH
T ss_pred cccCCCCCCCCcccccCccchhHHHHHHHHHHhcCCChHHHHHHHHHhcchhHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhc
Q 038355 81 CRMRAT 86 (93)
Q Consensus 81 ~~~Rk~ 86 (93)
++||++
T Consensus 93 ~~~rk~ 98 (98)
T PF01158_consen 93 AAMRKA 98 (98)
T ss_dssp HHHHH-
T ss_pred HHHhcC
Confidence 999985
No 2
>PTZ00196 60S ribosomal protein L36; Provisional
Probab=100.00 E-value=4.1e-47 Score=261.63 Aligned_cols=85 Identities=53% Similarity=0.763 Sum_probs=84.3
Q ss_pred CccccCCCCCCCCCCCCCCcchhHHHHHHHHHhhccchhHHhHHHHhhhcchhhHHHHHHHhhhhhHHHHHHHHHHHHHH
Q 038355 1 HIVTNKELLPRPVDPKGKTSKRIHFERNVIREVAGFAPYEKRIDALLKVGKDKRALKLAKRKLCTYERAKMKHGEMSNVL 80 (93)
Q Consensus 1 h~vtk~~~~~r~s~~kg~~tkr~kfvr~~IrEv~GfaPYEkr~~eLlk~~kdKrAlKf~KKrlGth~RAKrK~eel~~vl 80 (93)
|+||+++++||||+++|.+|+|++||||||+|||||||||+++||||++|+||+||||+|+|||||+|||+|+|||++||
T Consensus 13 h~vtk~~~~~r~s~rkg~~tkr~~fVr~vIrEV~GfaPYErr~mELLkv~kdKrAlKfaKkRlGth~RaK~Kreel~~vl 92 (98)
T PTZ00196 13 HIVTKRARKPSPSKRKGLLSKRKRLVKDVIREVCGFSPYERRMIELLKVGKDKRALKYAKKRLGTHKRAKAKRDEIQEAL 92 (98)
T ss_pred cccCcCCCCCCcccccCCCCchhHHHHHHHHHHhcccHHHHHHHHHHHhcchHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHh
Q 038355 81 CRMRA 85 (93)
Q Consensus 81 ~~~Rk 85 (93)
++||+
T Consensus 93 ~~~rk 97 (98)
T PTZ00196 93 RAQRK 97 (98)
T ss_pred HHHhc
Confidence 99997
No 3
>KOG3452 consensus 60S ribosomal protein L36 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.5e-45 Score=252.15 Aligned_cols=88 Identities=58% Similarity=0.781 Sum_probs=86.3
Q ss_pred CccccCCCCCCCCCCCCCCcchhHHHHHHHHHhhccchhHHhHHHHhhhcchhhHHHHHHHhhhhhHHHHHHHHHHHHHH
Q 038355 1 HIVTNKELLPRPVDPKGKTSKRIHFERNVIREVAGFAPYEKRIDALLKVGKDKRALKLAKRKLCTYERAKMKHGEMSNVL 80 (93)
Q Consensus 1 h~vtk~~~~~r~s~~kg~~tkr~kfvr~~IrEv~GfaPYEkr~~eLlk~~kdKrAlKf~KKrlGth~RAKrK~eel~~vl 80 (93)
|+||++++.||+|+++|.+|+||+||+|||+|||||||||+++||||++|+||+|+||+|+|||||+||++|+|||+|||
T Consensus 15 h~~tk~~~~pr~s~~kg~~sk~tkfvr~lirEv~G~aPyErr~meLlkvskdkrA~K~lKkRlGth~RAk~KrEELsnvl 94 (102)
T KOG3452|consen 15 HKVTKRVSKPRQSRRKGETSKRTKFVRDLIREVAGFAPYERRAMELLKVSKDKRALKLLKKRLGTHKRAKRKREELSNVL 94 (102)
T ss_pred chhhcccCCCCcCccccchhhhHHHHHHHHHHHhCCChHHHHHHHHHHHcccHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhccc
Q 038355 81 CRMRATGG 88 (93)
Q Consensus 81 ~~~Rk~~a 88 (93)
++||++++
T Consensus 95 ~~~rk~~~ 102 (102)
T KOG3452|consen 95 AAMRKAHA 102 (102)
T ss_pred HHHHhccC
Confidence 99999764
No 4
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.3e-30 Score=178.63 Aligned_cols=81 Identities=43% Similarity=0.690 Sum_probs=79.3
Q ss_pred ccccCCCCCCCCCCCCCCcchhHHHHHHHHHhhccchhHHhHHHHhhhcchhhHHHHHHHhhhhhHHHHHHHHHHHHHHH
Q 038355 2 IVTNKELLPRPVDPKGKTSKRIHFERNVIREVAGFAPYEKRIDALLKVGKDKRALKLAKRKLCTYERAKMKHGEMSNVLC 81 (93)
Q Consensus 2 ~vtk~~~~~r~s~~kg~~tkr~kfvr~~IrEv~GfaPYEkr~~eLlk~~kdKrAlKf~KKrlGth~RAKrK~eel~~vl~ 81 (93)
+||++.+.+|||.++|.+|+|+.||+++++|++||+|||+++||||.+|.|++|.|+++||||+|+||+.|.|||.++|+
T Consensus 16 kvt~r~p~~rps~kkgq~s~Rt~fvrsivrEiaGlsPyErr~i~Lirns~~krArKlakKRLGs~kRAkaKvEel~~~i~ 95 (97)
T COG5051 16 KVTKRQPPERPSRKKGQLSKRTEFVRSIVREIAGLSPYERRVIELIRNSQDKRARKLAKKRLGSLKRAKAKVEELTSVIQ 95 (97)
T ss_pred eeeeccCCCCcchhhhccccHHHHHHHHHHHHccCCHHHHHHHHHHHhcccHHHHHHHHHHhhhHHHHHHHHHHHHHHHh
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred H
Q 038355 82 R 82 (93)
Q Consensus 82 ~ 82 (93)
+
T Consensus 96 ~ 96 (97)
T COG5051 96 S 96 (97)
T ss_pred c
Confidence 5
No 5
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=45.12 E-value=38 Score=26.64 Aligned_cols=64 Identities=20% Similarity=0.271 Sum_probs=44.8
Q ss_pred CcchhHHHHHHHHHhhccch------hHHhHHHHhhhcchhhHHHHHHHhhhhhH-HHHHHHHHHHHHHHH
Q 038355 19 TSKRIHFERNVIREVAGFAP------YEKRIDALLKVGKDKRALKLAKRKLCTYE-RAKMKHGEMSNVLCR 82 (93)
Q Consensus 19 ~tkr~kfvr~~IrEv~GfaP------YEkr~~eLlk~~kdKrAlKf~KKrlGth~-RAKrK~eel~~vl~~ 82 (93)
...=..++.++-.|+..-.+ -..+.+|||+.++-..|+.|+.-+|-..- ..-.+.++|..++..
T Consensus 80 Ie~Aie~in~l~PeiLd~n~~l~F~Lq~q~lIEliR~~~~eeal~F~q~~LA~~a~e~~~~~~elE~~l~l 150 (228)
T KOG2659|consen 80 IEEAIEKVNQLNPEILDTNRELFFHLQQLHLIELIREGKTEEALEFAQTKLAPFAEENPKKMEELERTLAL 150 (228)
T ss_pred HHHHHHHHHHhChHHHccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHccccccccHHHHHHHHHHHHH
Confidence 33334556666666666554 35689999999999999999999884332 222678888777653
No 6
>PF08068 DKCLD: DKCLD (NUC011) domain; InterPro: IPR012960 This is an N-terminal domain of dyskerin-like proteins, which is often associated with the TruB N-terminal(IPR002501 from INTERPRO) and PUA(IPR002478 from INTERPRO) domains [].; PDB: 3ZV0_D 3UAI_A 3U28_A 2AUS_C 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=44.91 E-value=12 Score=24.00 Aligned_cols=19 Identities=26% Similarity=0.548 Sum_probs=13.5
Q ss_pred HhhccchhHHhHHHHhhhc
Q 038355 32 EVAGFAPYEKRIDALLKVG 50 (93)
Q Consensus 32 Ev~GfaPYEkr~~eLlk~~ 50 (93)
.-+|..|++|-+-|+|+.|
T Consensus 25 ~~~G~~P~~R~i~~~i~~G 43 (59)
T PF08068_consen 25 PPYGCSPLKRPIEEYIKYG 43 (59)
T ss_dssp TTSS--GGGS-HHHHHHTE
T ss_pred cccCcCcccCCHHHHHhCC
Confidence 4589999999999999854
No 7
>PRK14132 riboflavin kinase; Provisional
Probab=42.66 E-value=14 Score=26.56 Aligned_cols=17 Identities=35% Similarity=0.626 Sum_probs=14.2
Q ss_pred HHHHHHHHhhccchhHH
Q 038355 25 FERNVIREVAGFAPYEK 41 (93)
Q Consensus 25 fvr~~IrEv~GfaPYEk 41 (93)
..++-++|.+||.||.-
T Consensus 22 ~Y~~qf~~~LGf~PyPG 38 (126)
T PRK14132 22 PYKEKFKEKLGFTPYEG 38 (126)
T ss_pred HHHHHHHHHhCCcCCCC
Confidence 45788999999999963
No 8
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=42.21 E-value=83 Score=21.09 Aligned_cols=28 Identities=25% Similarity=0.358 Sum_probs=23.7
Q ss_pred cchhHHhHHHHhhhcchhhHHHHHHHhh
Q 038355 36 FAPYEKRIDALLKVGKDKRALKLAKRKL 63 (93)
Q Consensus 36 faPYEkr~~eLlk~~kdKrAlKf~KKrl 63 (93)
|.=+-...+|||+.++-..|+.|++..+
T Consensus 40 f~L~~q~fiell~~~~~~~Ai~y~r~~l 67 (145)
T PF10607_consen 40 FELRCQQFIELLREGDIMEAIEYARKHL 67 (145)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHh
Confidence 4445567899999999999999999988
No 9
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=34.86 E-value=1.4e+02 Score=19.92 Aligned_cols=54 Identities=20% Similarity=0.218 Sum_probs=36.0
Q ss_pred HHHHHhhccchhHH--hHHHHhhhcchhhHHHHHHHhhhhhHHHHHHHHHHHHHHH
Q 038355 28 NVIREVAGFAPYEK--RIDALLKVGKDKRALKLAKRKLCTYERAKMKHGEMSNVLC 81 (93)
Q Consensus 28 ~~IrEv~GfaPYEk--r~~eLlk~~kdKrAlKf~KKrlGth~RAKrK~eel~~vl~ 81 (93)
+-|+++.|..|.|. .+++.|-.++-..|+.++..=+-.-+-...=.++|.+.++
T Consensus 4 e~V~~~lG~v~~~~i~~l~~ai~~~d~~~~l~~~~~l~~~G~d~~~~l~~L~~~~R 59 (143)
T PF12169_consen 4 EDVREILGLVDEEQIFELLDAILEGDAAEALELLNELLEQGKDPKQFLDDLIEYLR 59 (143)
T ss_dssp HHHHHHHTHTSTHHHHHHHHHHHTT-HHHHHHHHHHHHHCT--HHHHHHHHHHHHH
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 56899999999997 5666666788888998888755444444444555554443
No 10
>PF01982 CTP-dep_RFKase: Domain of unknown function DUF120; InterPro: IPR023602 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents a CTP-dependent riboflavin kinase domain, found primarily in archaea, that catalyses the phosphorylation of riboflavin to form flavin mononucleotide in riboflavin biosynthesis. Its structure resembles a RIFT barrel, structurally similar to but topologically distinct from bacterial and eukaryotic examples []. The N-terminal is a winged helix-turn-helix DNA-binding domain, and the C-terminal half is most similar in sequence to a group of cradle-loop barrels.; GO: 0016773 phosphotransferase activity, alcohol group as acceptor; PDB: 2VBV_A 2VBU_A 2VBS_A 2VBT_A 2P3M_A 2OYN_A 3CTA_A.
Probab=32.59 E-value=31 Score=24.59 Aligned_cols=16 Identities=44% Similarity=0.636 Sum_probs=10.5
Q ss_pred HHHHHHHHhhccchhH
Q 038355 25 FERNVIREVAGFAPYE 40 (93)
Q Consensus 25 fvr~~IrEv~GfaPYE 40 (93)
..++-++|.+||.||.
T Consensus 16 ~Y~~qf~~~LGf~PyP 31 (121)
T PF01982_consen 16 GYRRQFREKLGFEPYP 31 (121)
T ss_dssp HHHHHHHHHCSS---S
T ss_pred HHHHHHHHHhCCCCCC
Confidence 3577889999999995
No 11
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=31.97 E-value=26 Score=26.96 Aligned_cols=17 Identities=29% Similarity=0.378 Sum_probs=14.1
Q ss_pred HHHHHHHHhhccchhHH
Q 038355 25 FERNVIREVAGFAPYEK 41 (93)
Q Consensus 25 fvr~~IrEv~GfaPYEk 41 (93)
..++-++|.+||.||.-
T Consensus 110 ~Y~~~f~~~lGf~PypG 126 (217)
T PRK14165 110 GYKIQFEEKLGFIPYPG 126 (217)
T ss_pred HHHHHHHHHhCCcCCCC
Confidence 35778999999999964
No 12
>PF13058 DUF3920: Protein of unknown function (DUF3920)
Probab=26.66 E-value=71 Score=23.26 Aligned_cols=28 Identities=46% Similarity=0.631 Sum_probs=22.3
Q ss_pred hccchhHHhHHHHhhhcchhhHHHHHHHhhhhhHH
Q 038355 34 AGFAPYEKRIDALLKVGKDKRALKLAKRKLCTYER 68 (93)
Q Consensus 34 ~GfaPYEkr~~eLlk~~kdKrAlKf~KKrlGth~R 68 (93)
.|-.|||.|.||- | |..|+-..|...+|
T Consensus 97 vg~e~yEeR~ie~-----D--Ar~FAe~kl~ey~~ 124 (126)
T PF13058_consen 97 VGKEPYEERWIEK-----D--ARAFAERKLDEYKR 124 (126)
T ss_pred eccchHHHHHHHH-----H--HHHHHHHHHHHHhc
Confidence 7999999999985 5 88898887765543
No 13
>cd01433 Ribosomal_L16_L10e Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus.
Probab=25.87 E-value=12 Score=25.36 Aligned_cols=47 Identities=30% Similarity=0.333 Sum_probs=35.2
Q ss_pred CccccCCCCCCCCCCCCCCcchhHHHH--HHHHHhhccchhHHhHHHHhh
Q 038355 1 HIVTNKELLPRPVDPKGKTSKRIHFER--NVIREVAGFAPYEKRIDALLK 48 (93)
Q Consensus 1 h~vtk~~~~~r~s~~kg~~tkr~kfvr--~~IrEv~GfaPYEkr~~eLlk 48 (93)
|.||++..-.|=..-+|...-....|+ ++|-|+.|..+ +..+.+.|+
T Consensus 51 ~~vt~k~~~~rMGkGKG~~~~~~a~v~~G~iifEi~~~~~-~~~~~~alk 99 (112)
T cd01433 51 HPVTKKPLETRMGKGKGKPEGWVARVKPGQILFEVRGVPE-EEVAKEALR 99 (112)
T ss_pred ccEEECccccccCCCCCCccEEEEEECCCCEEEEEeCcCc-HHHHHHHHH
Confidence 568888777777777888888777777 89999999988 444444444
No 14
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=25.62 E-value=39 Score=26.57 Aligned_cols=15 Identities=47% Similarity=0.822 Sum_probs=13.1
Q ss_pred HHHHHHhhccchhHH
Q 038355 27 RNVIREVAGFAPYEK 41 (93)
Q Consensus 27 r~~IrEv~GfaPYEk 41 (93)
+..++|..||.||.-
T Consensus 110 ~~qf~ekLGf~PyPG 124 (214)
T COG1339 110 RRQFREKLGFDPYPG 124 (214)
T ss_pred HHHHHHHhCCCCCCC
Confidence 678999999999963
No 15
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=24.42 E-value=47 Score=19.87 Aligned_cols=17 Identities=29% Similarity=0.380 Sum_probs=14.4
Q ss_pred HhhccchhHHhHHHHhh
Q 038355 32 EVAGFAPYEKRIDALLK 48 (93)
Q Consensus 32 Ev~GfaPYEkr~~eLlk 48 (93)
++.||+.+|.+++..|-
T Consensus 2 ~~~gLs~~E~~vy~~Ll 18 (68)
T PF01978_consen 2 EVLGLSENEAKVYLALL 18 (68)
T ss_dssp HHHCHHHHHHHHHHHHH
T ss_pred CcCCcCHHHHHHHHHHH
Confidence 47899999999997764
No 16
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=23.74 E-value=95 Score=23.95 Aligned_cols=52 Identities=23% Similarity=0.382 Sum_probs=40.5
Q ss_pred HHHHHHHh-hccchhHHhHHHHhh-------------hcchhhHHHHHHHhh-hhhHHHHHHHHHHHHH
Q 038355 26 ERNVIREV-AGFAPYEKRIDALLK-------------VGKDKRALKLAKRKL-CTYERAKMKHGEMSNV 79 (93)
Q Consensus 26 vr~~IrEv-~GfaPYEkr~~eLlk-------------~~kdKrAlKf~KKrl-Gth~RAKrK~eel~~v 79 (93)
++|+|+-+ -||.|=+ +|-||. ++....++.=+|-|+ |..-++++=.|+|+++
T Consensus 67 a~d~VkAIgrGF~pe~--A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~ 133 (194)
T COG1094 67 ARDVVKAIGRGFPPEK--ALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGV 133 (194)
T ss_pred HHHHHHHHhcCCCHHH--HHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCC
Confidence 57778777 7998854 666665 355677788888887 9999999999999864
No 17
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=22.48 E-value=72 Score=20.23 Aligned_cols=22 Identities=23% Similarity=0.211 Sum_probs=18.0
Q ss_pred hhHHHHHHHHHhhccchhHHhH
Q 038355 22 RIHFERNVIREVAGFAPYEKRI 43 (93)
Q Consensus 22 r~kfvr~~IrEv~GfaPYEkr~ 43 (93)
-.+.|+..+++++|..-||+=+
T Consensus 8 ~~~~~~~~~r~l~G~~~Ye~Yv 29 (65)
T PF04328_consen 8 AWRRVRWYARLLVGEPDYERYV 29 (65)
T ss_pred HHHHHHHHHHHhcCcHHHHHHH
Confidence 3456789999999999999844
No 18
>PF04836 IFRD_C: Interferon-related protein conserved region; InterPro: IPR006921 This domain, primarily C-terminal, is found in a family of proteins thought to be involved in regulating gene activity in the proliferative and/or differentiative pathways induced by NGF [].
Probab=22.27 E-value=47 Score=20.69 Aligned_cols=12 Identities=17% Similarity=0.531 Sum_probs=10.4
Q ss_pred HHHHHhhccchh
Q 038355 28 NVIREVAGFAPY 39 (93)
Q Consensus 28 ~~IrEv~GfaPY 39 (93)
+++|||+||.|=
T Consensus 2 e~lRdiF~Lgp~ 13 (54)
T PF04836_consen 2 EFLRDIFDLGPP 13 (54)
T ss_pred hHHHHHcCCCCc
Confidence 678999999995
No 19
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.75 E-value=94 Score=26.49 Aligned_cols=25 Identities=24% Similarity=0.464 Sum_probs=22.1
Q ss_pred hHHHHhhhcchhhHHHHHHHhhhhh
Q 038355 42 RIDALLKVGKDKRALKLAKRKLCTY 66 (93)
Q Consensus 42 r~~eLlk~~kdKrAlKf~KKrlGth 66 (93)
..+|||++++-..|.-|++|-+++-
T Consensus 197 efIELi~~~~~~~Ai~~akk~f~~~ 221 (389)
T KOG0396|consen 197 EFIELIKVDNYDKAIAFAKKHFAPW 221 (389)
T ss_pred HHHHHHHhccHHHHHHHHHHHHhhh
Confidence 5789999999999999999977654
Done!