Query 035256
Match_columns 69
No_of_seqs 101 out of 172
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 10:26:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035256.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035256hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3499 60S ribosomal protein 100.0 3.8E-46 8.3E-51 232.3 8.0 69 1-69 1-69 (69)
2 PTZ00181 60S ribosomal protein 100.0 3.7E-44 8E-49 230.0 8.1 69 1-69 1-69 (82)
3 PF01781 Ribosomal_L38e: Ribos 100.0 1.6E-43 3.4E-48 220.8 5.7 68 2-69 1-69 (69)
4 PTZ00193 60S ribosomal protein 70.1 5.9 0.00013 29.1 3.1 44 2-47 106-171 (188)
5 PF14223 UBN2: gag-polypeptide 44.0 14 0.00031 22.8 1.3 20 46-65 63-82 (119)
6 PTZ00039 40S ribosomal protein 43.9 97 0.0021 20.7 5.9 59 8-67 35-112 (115)
7 cd02413 40S_S3_KH K homology R 43.9 72 0.0016 19.6 4.4 35 7-41 6-41 (81)
8 PRK06302 acetyl-CoA carboxylas 41.5 58 0.0013 22.1 4.0 25 5-29 3-27 (155)
9 TIGR00531 BCCP acetyl-CoA carb 41.2 61 0.0013 22.1 4.1 26 4-29 2-27 (156)
10 PF14227 UBN2_2: gag-polypepti 41.0 14 0.00031 22.8 0.9 19 46-64 61-79 (119)
11 TIGR01451 B_ant_repeat conserv 37.2 10 0.00022 21.5 -0.2 29 39-67 12-44 (53)
12 cd04885 ACT_ThrD-I Tandem C-te 35.3 87 0.0019 17.7 4.2 56 2-62 6-61 (68)
13 COG4269 Predicted membrane pro 34.9 5 0.00011 32.0 -2.3 10 35-44 49-58 (364)
14 PF14259 RRM_6: RNA recognitio 34.6 39 0.00085 18.4 2.0 48 6-61 13-60 (70)
15 PF00703 Glyco_hydro_2: Glycos 30.8 36 0.00077 19.7 1.5 10 39-48 83-92 (110)
16 KOG3346 Phosphatidylethanolami 30.1 31 0.00068 24.8 1.3 14 38-51 61-74 (185)
17 TIGR01046 S10_Arc_S20_Euk ribo 29.3 1.6E+02 0.0035 18.9 6.7 59 8-67 19-96 (99)
18 COG2443 Sss1 Preprotein transl 29.2 42 0.00091 20.8 1.6 15 2-16 5-19 (65)
19 PF01345 DUF11: Domain of unkn 28.6 18 0.00039 20.9 -0.1 27 41-67 43-73 (76)
20 cd02411 archeal_30S_S3_KH K ho 27.6 1.5E+02 0.0032 18.0 4.6 34 7-40 14-48 (85)
21 cd02412 30S_S3_KH K homology R 27.6 1.7E+02 0.0037 18.6 4.6 35 6-40 36-71 (109)
22 cd01812 BAG1_N Ubiquitin-like 27.6 91 0.002 17.3 2.8 28 33-60 2-29 (71)
23 PF12746 GNAT_acetyltran: GNAT 27.2 32 0.0007 25.7 1.0 31 38-68 101-133 (265)
24 PRK01192 50S ribosomal protein 25.9 84 0.0018 20.2 2.7 39 2-40 27-76 (89)
25 PF08671 SinI: Anti-repressor 25.7 55 0.0012 17.3 1.5 11 4-14 18-28 (30)
26 PF10105 DUF2344: Uncharacteri 25.4 42 0.00092 23.5 1.3 22 47-68 72-93 (187)
27 PF06470 SMC_hinge: SMC protei 25.1 27 0.00058 21.2 0.2 23 39-61 27-49 (120)
28 cd01201 Neurobeachin Neurobeac 24.1 92 0.002 20.8 2.7 32 31-62 75-107 (108)
29 cd01759 PLAT_PL PLAT/LH2 domai 21.7 48 0.001 21.8 1.0 21 19-39 79-99 (113)
30 KOG4309 Transcription mediator 20.9 53 0.0011 24.6 1.1 16 29-44 107-122 (217)
31 PHA02683 ORF078 thioredoxin-li 20.8 80 0.0017 20.2 1.8 17 2-18 43-59 (75)
32 PRK12271 rps10p 30S ribosomal 20.5 2.1E+02 0.0046 18.5 3.8 59 8-67 20-97 (102)
33 PF01198 Ribosomal_L31e: Ribos 20.4 1.2E+02 0.0027 19.0 2.6 37 2-40 25-72 (83)
34 PRK10598 lipoprotein; Provisio 20.0 78 0.0017 22.8 1.8 25 42-67 152-176 (186)
No 1
>KOG3499 consensus 60S ribosomal protein L38 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.8e-46 Score=232.31 Aligned_cols=69 Identities=77% Similarity=1.184 Sum_probs=68.2
Q ss_pred CchhhhhHHHHHHHHhhcCCceEEEeeCCCeeeEEEeecCcEEEEEecChHHHHHhhhcCCCCCceecC
Q 035256 1 MPKQIHEIKDFLLTARRKDARSVKIKRSRDVVKFKVRCSKYLYTLCVFDSEKADKLKQSLPPGLSVQDL 69 (69)
Q Consensus 1 MPkei~diK~FL~~arrkdAk~v~IKk~k~~tKFKvRcsryLYTLvv~d~~KAeKl~qSLPp~l~v~~~ 69 (69)
||+||+||||||++|||+||+||+||+|+++||||||||||||||||.|++|||||+|||||||+|+|+
T Consensus 1 Mpr~i~eiK~FL~~arR~Da~s~kiKkn~~~~KFKvRcsryLYTLvv~D~~KAeKlkQSLPP~l~V~el 69 (69)
T KOG3499|consen 1 MPRQITEIKDFLLTARRKDAKSVKIKKNKNNVKFKVRCSRYLYTLVVADAEKAEKLKQSLPPGLTVKEL 69 (69)
T ss_pred CcchHHHHHHHHHHHHhcccceeEEEecCCceeEEEEeeeeeeeeeeccHHHHHHHHhcCCCCceeecC
Confidence 999999999999999999999999999999999999999999999999999999999999999999986
No 2
>PTZ00181 60S ribosomal protein L38; Provisional
Probab=100.00 E-value=3.7e-44 Score=229.98 Aligned_cols=69 Identities=49% Similarity=0.845 Sum_probs=67.9
Q ss_pred CchhhhhHHHHHHHHhhcCCceEEEeeCCCeeeEEEeecCcEEEEEecChHHHHHhhhcCCCCCceecC
Q 035256 1 MPKQIHEIKDFLLTARRKDARSVKIKRSRDVVKFKVRCSKYLYTLCVFDSEKADKLKQSLPPGLSVQDL 69 (69)
Q Consensus 1 MPkei~diK~FL~~arrkdAk~v~IKk~k~~tKFKvRcsryLYTLvv~d~~KAeKl~qSLPp~l~v~~~ 69 (69)
||+||+|||+||++|||+||++|+||+|+++||||||||||||||+|.|.+||+||+|||||||+++++
T Consensus 1 MPkeI~dIK~FL~~arrkDAksvkIKkn~~~tKFKvRcsrYLYTLvv~D~~KA~KlkqSLPp~l~v~~v 69 (82)
T PTZ00181 1 MPREIKTLKEFLAICSRKDARCVKVKHNPSATKFKVRCSRYLYTLVVADKKKADKIERSIHPSVKKITV 69 (82)
T ss_pred CchhHHHHHHHHHHhhccCceEEEeecCCcceEEEEEecceEEEEEeCCHHHHHHHHhcCCCCceEEEe
Confidence 999999999999999999999999999999999999999999999999999999999999999999875
No 3
>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=100.00 E-value=1.6e-43 Score=220.80 Aligned_cols=68 Identities=74% Similarity=1.123 Sum_probs=62.8
Q ss_pred chhhhhHHHHHHHHhhcCCceEEEeeCCCe-eeEEEeecCcEEEEEecChHHHHHhhhcCCCCCceecC
Q 035256 2 PKQIHEIKDFLLTARRKDARSVKIKRSRDV-VKFKVRCSKYLYTLCVFDSEKADKLKQSLPPGLSVQDL 69 (69)
Q Consensus 2 Pkei~diK~FL~~arrkdAk~v~IKk~k~~-tKFKvRcsryLYTLvv~d~~KAeKl~qSLPp~l~v~~~ 69 (69)
|+||+||||||++|||+||+||+||+|+++ ||||||||||||||+|+|++|||+|+|||||||+++++
T Consensus 1 Pkqi~~iK~FL~~arrkDAksv~iKk~~~~~tKFKvRcsryLYTLvv~d~~KAeklkqSLPp~l~v~~i 69 (69)
T PF01781_consen 1 PKQIKDIKDFLETARRKDAKSVKIKKNKDNGTKFKVRCSRYLYTLVVKDKEKAEKLKQSLPPGLKVKEI 69 (69)
T ss_dssp -THHHHHHHHHHHHCSS-EEEEEEECESSSTEEEEEECSS-EEEESS-SHHHHHHHHHSSSSSSEEEEE
T ss_pred CcchhhHHHHHHHHhhCCCceEEEEecCCCeeEEEEEecceEEEEEEcCHHHHHHHHhhCCCCCeEeeC
Confidence 899999999999999999999999999999 99999999999999999999999999999999999875
No 4
>PTZ00193 60S ribosomal protein L31; Provisional
Probab=70.10 E-value=5.9 Score=29.11 Aligned_cols=44 Identities=20% Similarity=0.342 Sum_probs=32.1
Q ss_pred chhhhhHHHHHHHHhhcCCceEEEee--CC-------C--eeeEEEeecCc-----------EEEEEe
Q 035256 2 PKQIHEIKDFLLTARRKDARSVKIKR--SR-------D--VVKFKVRCSKY-----------LYTLCV 47 (69)
Q Consensus 2 Pkei~diK~FL~~arrkdAk~v~IKk--~k-------~--~tKFKvRcsry-----------LYTLvv 47 (69)
|+-|.+|+.|+..... ...|+|-. |+ . -.++.||.||. ||||+-
T Consensus 106 PrAIKeIRkFA~K~Mg--T~DVRIDtrLNkaIWsrGIRnvP~RIRVRlsRKrNedEDs~~KklYTlVt 171 (188)
T PTZ00193 106 PIAIKRIKAFVGRLMK--TKDNRIDASLNTYIWHKGVKGVPGRVRVLVERKSETLEGGKRKHFYTVIS 171 (188)
T ss_pred HHHHHHHHHHHHHhcC--CCcEEECHHHHHHHHHccCcCCCceEEEEEEeecCccccCcccceEEEEE
Confidence 7889999999887754 56777643 22 2 25888899884 898864
No 5
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=44.03 E-value=14 Score=22.81 Aligned_cols=20 Identities=30% Similarity=0.517 Sum_probs=17.6
Q ss_pred EecChHHHHHhhhcCCCCCc
Q 035256 46 CVFDSEKADKLKQSLPPGLS 65 (69)
Q Consensus 46 vv~d~~KAeKl~qSLPp~l~ 65 (69)
.+.|.+...++..||||...
T Consensus 63 ~i~d~~~v~~iL~~Lp~~y~ 82 (119)
T PF14223_consen 63 PISDEDLVSKILRSLPPSYD 82 (119)
T ss_pred cccchhHHHHHHhcCCchhH
Confidence 57899999999999999764
No 6
>PTZ00039 40S ribosomal protein S20; Provisional
Probab=43.87 E-value=97 Score=20.70 Aligned_cols=59 Identities=20% Similarity=0.385 Sum_probs=42.0
Q ss_pred HHHHHHHHhhcCCc------------eEEEeeCCC-e-----eeEEEeecCcEEEEEecChHHHHHhh-hcCCCCCcee
Q 035256 8 IKDFLLTARRKDAR------------SVKIKRSRD-V-----VKFKVRCSKYLYTLCVFDSEKADKLK-QSLPPGLSVQ 67 (69)
Q Consensus 8 iK~FL~~arrkdAk------------~v~IKk~k~-~-----tKFKvRcsryLYTLvv~d~~KAeKl~-qSLPp~l~v~ 67 (69)
.+++.+.|++.+|+ .+.+-++.. + =.|..|.-+=|.-|.- +.+-++.|. .+||||..+.
T Consensus 35 ~~~Ii~~ak~~g~~v~GPipLPtK~~~~tvlrSPhg~~kksreqfE~RiHKRlIdI~~-~~~~v~~l~~~~lp~GV~Ie 112 (115)
T PTZ00039 35 CADIITGAKEKNLKVTGPVRMPVKTLRITTRKSPCGEGTNTWDRFEMRIYKRVIDLYS-SSDVVTQITSINIDPGVEVE 112 (115)
T ss_pred HHHHHHHHHHcCCEeECCccCCceeEEEEeeeCCCCCCCchHHHheeeeeeEEEEEeC-CHHHHHHHhCCCCCCCcEEE
Confidence 46788888888764 334555433 1 4689999998888855 556678766 6899999874
No 7
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=43.85 E-value=72 Score=19.63 Aligned_cols=35 Identities=14% Similarity=0.324 Sum_probs=26.8
Q ss_pred hHHHHHHHHh-hcCCceEEEeeCCCeeeEEEeecCc
Q 035256 7 EIKDFLLTAR-RKDARSVKIKRSRDVVKFKVRCSKY 41 (69)
Q Consensus 7 diK~FL~~ar-rkdAk~v~IKk~k~~tKFKvRcsry 41 (69)
.|++||...- +.+...|.|.+..+.+.+-+.|+|=
T Consensus 6 ~Ire~l~k~~~~agis~IeI~Rt~~~i~I~I~tarP 41 (81)
T cd02413 6 ELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRT 41 (81)
T ss_pred HHHHHHHHHHHhCCeeeEEEEEcCCeEEEEEEeCCC
Confidence 6788888643 3456689999988888888887774
No 8
>PRK06302 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=41.50 E-value=58 Score=22.14 Aligned_cols=25 Identities=20% Similarity=0.315 Sum_probs=22.7
Q ss_pred hhhHHHHHHHHhhcCCceEEEeeCC
Q 035256 5 IHEIKDFLLTARRKDARSVKIKRSR 29 (69)
Q Consensus 5 i~diK~FL~~arrkdAk~v~IKk~k 29 (69)
+++|++.+....+.|..++.++.+.
T Consensus 3 ~~~I~~Li~~~~~s~l~ele~~~~~ 27 (155)
T PRK06302 3 IRKIKKLIELVDESGISEFEIKEGE 27 (155)
T ss_pred HHHHHHHHHHHHHCCCeEEEEEcCC
Confidence 6799999999999999999998765
No 9
>TIGR00531 BCCP acetyl-CoA carboxylase, biotin carboxyl carrier protein. The gene name is accB or fabE.
Probab=41.18 E-value=61 Score=22.09 Aligned_cols=26 Identities=19% Similarity=0.381 Sum_probs=23.2
Q ss_pred hhhhHHHHHHHHhhcCCceEEEeeCC
Q 035256 4 QIHEIKDFLLTARRKDARSVKIKRSR 29 (69)
Q Consensus 4 ei~diK~FL~~arrkdAk~v~IKk~k 29 (69)
.+++||+.+....+.+..++.++.+.
T Consensus 2 d~~~Ik~Li~~~~~s~l~elei~~~~ 27 (156)
T TIGR00531 2 NIREIKELIKLIEESGITELELKEEE 27 (156)
T ss_pred CHHHHHHHHHHHHHCCCcEEEEEeCC
Confidence 36799999999999999999998875
No 10
>PF14227 UBN2_2: gag-polypeptide of LTR copia-type
Probab=41.00 E-value=14 Score=22.80 Aligned_cols=19 Identities=37% Similarity=0.429 Sum_probs=16.8
Q ss_pred EecChHHHHHhhhcCCCCC
Q 035256 46 CVFDSEKADKLKQSLPPGL 64 (69)
Q Consensus 46 vv~d~~KAeKl~qSLPp~l 64 (69)
.+.|.+.+.-|..||||+.
T Consensus 61 ~i~d~~~~~~lL~sLP~sy 79 (119)
T PF14227_consen 61 PIDDEDKVIILLSSLPPSY 79 (119)
T ss_pred cchHHHHHHHHHHcCCHhH
Confidence 4789999999999999974
No 11
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=37.20 E-value=10 Score=21.51 Aligned_cols=29 Identities=21% Similarity=0.365 Sum_probs=19.5
Q ss_pred cCcEEEEEecChHHHH----HhhhcCCCCCcee
Q 035256 39 SKYLYTLCVFDSEKAD----KLKQSLPPGLSVQ 67 (69)
Q Consensus 39 sryLYTLvv~d~~KAe----Kl~qSLPp~l~v~ 67 (69)
...-||+.+.+..-+. .+...||+|+...
T Consensus 12 d~v~Yti~v~N~g~~~a~~v~v~D~lP~g~~~v 44 (53)
T TIGR01451 12 DTITYTITVTNNGNVPATNVVVTDILPSGTTFV 44 (53)
T ss_pred CEEEEEEEEEECCCCceEeEEEEEcCCCCCEEE
Confidence 3445788877665443 3677899998754
No 12
>cd04885 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=35.33 E-value=87 Score=17.70 Aligned_cols=56 Identities=20% Similarity=0.188 Sum_probs=38.6
Q ss_pred chhhhhHHHHHHHHhhcCCceEEEeeCCCeeeEEEeecCcEEEEEecChHHHHHhhhcCCC
Q 035256 2 PKQIHEIKDFLLTARRKDARSVKIKRSRDVVKFKVRCSKYLYTLCVFDSEKADKLKQSLPP 62 (69)
Q Consensus 2 Pkei~diK~FL~~arrkdAk~v~IKk~k~~tKFKvRcsryLYTLvv~d~~KAeKl~qSLPp 62 (69)
|-.--.+.+|+..... +|.-+.+.-.... ..-.+.+.++-+.|++-.+.+.+.|..
T Consensus 6 pdkPG~l~~~~~~i~~-~~nI~~~~~~~~~----~~~~~v~v~ie~~~~~~~~~i~~~L~~ 61 (68)
T cd04885 6 PERPGALKKFLELLGP-PRNITEFHYRNQG----GDEARVLVGIQVPDREDLAELKERLEA 61 (68)
T ss_pred CCCCCHHHHHHHHhCC-CCcEEEEEEEcCC----CCceEEEEEEEeCCHHHHHHHHHHHHH
Confidence 4444457888888876 7765655443322 344667889999999999998887754
No 13
>COG4269 Predicted membrane protein [Function unknown]
Probab=34.87 E-value=5 Score=32.03 Aligned_cols=10 Identities=50% Similarity=0.936 Sum_probs=8.9
Q ss_pred EEeecCcEEE
Q 035256 35 KVRCSKYLYT 44 (69)
Q Consensus 35 KvRcsryLYT 44 (69)
||||.||+|+
T Consensus 49 ~VR~rrYfYg 58 (364)
T COG4269 49 KVRRRRYFYG 58 (364)
T ss_pred HHHHHHhhhc
Confidence 5899999996
No 14
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=34.64 E-value=39 Score=18.45 Aligned_cols=48 Identities=13% Similarity=0.306 Sum_probs=33.4
Q ss_pred hhHHHHHHHHhhcCCceEEEeeCCCeeeEEEeecCcEEEEEecChHHHHHhhhcCC
Q 035256 6 HEIKDFLLTARRKDARSVKIKRSRDVVKFKVRCSKYLYTLCVFDSEKADKLKQSLP 61 (69)
Q Consensus 6 ~diK~FL~~arrkdAk~v~IKk~k~~tKFKvRcsryLYTLvv~d~~KAeKl~qSLP 61 (69)
.||.+|+...- +...+++.++++. +++++-| +.+.+.+-|+...+.++
T Consensus 13 ~~l~~~f~~~g--~v~~v~~~~~~~~-----~~~~~a~-v~f~~~~~a~~al~~~~ 60 (70)
T PF14259_consen 13 EDLRNFFSRFG--PVEKVRLIKNKDG-----QSRGFAF-VEFSSEEDAKRALELLN 60 (70)
T ss_dssp HHHHHHCTTSS--BEEEEEEEESTTS-----SEEEEEE-EEESSHHHHHHHHHHHT
T ss_pred HHHHHHHHhcC--CcceEEEEeeecc-----ccCCEEE-EEeCCHHHHHHHHHHCC
Confidence 46667666552 4678888887662 4445544 66789999999988876
No 15
>PF00703 Glyco_hydro_2: Glycosyl hydrolases family 2; InterPro: IPR006102 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 2 GH2 from CAZY comprises enzymes with several known activities: beta-galactosidase (3.2.1.23 from EC); beta-mannosidase (3.2.1.25 from EC); beta-glucuronidase (3.2.1.31 from EC). These enzymes contain a conserved glutamic acid residue which has been shown [], in Escherichia coli lacZ (P00722 from SWISSPROT), to be the general acid/base catalyst in the active site of the enzyme. This entry describes the immunoglobulin-like beta-sandwich domain [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3FN9_C 3DEC_A 3OB8_A 3OBA_A 3CMG_A 3GM8_A 3HN3_E 1BHG_A 2VZU_A 2X09_A ....
Probab=30.83 E-value=36 Score=19.67 Aligned_cols=10 Identities=60% Similarity=0.750 Sum_probs=7.4
Q ss_pred cCcEEEEEec
Q 035256 39 SKYLYTLCVF 48 (69)
Q Consensus 39 sryLYTLvv~ 48 (69)
.-|||+|.+.
T Consensus 83 ~P~LY~l~v~ 92 (110)
T PF00703_consen 83 DPYLYTLEVE 92 (110)
T ss_dssp SBSEEEEEEE
T ss_pred CceEEEEEEE
Confidence 4589998873
No 16
>KOG3346 consensus Phosphatidylethanolamine binding protein [General function prediction only]
Probab=30.06 E-value=31 Score=24.84 Aligned_cols=14 Identities=36% Similarity=0.470 Sum_probs=13.0
Q ss_pred ecCcEEEEEecChH
Q 035256 38 CSKYLYTLCVFDSE 51 (69)
Q Consensus 38 csryLYTLvv~d~~ 51 (69)
+.+=+|||++.|++
T Consensus 61 ~~~~~yTLvm~DPD 74 (185)
T KOG3346|consen 61 DPGSLYTLVMTDPD 74 (185)
T ss_pred CCCCeEEEEEeCCC
Confidence 88999999999986
No 17
>TIGR01046 S10_Arc_S20_Euk ribosomal protein S10(archaeal)/S20(eukaryotic). its equivalents in eukaryotes.
Probab=29.30 E-value=1.6e+02 Score=18.91 Aligned_cols=59 Identities=19% Similarity=0.295 Sum_probs=42.2
Q ss_pred HHHHHHHHhhcCCc------------eEEEeeCCC----e--eeEEEeecCcEEEEEecChHHHHHhh-hcCCCCCcee
Q 035256 8 IKDFLLTARRKDAR------------SVKIKRSRD----V--VKFKVRCSKYLYTLCVFDSEKADKLK-QSLPPGLSVQ 67 (69)
Q Consensus 8 iK~FL~~arrkdAk------------~v~IKk~k~----~--tKFKvRcsryLYTLvv~d~~KAeKl~-qSLPp~l~v~ 67 (69)
.+++.+.|.+.+++ .+.+-++.. . =.|..|.-+=|.-+. .+.+-++.|. ..||||..+.
T Consensus 19 ~~~I~~~ak~~g~~~~GPipLPtk~~~~tv~rsPh~~~~ks~e~fE~r~hKRlidi~-~~~~~~~~l~~~~lp~gV~ve 96 (99)
T TIGR01046 19 CAQIKRIAEKTGVRMSGPVPLPTKRLRVPTRKSPDGEGSKTWDRWEMRIHKRLIDIE-ADERALRQIMRISVPEDVEIE 96 (99)
T ss_pred HHHHHHHHHHcCCEEECCccCCcceEEEEeeeCCCCCCCcchHheEEEEEEEEEEEE-CCHHHHHHHhCCCCCCCcEEE
Confidence 46777888888764 334555432 2 279999999998886 4567777766 6799999874
No 18
>COG2443 Sss1 Preprotein translocase subunit Sss1 [Intracellular trafficking and secretion]
Probab=29.17 E-value=42 Score=20.78 Aligned_cols=15 Identities=27% Similarity=0.456 Sum_probs=7.5
Q ss_pred chhhhhHHHHHHHHh
Q 035256 2 PKQIHEIKDFLLTAR 16 (69)
Q Consensus 2 Pkei~diK~FL~~ar 16 (69)
+...+++++|+...+
T Consensus 5 ~~~~e~~~~~lke~~ 19 (65)
T COG2443 5 MDKPEELREFLKEYR 19 (65)
T ss_pred HHHHHHHHHHHHHHH
Confidence 444555555555443
No 19
>PF01345 DUF11: Domain of unknown function DUF11; InterPro: IPR001434 This group of sequences is represented by a conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis (Streptococcus faecalis), and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydia trachomatis outer membrane proteins. In C. trachomatis, three cysteine-rich proteins (also believed to be lipoproteins), MOMP, OMP6 and OMP3, make up the extracellular matrix of the outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. They are thought to be involved in porin formation and, as these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.; GO: 0005727 extrachromosomal circular DNA
Probab=28.58 E-value=18 Score=20.94 Aligned_cols=27 Identities=30% Similarity=0.502 Sum_probs=16.1
Q ss_pred cEEEEEecChHHHH----HhhhcCCCCCcee
Q 035256 41 YLYTLCVFDSEKAD----KLKQSLPPGLSVQ 67 (69)
Q Consensus 41 yLYTLvv~d~~KAe----Kl~qSLPp~l~v~ 67 (69)
.-||+.|.+..-+. .|...||+|+...
T Consensus 43 v~ytitvtN~G~~~a~nv~v~D~lp~g~~~v 73 (76)
T PF01345_consen 43 VTYTITVTNTGPAPATNVVVTDTLPAGLTFV 73 (76)
T ss_pred EEEEEEEEECCCCeeEeEEEEEcCCCCCEEe
Confidence 34666665543322 3556899998764
No 20
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=27.60 E-value=1.5e+02 Score=17.95 Aligned_cols=34 Identities=15% Similarity=0.208 Sum_probs=23.5
Q ss_pred hHHHHHHHHh-hcCCceEEEeeCCCeeeEEEeecC
Q 035256 7 EIKDFLLTAR-RKDARSVKIKRSRDVVKFKVRCSK 40 (69)
Q Consensus 7 diK~FL~~ar-rkdAk~v~IKk~k~~tKFKvRcsr 40 (69)
.|++|+...- ..+...|.|.++.+.+..-+.+++
T Consensus 14 ~Ir~fl~~~~~~agIs~IeI~r~~~~i~V~I~t~~ 48 (85)
T cd02411 14 MIDEYLEKELERAGYGGMEILRTPLGTQITIYAER 48 (85)
T ss_pred HHHHHHHhhhhhCcccEEEEEEcCCcEEEEEEECC
Confidence 5788887653 335668899998777666666543
No 21
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=27.60 E-value=1.7e+02 Score=18.61 Aligned_cols=35 Identities=17% Similarity=0.439 Sum_probs=26.0
Q ss_pred hhHHHHHHHH-hhcCCceEEEeeCCCeeeEEEeecC
Q 035256 6 HEIKDFLLTA-RRKDARSVKIKRSRDVVKFKVRCSK 40 (69)
Q Consensus 6 ~diK~FL~~a-rrkdAk~v~IKk~k~~tKFKvRcsr 40 (69)
..|++||... .+.+...+.|.+..+.+.+-+-+.|
T Consensus 36 ~~IR~yL~k~~~~agis~I~I~R~~~~i~I~I~t~r 71 (109)
T cd02412 36 LKIRKFIKKKLKKAGISRIEIERKADRVEVTIHTAR 71 (109)
T ss_pred HHHHHHHHHHHhhCCccEEEEEEcCCCEEEEEEeCC
Confidence 3578888654 3557778999998888888777766
No 22
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=27.60 E-value=91 Score=17.30 Aligned_cols=28 Identities=18% Similarity=0.209 Sum_probs=20.7
Q ss_pred eEEEeecCcEEEEEecChHHHHHhhhcC
Q 035256 33 KFKVRCSKYLYTLCVFDSEKADKLKQSL 60 (69)
Q Consensus 33 KFKvRcsryLYTLvv~d~~KAeKl~qSL 60 (69)
++.||.+.-.|++.+.+.+-...|++.+
T Consensus 2 ~i~vk~~g~~~~i~v~~~~tv~~lK~~i 29 (71)
T cd01812 2 RVRVKHGGESHDLSISSQATFGDLKKML 29 (71)
T ss_pred EEEEEECCEEEEEEECCCCcHHHHHHHH
Confidence 4667777777888888877777777654
No 23
>PF12746 GNAT_acetyltran: GNAT acetyltransferase; PDB: 3G3S_B.
Probab=27.22 E-value=32 Score=25.70 Aligned_cols=31 Identities=26% Similarity=0.420 Sum_probs=20.4
Q ss_pred ecCcEEEEEec--ChHHHHHhhhcCCCCCceec
Q 035256 38 CSKYLYTLCVF--DSEKADKLKQSLPPGLSVQD 68 (69)
Q Consensus 38 csryLYTLvv~--d~~KAeKl~qSLPp~l~v~~ 68 (69)
-.||.|+..-. |.++-+++..+||.+..+..
T Consensus 101 ~~Ry~~~~~~~~Fd~~~l~~~~~~lp~~y~l~~ 133 (265)
T PF12746_consen 101 FTRYAFKKEPEVFDKEKLKKYVSALPEGYELKR 133 (265)
T ss_dssp EEEEEE-SS-----HHHHHHHHHCS-TTCEEEE
T ss_pred eeeeeeeeccccccHHHHHHHHhcCCCCeEEEE
Confidence 45888876443 67788888889999998764
No 24
>PRK01192 50S ribosomal protein L31e; Reviewed
Probab=25.89 E-value=84 Score=20.18 Aligned_cols=39 Identities=26% Similarity=0.457 Sum_probs=28.0
Q ss_pred chhhhhHHHHHHHHhhcCCceEEEee--CC-------C--eeeEEEeecC
Q 035256 2 PKQIHEIKDFLLTARRKDARSVKIKR--SR-------D--VVKFKVRCSK 40 (69)
Q Consensus 2 Pkei~diK~FL~~arrkdAk~v~IKk--~k-------~--~tKFKvRcsr 40 (69)
|+-|..|++|+.....-+...|+|-. |+ . -.++.||.||
T Consensus 27 ~rAik~Ir~f~~k~mkt~~~~V~iD~~lN~~IW~rGi~~~P~riRVr~~r 76 (89)
T PRK01192 27 DRAVKLVREFLARHFKADEDKVKIDPSINEKIWERGREKPPSKVRVRVAK 76 (89)
T ss_pred HHHHHHHHHHHHHHhCCCCCcEEEChHHHHHHHHccCCCCCceEEEEEEE
Confidence 67899999999998776666788744 21 2 2577777765
No 25
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=25.68 E-value=55 Score=17.29 Aligned_cols=11 Identities=36% Similarity=0.531 Sum_probs=8.5
Q ss_pred hhhhHHHHHHH
Q 035256 4 QIHEIKDFLLT 14 (69)
Q Consensus 4 ei~diK~FL~~ 14 (69)
.++||++||..
T Consensus 18 s~eeir~FL~~ 28 (30)
T PF08671_consen 18 SKEEIREFLEF 28 (30)
T ss_dssp -HHHHHHHHHH
T ss_pred CHHHHHHHHHh
Confidence 46899999975
No 26
>PF10105 DUF2344: Uncharacterized protein conserved in bacteria (DUF2344); InterPro: IPR018768 This domain, found in various hypothetical bacterial proteins and Radical Sam domain proteins, has no known function.
Probab=25.39 E-value=42 Score=23.54 Aligned_cols=22 Identities=27% Similarity=0.508 Sum_probs=17.4
Q ss_pred ecChHHHHHhhhcCCCCCceec
Q 035256 47 VFDSEKADKLKQSLPPGLSVQD 68 (69)
Q Consensus 47 v~d~~KAeKl~qSLPp~l~v~~ 68 (69)
++..+-.++|.+.||+|+.+.+
T Consensus 72 ~~~~~~~~rLn~~lP~Gl~i~~ 93 (187)
T PF10105_consen 72 IDPEEVLERLNAVLPEGLRILE 93 (187)
T ss_pred CCHHHHHHHHHHhCCCCCEEEE
Confidence 3345667889999999999865
No 27
>PF06470 SMC_hinge: SMC proteins Flexible Hinge Domain; InterPro: IPR010935 This entry represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction [].; GO: 0005515 protein binding, 0005524 ATP binding, 0051276 chromosome organization, 0005694 chromosome; PDB: 2WD5_A 1GXL_C 1GXK_A 1GXJ_A 3NWC_B 3L51_A.
Probab=25.14 E-value=27 Score=21.18 Aligned_cols=23 Identities=30% Similarity=0.297 Sum_probs=19.2
Q ss_pred cCcEEEEEecChHHHHHhhhcCC
Q 035256 39 SKYLYTLCVFDSEKADKLKQSLP 61 (69)
Q Consensus 39 sryLYTLvv~d~~KAeKl~qSLP 61 (69)
+.||.+++|.|.+-|.++.+.|.
T Consensus 27 G~~l~~iVV~~~~~a~~~i~~l~ 49 (120)
T PF06470_consen 27 GGRLQAIVVEDEETAKKIIEFLK 49 (120)
T ss_dssp GGGGGSEEESSHHHHHHHHHHHH
T ss_pred HHhhceEEECcHHHHHHHHHHHh
Confidence 46889999999999998877664
No 28
>cd01201 Neurobeachin Neurobeachin Pleckstrin homology-like domain. Neurobeachin Pleckstrin homology-like domain. This domain is found in the large multi-domain eukaryotic protein Nerubeachin, N-terminal to the BEACH domain. This PH-like domain interacts with the BEACH domain in the same manner used by other PH-like domains to bind peptides.
Probab=24.06 E-value=92 Score=20.83 Aligned_cols=32 Identities=13% Similarity=0.108 Sum_probs=24.2
Q ss_pred eeeEEEeecC-cEEEEEecChHHHHHhhhcCCC
Q 035256 31 VVKFKVRCSK-YLYTLCVFDSEKADKLKQSLPP 62 (69)
Q Consensus 31 ~tKFKvRcsr-yLYTLvv~d~~KAeKl~qSLPp 62 (69)
++-+.+.|+- --|=|...|++.+.++.++|||
T Consensus 75 ~~alEiF~~d~~~~f~~F~~~~~~k~vv~~lp~ 107 (108)
T cd01201 75 NTALELFLASRTSIFFAFPDQNAVKKVVYALPR 107 (108)
T ss_pred cceEEEEEeCCceEEEEeCcHHHHHHHHhhcCC
Confidence 3455666654 4556677799999999999998
No 29
>cd01759 PLAT_PL PLAT/LH2 domain of pancreatic triglyceride lipase. Lipases hydrolyze phospholipids and triglycerides to generate fatty acids for energy production or for storage and to release inositol phosphates that act as second messengers. The central role of triglyceride lipases is in energy production. The proposed function of PLAT/LH2 domains is to mediate interaction with lipids or membrane bound proteins.
Probab=21.69 E-value=48 Score=21.83 Aligned_cols=21 Identities=19% Similarity=0.314 Sum_probs=15.8
Q ss_pred CCceEEEeeCCCeeeEEEeec
Q 035256 19 DARSVKIKRSRDVVKFKVRCS 39 (69)
Q Consensus 19 dAk~v~IKk~k~~tKFKvRcs 39 (69)
.|+.|+|+.+.+..+|+...+
T Consensus 79 ~~~~I~Vq~Ge~~~~~~FC~~ 99 (113)
T cd01759 79 GAEKITVQSGKDGKVFNFCSS 99 (113)
T ss_pred EEEEEEEEeCCCccEEEECCC
Confidence 578899999888777766443
No 30
>KOG4309 consensus Transcription mediator-related factor [Transcription]
Probab=20.85 E-value=53 Score=24.56 Aligned_cols=16 Identities=25% Similarity=0.518 Sum_probs=13.7
Q ss_pred CCeeeEEEeecCcEEE
Q 035256 29 RDVVKFKVRCSKYLYT 44 (69)
Q Consensus 29 k~~tKFKvRcsryLYT 44 (69)
++.+|...|+.||+|-
T Consensus 107 ~ka~KIE~rG~ry~Y~ 122 (217)
T KOG4309|consen 107 AKASKIETRGTRYQYC 122 (217)
T ss_pred ccccceeeccceeeec
Confidence 3568999999999994
No 31
>PHA02683 ORF078 thioredoxin-like protein; Provisional
Probab=20.78 E-value=80 Score=20.19 Aligned_cols=17 Identities=41% Similarity=0.790 Sum_probs=14.5
Q ss_pred chhhhhHHHHHHHHhhc
Q 035256 2 PKQIHEIKDFLLTARRK 18 (69)
Q Consensus 2 Pkei~diK~FL~~arrk 18 (69)
|....-+|+||..+|.|
T Consensus 43 P~k~~iLk~FL~~~RNK 59 (75)
T PHA02683 43 PNKLRILKEFLATCRNK 59 (75)
T ss_pred ccHHHHHHHHHHHHhcc
Confidence 56677899999999987
No 32
>PRK12271 rps10p 30S ribosomal protein S10P; Reviewed
Probab=20.47 E-value=2.1e+02 Score=18.50 Aligned_cols=59 Identities=17% Similarity=0.241 Sum_probs=42.0
Q ss_pred HHHHHHHHhhcCCc------------eEEEeeCCC------eeeEEEeecCcEEEEEecChHHHHHhh-hcCCCCCcee
Q 035256 8 IKDFLLTARRKDAR------------SVKIKRSRD------VVKFKVRCSKYLYTLCVFDSEKADKLK-QSLPPGLSVQ 67 (69)
Q Consensus 8 iK~FL~~arrkdAk------------~v~IKk~k~------~tKFKvRcsryLYTLvv~d~~KAeKl~-qSLPp~l~v~ 67 (69)
.+++.+.|.+.+|+ .+.+-++.. .=.|..|.-+=|.-+ -.+.+-++.|. ..||+|+.+.
T Consensus 20 ~~~I~~~~k~~g~~~~GPipLPtk~~~~tv~rSPh~~gk~sreqfE~r~hKRlidi-~~~~~~~~~l~~~~lp~gV~ie 97 (102)
T PRK12271 20 CDQIKEIAEKTGVDMSGPIPLPTKRLVVPTRKSPDGEGTATWDHWEMRIHKRLIDI-DADERALRQLMRIRVPEDVQIE 97 (102)
T ss_pred HHHHHHHHHHcCCeEECCCcCCceeEEEEeeeCCCCCCCcchHHeEEEEeEEEEEe-eCCHHHHHHHhCCCCCCCcEEE
Confidence 46677888888764 334555432 137999999999988 45667777765 5799998874
No 33
>PF01198 Ribosomal_L31e: Ribosomal protein L31e; InterPro: IPR000054 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 large subunit ribosomal proteins can be grouped on the basis of sequence similarities. These proteins have 87 to 128 amino-acid residues. This family consists of: Yeast L34 Archaeal L31 [] Plants L31 Mammalian L31 [] ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3G6E_X 3I56_X 1YIT_X 1NJI_Y 3CC4_X 1VQM_X 1KC8_Y 1VQ9_X 1VQN_X 1M1K_Y ....
Probab=20.37 E-value=1.2e+02 Score=19.03 Aligned_cols=37 Identities=27% Similarity=0.509 Sum_probs=24.7
Q ss_pred chhhhhHHHHHHHHhhcCCceEEEee--C-------CC--eeeEEEeecC
Q 035256 2 PKQIHEIKDFLLTARRKDARSVKIKR--S-------RD--VVKFKVRCSK 40 (69)
Q Consensus 2 Pkei~diK~FL~~arrkdAk~v~IKk--~-------k~--~tKFKvRcsr 40 (69)
|+-|..|++|+..-..-+ .|+|-. | -. -.++.||.+|
T Consensus 25 ~rAvk~Ir~f~~k~mkt~--dV~iD~~lN~~IWsrGi~~pP~rIRVr~~r 72 (83)
T PF01198_consen 25 PRAVKEIRKFAQKHMKTE--DVKIDPELNKAIWSRGIRKPPRRIRVRVSR 72 (83)
T ss_dssp HHHHHHHHHHHHHHHTTS--CEEE-HHHHHHHHTTTSSS--SEEEEEEEE
T ss_pred HHHHHHHHHHHHHHhCCC--ceEEchHHHHHHHhcccCCCCceEEEEEEE
Confidence 567899999998887775 677633 1 11 2567777765
No 34
>PRK10598 lipoprotein; Provisional
Probab=20.05 E-value=78 Score=22.83 Aligned_cols=25 Identities=40% Similarity=0.561 Sum_probs=19.7
Q ss_pred EEEEEecChHHHHHhhhcCCCCCcee
Q 035256 42 LYTLCVFDSEKADKLKQSLPPGLSVQ 67 (69)
Q Consensus 42 LYTLvv~d~~KAeKl~qSLPp~l~v~ 67 (69)
.|+|- +|.+++|.+..++++++.|+
T Consensus 152 VY~L~-d~~~~~eal~kk~~k~i~Vk 176 (186)
T PRK10598 152 AYVLR-EDKSKAEALAKKLAKGLEVK 176 (186)
T ss_pred eEEEC-CCCCHHHHHHHhccCCCEEE
Confidence 46662 35788999999999999886
Done!