Query psy3566
Match_columns 105
No_of_seqs 103 out of 168
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 19:55:12 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3566.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3566hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00135 rps10 ribosomal prote 99.9 3.1E-26 6.7E-31 159.3 6.4 70 36-105 7-78 (101)
2 COG0051 RpsJ Ribosomal protein 99.9 7.8E-26 1.7E-30 158.5 6.1 70 36-105 4-75 (104)
3 PRK00596 rpsJ 30S ribosomal pr 99.9 7.7E-26 1.7E-30 156.7 5.9 71 35-105 3-75 (102)
4 PF00338 Ribosomal_S10: Riboso 99.9 1E-25 2.2E-30 151.9 6.2 68 38-105 1-70 (97)
5 TIGR01049 rpsJ_bact ribosomal 99.9 1E-25 2.2E-30 155.1 5.7 70 36-105 1-72 (99)
6 KOG4060|consensus 99.9 2.4E-25 5.3E-30 166.0 6.3 85 19-105 38-122 (176)
7 PRK12271 rps10p 30S ribosomal 99.9 2E-23 4.4E-28 145.3 7.5 70 36-105 2-74 (102)
8 TIGR01046 S10_Arc_S20_Euk ribo 99.9 7.1E-23 1.5E-27 141.8 7.5 69 37-105 2-73 (99)
9 PTZ00039 40S ribosomal protein 99.9 1.1E-22 2.4E-27 144.5 7.0 73 33-105 14-89 (115)
10 KOG3321|consensus 99.9 6.9E-23 1.5E-27 153.6 -0.0 85 21-105 31-118 (175)
11 KOG0900|consensus 98.2 5.4E-07 1.2E-11 65.0 1.5 69 37-105 21-92 (121)
12 PRK08351 DNA-directed RNA poly 53.7 6.2 0.00013 25.4 0.7 16 59-74 43-58 (61)
13 PF09288 UBA_3: Fungal ubiquit 52.3 9.4 0.0002 24.2 1.4 30 41-70 4-39 (55)
14 COG2093 DNA-directed RNA polym 44.2 10 0.00023 24.7 0.7 17 59-75 46-62 (64)
15 PF00298 Ribosomal_L11: Riboso 35.5 36 0.00078 21.9 2.2 21 48-68 49-69 (69)
16 KOG0046|consensus 27.7 22 0.00047 32.0 0.2 60 16-81 540-599 (627)
17 PRK14556 pyrH uridylate kinase 27.6 84 0.0018 25.0 3.5 38 33-70 13-63 (249)
18 COG1761 RPB11 DNA-directed RNA 27.1 76 0.0016 22.1 2.8 37 36-76 15-51 (99)
19 PRK06393 rpoE DNA-directed RNA 26.0 31 0.00068 22.4 0.7 17 59-75 45-61 (64)
20 COG0080 RplK Ribosomal protein 25.9 52 0.0011 24.5 1.9 28 43-70 113-140 (141)
21 PRK01143 rpl11p 50S ribosomal 25.8 58 0.0013 24.4 2.2 24 47-70 115-138 (163)
22 TIGR03653 arch_L6P archaeal ri 25.1 98 0.0021 23.1 3.3 25 39-63 129-153 (170)
23 cd00460 RNAP_RPB11_RPB3 RPB11 24.8 96 0.0021 20.3 2.9 24 36-59 9-32 (86)
24 COG0528 PyrH Uridylate kinase 22.8 1.9E+02 0.004 23.2 4.6 35 33-68 3-47 (238)
25 COG0440 IlvH Acetolactate synt 22.5 1E+02 0.0022 23.3 3.0 52 15-67 25-76 (163)
26 TIGR01632 L11_bact 50S ribosom 22.3 41 0.00089 24.6 0.8 26 45-70 115-140 (140)
27 KOG3257|consensus 22.2 76 0.0016 24.3 2.2 25 47-71 134-158 (168)
28 cd02641 R3H_Smubp-2_like R3H d 21.9 70 0.0015 19.8 1.7 16 54-69 31-46 (60)
29 PTZ00105 60S ribosomal protein 21.8 51 0.0011 24.1 1.2 24 47-70 97-120 (140)
30 PF12444 Sox_N: Sox developmen 20.5 25 0.00053 23.9 -0.7 10 41-50 69-78 (84)
No 1
>CHL00135 rps10 ribosomal protein S10; Validated
Probab=99.93 E-value=3.1e-26 Score=159.26 Aligned_cols=70 Identities=16% Similarity=0.283 Sum_probs=68.2
Q ss_pred ceEEEEEeecChhHHhhHHHHHHHHHHHcCCeeeccccCCC--ceEEEEecCCCCcceeeeEEecceeeecC
Q psy3566 36 DEVNVQLKGYDFPVLESYQKFVYKIAASLSIQSDESWALPP--QKFNITRMEPNSSVVDANYHLRIYERNVQ 105 (105)
Q Consensus 36 ~~inIklkgyD~~lLe~~~~~I~~~a~~~gi~V~g~~aLPt--~~~tVlrs~hv~kk~r~qfelrth~R~Iq 105 (105)
++|+|+|+|||+.+||+++.+|.++|+.+|+.+.||+|||| .++||+||||++|++|||||+|+|+|+|+
T Consensus 7 ~kirI~LkS~d~~~L~~~~~~I~~~~k~~~~~~~GpipLPtk~~~~TvlrSPhv~KkSrEqfE~r~hKRlI~ 78 (101)
T CHL00135 7 AKIRIKLKSFNHELLNSSCKKIIDTASRTNATAVGPIPLPTKRRIYCVLRSPHVDKDSREHFEIRTHKRIID 78 (101)
T ss_pred CeEEEEEEECCHHHHHHHHHHHHHHHHHcCCeEeCCcCCCcEEEEEEEecCCCCCCchHHhhhheeeeEEEE
Confidence 57999999999999999999999999999999999999999 79999999999999999999999999985
No 2
>COG0051 RpsJ Ribosomal protein S10 [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=7.8e-26 Score=158.54 Aligned_cols=70 Identities=14% Similarity=0.317 Sum_probs=68.1
Q ss_pred ceEEEEEeecChhHHhhHHHHHHHHHHHcCCeeeccccCCC--ceEEEEecCCCCcceeeeEEecceeeecC
Q psy3566 36 DEVNVQLKGYDFPVLESYQKFVYKIAASLSIQSDESWALPP--QKFNITRMEPNSSVVDANYHLRIYERNVQ 105 (105)
Q Consensus 36 ~~inIklkgyD~~lLe~~~~~I~~~a~~~gi~V~g~~aLPt--~~~tVlrs~hv~kk~r~qfelrth~R~Iq 105 (105)
++++|+|+|||+.+||.++++|+++|+++|+.|.||+|||| .++||+||||++++++||||+|||+|+|+
T Consensus 4 ~kirI~L~s~d~~~LD~~~~~Ive~akrtg~~v~GPiPLPTk~~~~tvlrsP~~~k~s~e~fEmr~HkRlid 75 (104)
T COG0051 4 QKIRIRLKSFDHRLLDQVCREIVETAKRTGADVKGPIPLPTKRERVTVLRSPHGEKDSREQFEMRTHKRLID 75 (104)
T ss_pred ceEEEEEecCCHHHHHHHHHHHHHHHHHhCCeeeCCccCCCceEEEEEEeCCCCCCchHHHhhhheeeeEEE
Confidence 48999999999999999999999999999999999999999 69999999999999999999999999985
No 3
>PRK00596 rpsJ 30S ribosomal protein S10; Reviewed
Probab=99.92 E-value=7.7e-26 Score=156.70 Aligned_cols=71 Identities=18% Similarity=0.343 Sum_probs=68.6
Q ss_pred cceEEEEEeecChhHHhhHHHHHHHHHHHcCCeeeccccCCC--ceEEEEecCCCCcceeeeEEecceeeecC
Q psy3566 35 YDEVNVQLKGYDFPVLESYQKFVYKIAASLSIQSDESWALPP--QKFNITRMEPNSSVVDANYHLRIYERNVQ 105 (105)
Q Consensus 35 y~~inIklkgyD~~lLe~~~~~I~~~a~~~gi~V~g~~aLPt--~~~tVlrs~hv~kk~r~qfelrth~R~Iq 105 (105)
.++|+|+|+|||+.+||+++++|.++|+.+|++|.||+|||| .++||+||||++|++|||||+|||+|+|+
T Consensus 3 ~~~irI~l~S~d~~~L~~~~~~i~~~a~~~~i~v~GpipLPtk~~r~tvlrSPhv~KksreqfE~r~hkR~i~ 75 (102)
T PRK00596 3 KQKIRIRLKAFDHRLLDQSAKKIVETAKRTGAQVRGPIPLPTKKERFTVLRSPHVNKDSREQFEIRTHKRLID 75 (102)
T ss_pred CcEEEEEEEECCHHHHHHHHHHHHHHHHHcCCeEECCcCCCcEEEEEEEeeCCCCCCCHHHHhhhhhheEEEE
Confidence 467999999999999999999999999999999999999999 79999999999999999999999999985
No 4
>PF00338 Ribosomal_S10: Ribosomal protein S10p/S20e; InterPro: IPR001848 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 [, ]. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S10 consists of about 100 amino acid residues. In Escherichia coli, S10 is involved in binding tRNA to the ribosome, and also operates as a transcriptional elongation factor []. Experimental evidence [] has revealed that S10 has virtually no groups exposed on the ribosomal surface, and is one of the "split proteins": these are a discrete group that are selectively removed from 30S subunits under low salt conditions and are required for the formation of activated 30S reconstitution intermediate (RI*) particles. S10 belongs to a family of proteins [] that includes: bacteria S10; algal chloroplast S10; cyanelle S10; archaebacterial S10; Marchantia polymorpha and Prototheca wickerhamii mitochondrial S10; Arabidopsis thaliana mitochondrial S10 (nuclear encoded); vertebrate S20; plant S20; and yeast URP2.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1S1H_J 3U5G_U 3O30_N 3O2Z_N 3IZB_J 3U5C_U 3R2C_J 3R2D_J 2ZKQ_j 2XQD_J ....
Probab=99.92 E-value=1e-25 Score=151.86 Aligned_cols=68 Identities=31% Similarity=0.547 Sum_probs=66.3
Q ss_pred EEEEEeecChhHHhhHHHHHHHHHHHcCCeeeccccCCC--ceEEEEecCCCCcceeeeEEecceeeecC
Q psy3566 38 VNVQLKGYDFPVLESYQKFVYKIAASLSIQSDESWALPP--QKFNITRMEPNSSVVDANYHLRIYERNVQ 105 (105)
Q Consensus 38 inIklkgyD~~lLe~~~~~I~~~a~~~gi~V~g~~aLPt--~~~tVlrs~hv~kk~r~qfelrth~R~Iq 105 (105)
|+|+|+|||+.+||+|+++|+++|+.+|+++.||||||| .++|++||||++|++|+|||+++|+|+||
T Consensus 1 i~I~l~s~d~~~l~~~~~~i~~~~~~~~~~~~~~~~lPtk~~~~tvlrSPhv~kks~eqfe~~~~kr~i~ 70 (97)
T PF00338_consen 1 IRIKLKSYDKKLLESYVKFIHKLAKNLGIKVSGPIPLPTKKKRFTVLRSPHVDKKSREQFEIRTHKRLIQ 70 (97)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHHHHCTSSCEEEEEEEEEEEEEEEEESSSSSSTTSEEEEEEEEEEEEEE
T ss_pred CEEEEEECCHHHHHHHHHHHHHHHHHhCCcccccccCCccEEEEEEeecCcCCcchhhheeeeeeEEEEE
Confidence 799999999999999999999999999999999999999 69999999999999999999999999985
No 5
>TIGR01049 rpsJ_bact ribosomal protein S10, bacterial/organelle. This model describes bacterial 30S ribosomal protein S10. In species that have a transcription antitermination complex, or N utilization substance, with NusA, NusB, NusG, and NusE, this ribosomal protein is responsible for NusE activity. Included in the family are one member each from Saccharomyces cerevisiae and Schizosaccharomyces pombe. These proteins lack an N-terminal mitochondrial transit peptide but contain additional sequence C-terminal to the ribosomal S10 protein region.
Probab=99.92 E-value=1e-25 Score=155.11 Aligned_cols=70 Identities=19% Similarity=0.366 Sum_probs=67.7
Q ss_pred ceEEEEEeecChhHHhhHHHHHHHHHHHcCCeeeccccCCC--ceEEEEecCCCCcceeeeEEecceeeecC
Q psy3566 36 DEVNVQLKGYDFPVLESYQKFVYKIAASLSIQSDESWALPP--QKFNITRMEPNSSVVDANYHLRIYERNVQ 105 (105)
Q Consensus 36 ~~inIklkgyD~~lLe~~~~~I~~~a~~~gi~V~g~~aLPt--~~~tVlrs~hv~kk~r~qfelrth~R~Iq 105 (105)
++|+|+|+|||+.+||+|+++|.++|+.+|+++.||+|||| .++||+||||++||+|||||+|||+|+|+
T Consensus 1 ~~irI~l~s~d~~~L~~~~~~i~~~a~~~gi~~~gpi~LPtk~~~~tvlrSPhv~kksreqfE~r~hkR~i~ 72 (99)
T TIGR01049 1 QKIRIKLKSYDHRLLDQSTKKIVETAKRTGAQVKGPIPLPTKKERYTVLRSPHVNKDSREQFEIRTHKRLID 72 (99)
T ss_pred CeEEEEEEECCHHHHHHHHHHHHHHHHHcCCceecccCCCCEEEEEEEeeCCCCCCCHHHHhhhhhheEEEE
Confidence 46999999999999999999999999999999999999999 69999999999999999999999999985
No 6
>KOG4060|consensus
Probab=99.92 E-value=2.4e-25 Score=165.97 Aligned_cols=85 Identities=40% Similarity=0.706 Sum_probs=79.7
Q ss_pred CCCccccccCCCCCCccceEEEEEeecChhHHhhHHHHHHHHHHHcCCeeeccccCCCceEEEEecCCCCcceeeeEEec
Q psy3566 19 LFEPDYLDHLNPEIPLYDEVNVQLKGYDFPVLESYQKFVYKIAASLSIQSDESWALPPQKFNITRMEPNSSVVDANYHLR 98 (105)
Q Consensus 19 l~eP~yl~~~~~~~ply~~inIklkgyD~~lLe~~~~~I~~~a~~~gi~V~g~~aLPt~~~tVlrs~hv~kk~r~qfelr 98 (105)
++||++.+. .++|+|+.|||+++|||+.+||+||.|||++|+.+|++|.+|||+||++.+|++.++.+++|..++.|.
T Consensus 38 ~~ePKf~~~--re~~ey~~lNV~i~gyD~~~lEsYq~yvH~la~~l~~~V~dsYA~p~qt~~v~~l~p~stv~ese~~lt 115 (176)
T KOG4060|consen 38 AEEPKFKKE--REINEYGVLNVHITGYDMTLLESYQQYVHNLANSLSIKVEDSYAMPTQTIEVLQLQPQSTVMESESVLT 115 (176)
T ss_pred hhCCcccch--hcccccceEEEEEEecccchHHHHHHHHHHHHHHcCceeEeeeccCccceeEEEecCCceeeehhhhhh
Confidence 566666664 677889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeecC
Q psy3566 99 IYERNVQ 105 (105)
Q Consensus 99 th~R~Iq 105 (105)
||+|+||
T Consensus 116 TyeRvvq 122 (176)
T KOG4060|consen 116 TYERVVQ 122 (176)
T ss_pred hhhheee
Confidence 9999997
No 7
>PRK12271 rps10p 30S ribosomal protein S10P; Reviewed
Probab=99.89 E-value=2e-23 Score=145.33 Aligned_cols=70 Identities=13% Similarity=0.195 Sum_probs=66.8
Q ss_pred ceEEEEEeecChhHHhhHHHHHHHHHHHcCCeeeccccCCC--ceEEEEecCCCC-cceeeeEEecceeeecC
Q psy3566 36 DEVNVQLKGYDFPVLESYQKFVYKIAASLSIQSDESWALPP--QKFNITRMEPNS-SVVDANYHLRIYERNVQ 105 (105)
Q Consensus 36 ~~inIklkgyD~~lLe~~~~~I~~~a~~~gi~V~g~~aLPt--~~~tVlrs~hv~-kk~r~qfelrth~R~Iq 105 (105)
++|+|+|+|||+.+||.+++.|.++|+++|+++.||+|||| .++||+||||++ |++|+|||+|+|+|+|+
T Consensus 2 ~~irI~L~S~d~~~Ld~~~~~I~~~~k~~g~~~~GPipLPtk~~~~tv~rSPh~~gk~sreqfE~r~hKRlid 74 (102)
T PRK12271 2 QKARIRLSSTNPEDLDEVCDQIKEIAEKTGVDMSGPIPLPTKRLVVPTRKSPDGEGTATWDHWEMRIHKRLID 74 (102)
T ss_pred ceEEEEEEeCCHHHHHHHHHHHHHHHHHcCCeEECCCcCCceeEEEEeeeCCCCCCCcchHHeEEEEeEEEEE
Confidence 46999999999999999999999999999999999999999 699999999965 99999999999999984
No 8
>TIGR01046 S10_Arc_S20_Euk ribosomal protein S10(archaeal)/S20(eukaryotic). its equivalents in eukaryotes.
Probab=99.88 E-value=7.1e-23 Score=141.77 Aligned_cols=69 Identities=16% Similarity=0.238 Sum_probs=65.5
Q ss_pred eEEEEEeecChhHHhhHHHHHHHHHHHcCCeeeccccCCC--ceEEEEecCCC-CcceeeeEEecceeeecC
Q psy3566 37 EVNVQLKGYDFPVLESYQKFVYKIAASLSIQSDESWALPP--QKFNITRMEPN-SSVVDANYHLRIYERNVQ 105 (105)
Q Consensus 37 ~inIklkgyD~~lLe~~~~~I~~~a~~~gi~V~g~~aLPt--~~~tVlrs~hv-~kk~r~qfelrth~R~Iq 105 (105)
+|+|+|+|||+.+||++++.|.++|++.|+++.||+|||| .++||+||||+ ++++++|||+|+|+|+|+
T Consensus 2 ~irI~L~S~d~~~Ld~~~~~I~~~ak~~g~~~~GPipLPtk~~~~tv~rsPh~~~~ks~e~fE~r~hKRlid 73 (99)
T TIGR01046 2 KARIKLTSTNVRSLEKVCAQIKRIAEKTGVRMSGPVPLPTKRLRVPTRKSPDGEGSKTWDRWEMRIHKRLID 73 (99)
T ss_pred cEEEEEEECCHHHHHHHHHHHHHHHHHcCCEEECCccCCcceEEEEeeeCCCCCCCcchHheEEEEEEEEEE
Confidence 6999999999999999999999999999999999999999 68999999995 458999999999999984
No 9
>PTZ00039 40S ribosomal protein S20; Provisional
Probab=99.88 E-value=1.1e-22 Score=144.47 Aligned_cols=73 Identities=11% Similarity=0.195 Sum_probs=68.5
Q ss_pred CccceEEEEEeecChhHHhhHHHHHHHHHHHcCCeeeccccCCC--ceEEEEecCCC-CcceeeeEEecceeeecC
Q psy3566 33 PLYDEVNVQLKGYDFPVLESYQKFVYKIAASLSIQSDESWALPP--QKFNITRMEPN-SSVVDANYHLRIYERNVQ 105 (105)
Q Consensus 33 ply~~inIklkgyD~~lLe~~~~~I~~~a~~~gi~V~g~~aLPt--~~~tVlrs~hv-~kk~r~qfelrth~R~Iq 105 (105)
+.-++|+|+|+|||+.+||+++..|.+.|+++|++|.||+|||| .++|++||||+ +|++++|||+|+|+|+|+
T Consensus 14 ~~~~kirI~L~S~d~~~Ld~~~~~Ii~~ak~~g~~v~GPipLPtK~~~~tvlrSPhg~~kksreqfE~RiHKRlId 89 (115)
T PTZ00039 14 NRLHKIRITLTSKNLKSIEKVCADIITGAKEKNLKVTGPVRMPVKTLRITTRKSPCGEGTNTWDRFEMRIYKRVID 89 (115)
T ss_pred heeeEEEEEEEECCHHHHHHHHHHHHHHHHHcCCEeECCccCCceeEEEEeeeCCCCCCCchHHHheeeeeeEEEE
Confidence 34568999999999999999999999999999999999999999 68999999996 599999999999999985
No 10
>KOG3321|consensus
Probab=99.85 E-value=6.9e-23 Score=153.60 Aligned_cols=85 Identities=27% Similarity=0.389 Sum_probs=77.9
Q ss_pred CccccccCC-CCCCccceEEEEEeecChhHHhhHHHHHHHHHHHcCCeeeccccCCC--ceEEEEecCCCCcceeeeEEe
Q psy3566 21 EPDYLDHLN-PEIPLYDEVNVQLKGYDFPVLESYQKFVYKIAASLSIQSDESWALPP--QKFNITRMEPNSSVVDANYHL 97 (105)
Q Consensus 21 eP~yl~~~~-~~~ply~~inIklkgyD~~lLe~~~~~I~~~a~~~gi~V~g~~aLPt--~~~tVlrs~hv~kk~r~qfel 97 (105)
++.|..-++ -+.-+|..+.|+++|||.++||+|..||.++|..+||.+.||+|||+ ++||+|||||++||+++|||.
T Consensus 31 ~a~~~~~lk~~Pdkly~~~ai~lrg~D~avLdsYt~Fi~~ta~~LgIp~~~~~plp~~~Er~TlLrS~fIhKK~k~~yE~ 110 (175)
T KOG3321|consen 31 AAVYQNPLKKLPDKLYSLVAIELRGHDKAVLDSYTDFICRTAYYLGIPIKGPEPLPKKRERWTLLRSPFIHKKSKENYER 110 (175)
T ss_pred cccccCccccCchhhcceeeEEeccCchHHHHHHHHHHHHHHHHhCCccCCCCCCchhhhhhhhhhchhhhhHHhhhHHH
Confidence 466766666 44457888999999999999999999999999999999999999999 899999999999999999999
Q ss_pred cceeeecC
Q psy3566 98 RIYERNVQ 105 (105)
Q Consensus 98 rth~R~Iq 105 (105)
|||.|+|+
T Consensus 111 rTH~R~i~ 118 (175)
T KOG3321|consen 111 RTHSRLIE 118 (175)
T ss_pred HHHHHHHH
Confidence 99999985
No 11
>KOG0900|consensus
Probab=98.21 E-value=5.4e-07 Score=65.01 Aligned_cols=69 Identities=14% Similarity=0.189 Sum_probs=62.7
Q ss_pred eEEEEEeecChhHHhhHHHHHHHHHHHcCCeeeccccCCC--ceEEEEecCC-CCcceeeeEEecceeeecC
Q psy3566 37 EVNVQLKGYDFPVLESYQKFVYKIAASLSIQSDESWALPP--QKFNITRMEP-NSSVVDANYHLRIYERNVQ 105 (105)
Q Consensus 37 ~inIklkgyD~~lLe~~~~~I~~~a~~~gi~V~g~~aLPt--~~~tVlrs~h-v~kk~r~qfelrth~R~Iq 105 (105)
.++|.+.+--..-||.-.+-|.+.|+.-++++.||..+|| +++|+.+.|+ .+++-...|++|+|+|+|+
T Consensus 21 ~~~it~~~~~~kslekvC~dl~~~ak~~nl~~kg~vr~Ptk~~~itt~k~p~g~g~k~w~~f~mRiH~R~id 92 (121)
T KOG0900|consen 21 KIRITLTSQKVKSLEKVCADLVRGAKEKNLKVKGPVRLPTKVLKITTRKTPCGEGSKTWDRFEMRVHKRLID 92 (121)
T ss_pred ccceeeeHHHHHHHHHHHHHHHHHHhhcCCcccCcccCCceeEEEEEeecCCcCCccHHHHHHHHHHHHHhc
Confidence 3566677777888999999999999999999999999999 6889999999 7999999999999999985
No 12
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=53.75 E-value=6.2 Score=25.39 Aligned_cols=16 Identities=25% Similarity=0.434 Sum_probs=14.6
Q ss_pred HHHHHcCCeeeccccC
Q psy3566 59 KIAASLSIQSDESWAL 74 (105)
Q Consensus 59 ~~a~~~gi~V~g~~aL 74 (105)
..|+++|+++.|-|||
T Consensus 43 ~IAk~l~i~~pG~YAl 58 (61)
T PRK08351 43 RIAKKLGAKVPGKYAI 58 (61)
T ss_pred HHHHHhCCCCCCeEEE
Confidence 5789999999999997
No 13
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=52.31 E-value=9.4 Score=24.18 Aligned_cols=30 Identities=23% Similarity=0.376 Sum_probs=19.2
Q ss_pred EEeecChhHHhhHHH------HHHHHHHHcCCeeec
Q psy3566 41 QLKGYDFPVLESYQK------FVYKIAASLSIQSDE 70 (105)
Q Consensus 41 klkgyD~~lLe~~~~------~I~~~a~~~gi~V~g 70 (105)
++-|||..++++|.. +|+++-+++|++=.+
T Consensus 4 ~~~Gi~~~lVd~F~~mGF~~dkVvevlrrlgik~~n 39 (55)
T PF09288_consen 4 ALYGIDKDLVDQFENMGFERDKVVEVLRRLGIKSMN 39 (55)
T ss_dssp S----SHHHHHHHHHHT--HHHHHHHHHHS--SS--
T ss_pred HHcCCCHHHHHHHHHcCCcHHHHHHHHHHhCCCCCC
Confidence 467999999999974 799999999987533
No 14
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=44.23 E-value=10 Score=24.72 Aligned_cols=17 Identities=35% Similarity=0.458 Sum_probs=15.0
Q ss_pred HHHHHcCCeeeccccCC
Q psy3566 59 KIAASLSIQSDESWALP 75 (105)
Q Consensus 59 ~~a~~~gi~V~g~~aLP 75 (105)
..|+++|+++.|-|||-
T Consensus 46 eIAkrlgi~~Pg~yAl~ 62 (64)
T COG2093 46 EIAKRLGIKIPGKYALR 62 (64)
T ss_pred HHHHHhCCCCCceEEEE
Confidence 57999999999999873
No 15
>PF00298 Ribosomal_L11: Ribosomal protein L11, RNA binding domain; InterPro: IPR020783 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 L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacteria, plant chloroplast, red algal chloroplast, cyanelle and archaeabacterial L11; and mammalian, plant and yeast L12 (YL15). L11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of L11 has been shown [] to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 1VQN_I 2OTJ_I 3G6E_I 3CME_I 1YIJ_I 1YI2_I 3G4S_I 3CMA_I 3I55_I 1VQ7_I ....
Probab=35.53 E-value=36 Score=21.92 Aligned_cols=21 Identities=38% Similarity=0.281 Sum_probs=18.5
Q ss_pred hHHhhHHHHHHHHHHHcCCee
Q psy3566 48 PVLESYQKFVYKIAASLSIQS 68 (105)
Q Consensus 48 ~lLe~~~~~I~~~a~~~gi~V 68 (105)
.-|++-.+-|.-+|+.+|++|
T Consensus 49 ~~l~~~~k~v~Gta~SmGi~V 69 (69)
T PF00298_consen 49 KSLESAVKSVIGTARSMGIKV 69 (69)
T ss_dssp SSHHHHHHHHHHHHHTTTEEE
T ss_pred CCHHHHHHHHHHHHhcCceEC
Confidence 347889999999999999987
No 16
>KOG0046|consensus
Probab=27.68 E-value=22 Score=31.96 Aligned_cols=60 Identities=23% Similarity=0.348 Sum_probs=36.6
Q ss_pred CCCCCCccccccCCCCCCccceEEEEEeecChhHHhhHHHHHHHHHHHcCCeeeccccCCCceEEE
Q psy3566 16 TTNLFEPDYLDHLNPEIPLYDEVNVQLKGYDFPVLESYQKFVYKIAASLSIQSDESWALPPQKFNI 81 (105)
Q Consensus 16 ~~~l~eP~yl~~~~~~~ply~~inIklkgyD~~lLe~~~~~I~~~a~~~gi~V~g~~aLPt~~~tV 81 (105)
+.+++==|-|++.+|..-.|+ +.-+|-.---=-+=|+|++..|+++|+.| |+||-...+|
T Consensus 540 S~g~~vLDLidaI~P~~Vn~~---LV~~G~t~EdK~~NAkYaIS~ARKiGa~I---yaLPEDIvEV 599 (627)
T KOG0046|consen 540 SDGLFVLDLLDAIKPGVVNYS---LVTSGNTDEEKLLNAKYAISVARKLGASI---YALPEDIVEV 599 (627)
T ss_pred ccCcchHHHHhhcCcCccchh---hccCCCChhhhhhcchhhHhHHHhhCceE---EeccHHHhhh
Confidence 344454555666555554443 22233322112234799999999999999 9999855544
No 17
>PRK14556 pyrH uridylate kinase; Provisional
Probab=27.57 E-value=84 Score=24.99 Aligned_cols=38 Identities=11% Similarity=0.232 Sum_probs=29.6
Q ss_pred CccceEEEEEee----------cChhHHhhHHHHHHHHHH---HcCCeeec
Q psy3566 33 PLYDEVNVQLKG----------YDFPVLESYQKFVYKIAA---SLSIQSDE 70 (105)
Q Consensus 33 ply~~inIklkg----------yD~~lLe~~~~~I~~~a~---~~gi~V~g 70 (105)
+.|++|=++|.| +|...|+.++..|.++++ +.++-|.|
T Consensus 13 ~~~~rvllKlsGe~l~~~~~~~~d~~~~~~~a~~i~~~~~~g~~i~iVvGG 63 (249)
T PRK14556 13 PKLKRILLKLSGESLSADQGFGINVESAQPIINQIKTLTNFGVELALVVGG 63 (249)
T ss_pred hhhCEEEEEEehhhCcCCCCCCcCHHHHHHHHHHHHHHHhCCcEEEEEECC
Confidence 348888888865 899999999999999877 44454544
No 18
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=27.07 E-value=76 Score=22.06 Aligned_cols=37 Identities=11% Similarity=0.322 Sum_probs=25.4
Q ss_pred ceEEEEEeecChhHHhhHHHHHHHHHHHcCCeeeccccCCC
Q psy3566 36 DEVNVQLKGYDFPVLESYQKFVYKIAASLSIQSDESWALPP 76 (105)
Q Consensus 36 ~~inIklkgyD~~lLe~~~~~I~~~a~~~gi~V~g~~aLPt 76 (105)
+.+.|++.|.||++..-=...|.+ .-+....+ |-+|.
T Consensus 15 n~~~i~i~gEdHTL~NlL~~~L~~---d~~V~~a~-Y~i~H 51 (99)
T COG1761 15 NSLELEIEGEDHTLGNLLREELLK---DEDVEFAA-YSIPH 51 (99)
T ss_pred CEEEEEEecCCchHHHHHHHHHhC---CCCeeEEE-EeCCC
Confidence 348999999999999887777665 34444432 44444
No 19
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=25.99 E-value=31 Score=22.38 Aligned_cols=17 Identities=24% Similarity=0.288 Sum_probs=14.4
Q ss_pred HHHHHcCCeeeccccCC
Q psy3566 59 KIAASLSIQSDESWALP 75 (105)
Q Consensus 59 ~~a~~~gi~V~g~~aLP 75 (105)
..|+.+||++.|.|||-
T Consensus 45 ~vAk~~~i~~pG~YAlk 61 (64)
T PRK06393 45 AIAKRAGITEPGMYAIK 61 (64)
T ss_pred HHHHHhCCCCCCeEEEE
Confidence 46899999999999873
No 20
>COG0080 RplK Ribosomal protein L11 [Translation, ribosomal structure and biogenesis]
Probab=25.88 E-value=52 Score=24.46 Aligned_cols=28 Identities=18% Similarity=0.154 Sum_probs=23.1
Q ss_pred eecChhHHhhHHHHHHHHHHHcCCeeec
Q psy3566 43 KGYDFPVLESYQKFVYKIAASLSIQSDE 70 (105)
Q Consensus 43 kgyD~~lLe~~~~~I~~~a~~~gi~V~g 70 (105)
....-.-||+..+-|.-+|+.||++|.|
T Consensus 113 ~dl~a~~l~aA~k~I~GTa~SMGv~Veg 140 (141)
T COG0080 113 PDLNAKDLEAAVKEILGTARSMGVTVEG 140 (141)
T ss_pred hhhhhHHHHHHHHHHhhhhhhceEEeec
Confidence 3344456899999999999999999987
No 21
>PRK01143 rpl11p 50S ribosomal protein L11P; Validated
Probab=25.78 E-value=58 Score=24.42 Aligned_cols=24 Identities=17% Similarity=0.069 Sum_probs=21.7
Q ss_pred hhHHhhHHHHHHHHHHHcCCeeec
Q psy3566 47 FPVLESYQKFVYKIAASLSIQSDE 70 (105)
Q Consensus 47 ~~lLe~~~~~I~~~a~~~gi~V~g 70 (105)
..-|++..+-|.-+|+.+|++|.|
T Consensus 115 ~~~l~~~vk~VlGTarSmGi~V~g 138 (163)
T PRK01143 115 SYDLKAAVKEVLGTCVSMGVTVEG 138 (163)
T ss_pred cccHHHHHHHHHhhHhhceEEEec
Confidence 456899999999999999999987
No 22
>TIGR03653 arch_L6P archaeal ribosomal protein L6P. Members of this protein family are the archaeal ribosomal protein L6P. The top-scoring proteins not selected by this model are eukaryotic cytosolic ribosomal protein L9. Bacterial ribosomal protein L6 scores lower and is described by a distinct model.
Probab=25.10 E-value=98 Score=23.09 Aligned_cols=25 Identities=12% Similarity=0.044 Sum_probs=23.3
Q ss_pred EEEEeecChhHHhhHHHHHHHHHHH
Q psy3566 39 NVQLKGYDFPVLESYQKFVYKIAAS 63 (105)
Q Consensus 39 nIklkgyD~~lLe~~~~~I~~~a~~ 63 (105)
+|-++|.|--.|-++|..|..+|+-
T Consensus 129 ~I~i~G~DKq~Vgq~AA~Ir~~~~~ 153 (170)
T TIGR03653 129 EVIVTGIDKEDVGQTAANIEQATRI 153 (170)
T ss_pred EEEEEeCCHHHHHHHHHHHHHhhcc
Confidence 6999999999999999999998873
No 23
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=24.78 E-value=96 Score=20.25 Aligned_cols=24 Identities=21% Similarity=0.307 Sum_probs=21.3
Q ss_pred ceEEEEEeecChhHHhhHHHHHHH
Q psy3566 36 DEVNVQLKGYDFPVLESYQKFVYK 59 (105)
Q Consensus 36 ~~inIklkgyD~~lLe~~~~~I~~ 59 (105)
+.+.+.+.|.||++...=...+.+
T Consensus 9 ~~~~~~~~~edhTl~n~L~~~l~~ 32 (86)
T cd00460 9 NYVDFVLENEDHTLGNSLRRILLK 32 (86)
T ss_pred CEEEEEEeCCCchHHHHHHHHHhC
Confidence 568999999999999988888777
No 24
>COG0528 PyrH Uridylate kinase [Nucleotide transport and metabolism]
Probab=22.77 E-value=1.9e+02 Score=23.24 Aligned_cols=35 Identities=20% Similarity=0.357 Sum_probs=28.1
Q ss_pred CccceEEEEEee----------cChhHHhhHHHHHHHHHHHcCCee
Q psy3566 33 PLYDEVNVQLKG----------YDFPVLESYQKFVYKIAASLSIQS 68 (105)
Q Consensus 33 ply~~inIklkg----------yD~~lLe~~~~~I~~~a~~~gi~V 68 (105)
|.|..+=|+|.| .|..+++.++..|-++.+. |.+|
T Consensus 3 ~~~~rillkLsGe~l~g~~~~gid~~~i~~~a~~i~~~~~~-g~eV 47 (238)
T COG0528 3 PKYMRILLKLSGEALAGEQGFGIDPEVLDRIANEIKELVDL-GVEV 47 (238)
T ss_pred cceEEEEEEeecceecCCCCCCCCHHHHHHHHHHHHHHHhc-CcEE
Confidence 567777777654 7999999999999999876 6665
No 25
>COG0440 IlvH Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]
Probab=22.54 E-value=1e+02 Score=23.32 Aligned_cols=52 Identities=21% Similarity=0.229 Sum_probs=42.9
Q ss_pred CCCCCCCccccccCCCCCCccceEEEEEeecChhHHhhHHHHHHHHHHHcCCe
Q psy3566 15 KTTNLFEPDYLDHLNPEIPLYDEVNVQLKGYDFPVLESYQKFVYKIAASLSIQ 67 (105)
Q Consensus 15 ~~~~l~eP~yl~~~~~~~ply~~inIklkgyD~~lLe~~~~~I~~~a~~~gi~ 67 (105)
++..=|..+=|-.+..+-|.-..|.|.+.| |..++|+-.+.++++....+..
T Consensus 25 fsrRG~NIeSltv~~tE~~~~SRiTivv~g-~~~~~EQi~kQL~kLidV~kV~ 76 (163)
T COG0440 25 FSRRGYNIESLTVGPTETPGLSRITIVVSG-DEQVLEQIIKQLNKLIDVLKVL 76 (163)
T ss_pred HHhcCcccceEEEEecCCCCceEEEEEEcC-CcchHHHHHHHHHhhccceeEE
Confidence 334446677777778889999999999999 9999999999999998876543
No 26
>TIGR01632 L11_bact 50S ribosomal protein L11. This model represents bacterial, chloroplast, and most mitochondrial forms of 50S ribosomal protein L11.
Probab=22.35 E-value=41 Score=24.59 Aligned_cols=26 Identities=19% Similarity=0.153 Sum_probs=22.4
Q ss_pred cChhHHhhHHHHHHHHHHHcCCeeec
Q psy3566 45 YDFPVLESYQKFVYKIAASLSIQSDE 70 (105)
Q Consensus 45 yD~~lLe~~~~~I~~~a~~~gi~V~g 70 (105)
....-|++..+-|.-+|+.+|++|.|
T Consensus 115 ~~~~~l~~~vk~v~GTarSmGi~V~~ 140 (140)
T TIGR01632 115 LNTKDIEAAMKIIAGTAKSMGIEIVG 140 (140)
T ss_pred hCcccHHHHHHHhheeHeeceEEEeC
Confidence 44567899999999999999999975
No 27
>KOG3257|consensus
Probab=22.24 E-value=76 Score=24.28 Aligned_cols=25 Identities=24% Similarity=0.206 Sum_probs=22.4
Q ss_pred hhHHhhHHHHHHHHHHHcCCeeecc
Q psy3566 47 FPVLESYQKFVYKIAASLSIQSDES 71 (105)
Q Consensus 47 ~~lLe~~~~~I~~~a~~~gi~V~g~ 71 (105)
+.-||+-.+-|.-+|+.|||+|.-+
T Consensus 134 ~~~lesi~rsiigtA~smGIkVvp~ 158 (168)
T KOG3257|consen 134 CTTLESICRSIIGTARSMGIKVVPP 158 (168)
T ss_pred cccHHHHHHHHHHHHHhCccccchh
Confidence 5679999999999999999999764
No 28
>cd02641 R3H_Smubp-2_like R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
Probab=21.86 E-value=70 Score=19.84 Aligned_cols=16 Identities=19% Similarity=0.426 Sum_probs=13.2
Q ss_pred HHHHHHHHHHcCCeee
Q psy3566 54 QKFVYKIAASLSIQSD 69 (105)
Q Consensus 54 ~~~I~~~a~~~gi~V~ 69 (105)
-+.||++|+.+|..-.
T Consensus 31 R~~vH~lA~~~gL~s~ 46 (60)
T cd02641 31 RLLVHELAEELGLRHE 46 (60)
T ss_pred HHHHHHHHHHcCCceE
Confidence 4689999999998754
No 29
>PTZ00105 60S ribosomal protein L12; Provisional
Probab=21.81 E-value=51 Score=24.11 Aligned_cols=24 Identities=17% Similarity=0.087 Sum_probs=21.4
Q ss_pred hhHHhhHHHHHHHHHHHcCCeeec
Q psy3566 47 FPVLESYQKFVYKIAASLSIQSDE 70 (105)
Q Consensus 47 ~~lLe~~~~~I~~~a~~~gi~V~g 70 (105)
..=|++-.+-|.-+|+.+|++|.|
T Consensus 97 ~~~l~~a~k~V~GTarSmGi~V~g 120 (140)
T PTZ00105 97 AKTFKGTVKEVLGTCVSIGCTVDG 120 (140)
T ss_pred CCcHHHHHHHHHhhheeeeEEEEC
Confidence 455888999999999999999987
No 30
>PF12444 Sox_N: Sox developmental protein N terminal ; InterPro: IPR022151 This domain family is found in eukaryotes, and is typically between 69 and 88 amino acids in length. The family is found in association with PF00505 from PFAM. There are two conserved sequence motifs: YDW and PVR. This family contains Sox8, Sox9 and Sox10 proteins which have structural similarity. Sox proteins are involved in developmental processes.
Probab=20.46 E-value=25 Score=23.90 Aligned_cols=10 Identities=50% Similarity=1.069 Sum_probs=7.7
Q ss_pred EEeecChhHH
Q psy3566 41 QLKGYDFPVL 50 (105)
Q Consensus 41 klkgyD~~lL 50 (105)
.|||||-.|+
T Consensus 69 VLkGYDWtLV 78 (84)
T PF12444_consen 69 VLKGYDWTLV 78 (84)
T ss_pred HhccCCceee
Confidence 4789998775
Done!