Query 025449
Match_columns 252
No_of_seqs 227 out of 800
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 05:57:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025449.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025449hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00069 60S ribosomal protein 100.0 1.4E-84 3.1E-89 595.0 16.8 184 1-184 1-189 (300)
2 KOG0875 60S ribosomal protein 100.0 9.8E-76 2.1E-80 527.1 11.3 182 1-182 1-186 (264)
3 PRK08569 rpl18p 50S ribosomal 100.0 1.7E-53 3.7E-58 371.9 12.7 149 11-192 2-155 (193)
4 COG0256 RplR Ribosomal protein 100.0 6E-34 1.3E-38 234.9 7.7 120 14-167 1-120 (125)
5 PF00861 Ribosomal_L18p: Ribos 99.9 2.4E-27 5.3E-32 192.0 7.4 113 20-167 2-114 (119)
6 PRK05593 rplR 50S ribosomal pr 99.9 5.7E-25 1.2E-29 179.2 8.7 104 28-167 8-112 (117)
7 CHL00139 rpl18 ribosomal prote 99.9 3.2E-25 6.9E-30 178.8 6.0 101 33-167 4-104 (109)
8 cd00432 Ribosomal_L18_L5e Ribo 99.9 1.4E-24 3.1E-29 170.4 8.3 93 45-167 8-100 (103)
9 TIGR00060 L18_bact ribosomal p 99.9 1.6E-22 3.4E-27 164.7 9.0 101 29-167 7-109 (114)
10 PTZ00032 60S ribosomal protein 99.6 5.7E-16 1.2E-20 137.4 9.1 74 37-125 99-184 (211)
11 KOG3333 Mitochondrial/chloropl 95.5 0.038 8.2E-07 48.8 6.1 66 49-126 61-127 (188)
12 PTZ00090 40S ribosomal protein 94.3 0.26 5.5E-06 45.4 8.5 67 46-125 116-184 (233)
13 PF00411 Ribosomal_S11: Riboso 88.3 4.2 9E-05 32.8 8.4 62 51-125 3-64 (110)
14 CHL00041 rps11 ribosomal prote 87.5 4.3 9.2E-05 33.3 8.2 71 41-125 6-77 (116)
15 TIGR03632 bact_S11 30S ribosom 86.2 4.7 0.0001 32.6 7.6 61 52-125 4-64 (108)
16 PRK05309 30S ribosomal protein 86.2 5 0.00011 33.5 8.0 61 47-112 16-76 (128)
17 PF02109 DAD: DAD family; Int 78.7 1.5 3.2E-05 36.4 2.1 34 170-203 78-111 (112)
18 PTZ00129 40S ribosomal protein 78.6 12 0.00026 32.5 7.7 59 53-125 33-93 (149)
19 PRK09607 rps11p 30S ribosomal 76.6 17 0.00037 30.9 7.9 62 51-125 12-74 (132)
20 TIGR03628 arch_S11P archaeal r 76.3 16 0.00034 30.4 7.5 61 53-125 7-67 (114)
21 KOG1746 Defender against cell 63.9 4.9 0.00011 33.6 1.9 34 170-203 81-114 (115)
22 COG0100 RpsK Ribosomal protein 48.0 79 0.0017 27.0 6.7 101 51-179 21-126 (129)
23 PRK05337 beta-hexosaminidase; 42.3 29 0.00062 33.1 3.6 64 95-182 96-173 (337)
24 KOG0408 Mitochondrial/chloropl 35.3 1.8E+02 0.0039 26.3 7.1 63 48-125 79-143 (190)
25 PF13069 DUF3933: Protein of u 29.2 15 0.00033 26.7 -0.4 9 58-66 3-11 (53)
26 PF13216 DUF4024: Protein of u 28.7 16 0.00035 24.6 -0.3 10 200-209 17-26 (35)
27 cd04518 TBP_archaea archaeal T 27.6 4.2E+02 0.009 23.2 8.7 54 42-112 29-83 (174)
28 COG5329 Phosphoinositide polyp 21.8 3.2E+02 0.0068 28.7 7.1 104 47-182 7-114 (570)
No 1
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=100.00 E-value=1.4e-84 Score=594.98 Aligned_cols=184 Identities=67% Similarity=1.019 Sum_probs=179.7
Q ss_pred CceeeeecCcccccccccccchhccCchhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeccCCCEEEEEEec
Q 025449 1 MAFAKAQKSKAYFKRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYA 80 (252)
Q Consensus 1 M~fvk~~knkayfkRyqVk~RRRREGKTDY~~R~rLi~qdKnKynspKpRLVVrrTNrhIiaQII~~~~eGD~tLaSAsS 80 (252)
|+|||++||+||||||||||||||||||||++|++|+.||||||||||||||||+||++|||||+++.++||+|||||+|
T Consensus 1 M~fvKv~KnkaY~~ryqvkfRRRREGKTdY~~R~rLi~q~knKynspK~RlVVR~TN~~ii~Qiv~~~~~GD~vl~sA~S 80 (300)
T PTZ00069 1 MAFVKVVKNKAYFKRFQVKYRRRREGKTDYYARRRLILQDKNKYNSPKYRLVVRITNKDIICQIVYATIVGDKVLAAAYS 80 (300)
T ss_pred CCceeeeecccccccccchhhhhhcccccHHHHHHHHHccccccCCCCceEEEEEECCcEEEEEEEeecCCCEEEEEeeh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccccCCCcHHHHHHHHHHHHHHHHhhhccccccCCceeecCccccc-ccCC-CCCcceEEEeecccccccCcce
Q 025449 81 HELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDYSV-EPTE-NRRPFRALLDVGLVKTTTGNRV 158 (252)
Q Consensus 81 ~EL~kyG~k~gltN~aAAYltGlLlArRAL~k~~~d~~y~Gi~eV~g~~~~v-e~~d-~~~~f~~~LDiGL~rtt~G~rV 158 (252)
+||++|||++|++|++||||||+|+|+|+|++||||+.|+|++|++|++|+| |+.| +|+||+|+|||||+|||+||||
T Consensus 81 ~eL~kyG~k~gl~N~~AAY~TGlL~arR~L~kl~ld~~y~G~~e~~g~~y~v~e~~~~~~rpf~a~LDiGL~rtt~G~RV 160 (300)
T PTZ00069 81 HELPRFGIPVGLTNYAAAYATGLLLARRLLKKLGLDKQFEGVKEADGEYYHVDEEDDEERRPFKAILDVGLARTTTGNRV 160 (300)
T ss_pred hhHhhcCcCCCCccHHHHHHHHHHHHHHHHHhhcccccccCcccccCcccccccccccCCCCceEEEeeccccCCCCcee
Confidence 9999999999999999999999999999999999999999999999999999 7766 5999999999999999999999
Q ss_pred eeeeccccc---ccccCCCccCCCCCCcC
Q 025449 159 FGALKVIFK---FIQTSYDYINGFSTTLD 184 (252)
Q Consensus 159 FaalKGavD---~IPhs~~~fpg~d~~~~ 184 (252)
|||||||+| +||||+++|||||.|++
T Consensus 161 FaalKGa~DgGl~IPhs~~rfpg~d~e~~ 189 (300)
T PTZ00069 161 FGALKGAVDGGLHIPHSPNRFPGYSKEKD 189 (300)
T ss_pred eeehhcccccCcccCCCCCcCCCCCcccc
Confidence 999999999 99999999999985544
No 2
>KOG0875 consensus 60S ribosomal protein L5 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.8e-76 Score=527.06 Aligned_cols=182 Identities=62% Similarity=0.974 Sum_probs=178.9
Q ss_pred CceeeeecCcccccccccccchhccCchhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeccCCCEEEEEEec
Q 025449 1 MAFAKAQKSKAYFKRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYA 80 (252)
Q Consensus 1 M~fvk~~knkayfkRyqVk~RRRREGKTDY~~R~rLi~qdKnKynspKpRLVVrrTNrhIiaQII~~~~eGD~tLaSAsS 80 (252)
|+|||++|+++||+||||||||||||||||++|++|+.|||||||+||+||+||+||++|+|||+++.++||+++|+|+|
T Consensus 1 m~fvk~~k~~~y~kryqvk~rrrreGkTdy~arkrl~~qdknk~nt~kyR~ivr~~n~~iicqi~~~~i~gd~v~~~a~s 80 (264)
T KOG0875|consen 1 MGFVKVVKSKAYFKRYQVKFRRRREGKTDYYARKRLVVQDKNKYNTPKYRMIVRVINKDIICQIAYATIEGDVIVRAAYA 80 (264)
T ss_pred CcchheeccccccccccceEEEecCCCccHHHHHHHHhhcccccCCCceEEEEEEechhhHHHHHhheecceEEEEeecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccccCCCcHHHHHHHHHHHHHHHHhhhccccccCCceeecCcccccccCC-CCCcceEEEeecccccccCccee
Q 025449 81 HELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDYSVEPTE-NRRPFRALLDVGLVKTTTGNRVF 159 (252)
Q Consensus 81 ~EL~kyG~k~gltN~aAAYltGlLlArRAL~k~~~d~~y~Gi~eV~g~~~~ve~~d-~~~~f~~~LDiGL~rtt~G~rVF 159 (252)
||||+||+++|++|++||||||+|||+|+|++||||++|+|++|++|+||++|++| +|+||+|+||+||+|||||||||
T Consensus 81 ~elpkyg~~~GLtNyaAay~TglLLarR~l~~~gmD~~yeg~~e~~gde~~~e~idgq~~aFt~~Ld~GLaRtttg~kvF 160 (264)
T KOG0875|consen 81 HELPKYGVKVGLTNYAAAYCTGLLLACRLLKRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVF 160 (264)
T ss_pred ccccccccccccchhHHHHhhHHHHHHHHHHHhCcccccccceeecCcccccccccCCCCCeEEEecccccccCCCceee
Confidence 99999999999999999999999999999999999999999999999999999998 59999999999999999999999
Q ss_pred eeeccccc---ccccCCCccCCCCCC
Q 025449 160 GALKVIFK---FIQTSYDYINGFSTT 182 (252)
Q Consensus 160 aalKGavD---~IPhs~~~fpg~d~~ 182 (252)
||||||+| +||||+++|||..++
T Consensus 161 GAlkga~dGGL~IPHs~krFpGl~e~ 186 (264)
T KOG0875|consen 161 GALKGAVDGGLSIPHSTKRFPGLTEE 186 (264)
T ss_pred eeeehhcccceecCCccccCCCcccc
Confidence 99999999 999999999997533
No 3
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=100.00 E-value=1.7e-53 Score=371.85 Aligned_cols=149 Identities=44% Similarity=0.610 Sum_probs=141.8
Q ss_pred ccccccccccchhccCchhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeccCCCEEEEEEeccccccccccc
Q 025449 11 AYFKRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEV 90 (252)
Q Consensus 11 ayfkRyqVk~RRRREGKTDY~~R~rLi~qdKnKynspKpRLVVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k~ 90 (252)
|..+|||||||||||||||||+|++|+.++ +||||||+||+|||||||+++++||+|||||||+||+++||++
T Consensus 2 a~g~ry~v~~rRrRegkTdY~~R~rl~~~~-------kpRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el~~~g~~~ 74 (193)
T PRK08569 2 ATGPRYKVPFRRRREGKTDYRKRLKLLLSG-------KPRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKYGWKG 74 (193)
T ss_pred CCCCccccceeccccccccHHHHHHHHhcC-------CCEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCchhhccccC
Confidence 568999999999999999999999999998 6999999999999999998888999999999999999999999
Q ss_pred CCCcHHHHHHHHHHHHHHHHhhhccccccCCceeecCcccccccCCCCCcceEEEeecccccccCcceeeeeccccc---
Q 025449 91 GLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKVIFK--- 167 (252)
Q Consensus 91 gltN~aAAYltGlLlArRAL~k~~~d~~y~Gi~eV~g~~~~ve~~d~~~~f~~~LDiGL~rtt~G~rVFaalKGavD--- 167 (252)
+++|++|||+||+|+|+||+++ ||++ |++|+|+.++++|+||||++|||.|
T Consensus 75 ~~~N~~AAy~vG~llA~ral~k--------Gi~~------------------vvfDrGg~~yh~gGRV~A~akgArd~GL 128 (193)
T PRK08569 75 DTGNTPAAYLTGLLAGKKALKA--------GVEE------------------AVLDIGLHRPTKGSRVFAALKGAIDAGL 128 (193)
T ss_pred CCCCHHHHHHHHHHHHHHHHHC--------CCCE------------------EEEecCCccccCCccHHHHHHHHHHcCC
Confidence 9999999999999999999999 9987 9999999999999999999999999
Q ss_pred ccccCCCccCCCCCC--cChhhHHHHH
Q 025449 168 FIQTSYDYINGFSTT--LDLSDYLLSI 192 (252)
Q Consensus 168 ~IPhs~~~fpg~d~~--~~~~~~~~~~ 192 (252)
+||||+++|||+|++ .++.+|...+
T Consensus 129 ~fPh~~~~~p~~~ri~G~Hia~y~~~l 155 (193)
T PRK08569 129 EIPHGEEVLPDEDRIRGEHIAEYAESL 155 (193)
T ss_pred cCCCCCCcCCCccccccchHHHHHHHH
Confidence 999999999999987 6778886654
No 4
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6e-34 Score=234.94 Aligned_cols=120 Identities=37% Similarity=0.490 Sum_probs=108.6
Q ss_pred cccccccchhccCchhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeccCCCEEEEEEecccccccccccCCC
Q 025449 14 KRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLT 93 (252)
Q Consensus 14 kRyqVk~RRRREGKTDY~~R~rLi~qdKnKynspKpRLVVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k~glt 93 (252)
++|++++||++++||+|+.|.+|. + ++++|||+||+||+|||||||++...+|.+.+|+.+.||+++||+.+++
T Consensus 1 ~~~~~~~rr~~~~kr~~r~R~kl~--g----~~~rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~g~~~~~~ 74 (125)
T COG0256 1 PRYKVKFRRRRRGKRAYRIRKKLL--G----TSGRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKKGGGG 74 (125)
T ss_pred CccchhhHHHHHHhHHHHHHHhhc--c----CCCCcEEEEEEeCCcEEEEEEEcCCCceEEEEEcchHHHHhhcccCCCC
Confidence 589999999999999999999999 4 7899999999999999999999976665555555555777899998899
Q ss_pred cHHHHHHHHHHHHHHHHhhhccccccCCceeecCcccccccCCCCCcceEEEeecccccccCcceeeeeccccc
Q 025449 94 NYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKVIFK 167 (252)
Q Consensus 94 N~aAAYltGlLlArRAL~k~~~d~~y~Gi~eV~g~~~~ve~~d~~~~f~~~LDiGL~rtt~G~rVFaalKGavD 167 (252)
|++|||+||+|+|+||+++ ||++ ++ +|+..++.|+||||+++||.|
T Consensus 75 N~~aA~~vG~lia~ra~~k--------gi~~------------------vV--fdr~g~~yhgRV~Ala~~Are 120 (125)
T COG0256 75 NTEAAYLVGKLIAERALAK--------GIEE------------------VV--FDRGGYKYHGRVAALADGARE 120 (125)
T ss_pred CHHHHHHHHHHHHHHHHHc--------CCcE------------------EE--EcCCCCCcchHHHHHHHHHHH
Confidence 9999999999999999999 9998 56 889999999999999999987
No 5
>PF00861 Ribosomal_L18p: Ribosomal L18p/L5e family; InterPro: IPR005484 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 [, ]. This family includes L18 from bacteria and L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits []. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA, while in bacteria it binds two or three different protein species []. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_M 4A1C_M 4A1A_M 4A17_M 3IZR_Q 3O58_E 1S1I_E 3IZS_Q 3O5H_E 1KQS_M ....
Probab=99.94 E-value=2.4e-27 Score=191.98 Aligned_cols=113 Identities=32% Similarity=0.286 Sum_probs=93.8
Q ss_pred cchhccCchhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeccCCCEEEEEEecccccccccccCCCcHHHHH
Q 025449 20 YKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAY 99 (252)
Q Consensus 20 ~RRRREGKTDY~~R~rLi~qdKnKynspKpRLVVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k~gltN~aAAY 99 (252)
++++|+.|++|..|+.+ +++++|||+|++||+|||||||++...++.+.||+.+.||+++||+.+++|++|||
T Consensus 2 k~~~~~~r~~~~r~~~~-------~~~~~~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~~l~~~~~~~~~~n~~aa~ 74 (119)
T PF00861_consen 2 KKRRRRRRKLRIRRKIK-------GTAERPRLVVFRSNKHIYAQIIDDSKGGTLASASTLSKELKKYGWKGSTKNVEAAY 74 (119)
T ss_dssp SCHHHHHHHHHHHHHHH-------HTTSSEEEEEEEESSEEEEEEEECTTTEEEEEEEEETTTGGGTT-SSTTSSHHHHH
T ss_pred hhHHHHHHHHHHHHHHh-------cCCCCCEEEEEeccCeEEEEEEeeCCCCeEEEEEecchhhhhhhhccCCCCEehHH
Confidence 44555566666655554 45568999999999999999999976666666666677788999999999999999
Q ss_pred HHHHHHHHHHHhhhccccccCCceeecCcccccccCCCCCcceEEEeecccccccCcceeeeeccccc
Q 025449 100 CTGLLLARRVLKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKVIFK 167 (252)
Q Consensus 100 ltGlLlArRAL~k~~~d~~y~Gi~eV~g~~~~ve~~d~~~~f~~~LDiGL~rtt~G~rVFaalKGavD 167 (252)
++|++||+|++++ ||. .+|.|+.+.+.++||+|+++|+.|
T Consensus 75 ~vG~lla~ra~~~--------gi~--------------------~v~fdr~~~~y~grv~a~~~~~re 114 (119)
T PF00861_consen 75 LVGELLAKRALEK--------GIA--------------------KVVFDRGGYKYHGRVKALADGARE 114 (119)
T ss_dssp HHHHHHHHHHHHT--------TSS--------------------EEEECTSTSSSSSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHc--------CCc--------------------EEEEcCCCCcccHHHHHHHHHHHH
Confidence 9999999999999 885 477778899999999999999987
No 6
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=99.92 E-value=5.7e-25 Score=179.16 Aligned_cols=104 Identities=29% Similarity=0.233 Sum_probs=93.4
Q ss_pred hhHHHHHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeccCCCEEEEEEeccccc-ccccccCCCcHHHHHHHHHHHH
Q 025449 28 TDYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELP-RYGLEVGLTNYAAAYCTGLLLA 106 (252)
Q Consensus 28 TDY~~R~rLi~qdKnKynspKpRLVVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~-kyG~k~gltN~aAAYltGlLlA 106 (252)
..++.|.|..++| ++.+|||+|++||+|||||||++ ++|+|||||||.|++ +++|+ ++|++|||++|+++|
T Consensus 8 ~~r~~r~r~ki~g----~~~rpRL~V~~SnkhiyAQvidd--~~~~tl~saST~e~~~k~~~~--~~n~~aa~~vG~~la 79 (117)
T PRK05593 8 LRRHRRVRKKISG----TAERPRLSVFRSNRHIYAQVIDD--VKGKTLASASTLEKDVRAGLK--GGNKEAAKKVGKLIA 79 (117)
T ss_pred HHHHHHHHHHhcC----CCCCCEEEEEEeCCeEEEEEEEC--CCCEEEEEEecCcHhHhcccc--CCCHHHHHHHHHHHH
Confidence 3456677777777 78899999999999999999987 799999999999998 57886 799999999999999
Q ss_pred HHHHhhhccccccCCceeecCcccccccCCCCCcceEEEeecccccccCcceeeeeccccc
Q 025449 107 RRVLKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKVIFK 167 (252)
Q Consensus 107 rRAL~k~~~d~~y~Gi~eV~g~~~~ve~~d~~~~f~~~LDiGL~rtt~G~rVFaalKGavD 167 (252)
+|++++ ||++ +++|.|..+. ++||+|.++||.|
T Consensus 80 ~ra~~~--------gi~~------------------vvfDrg~~~y--hGrV~a~a~~are 112 (117)
T PRK05593 80 ERAKAK--------GIKQ------------------VVFDRGGYKY--HGRVKALADAARE 112 (117)
T ss_pred HHHHHC--------CCCE------------------EEEcCCCCcc--cHHHHHHHHHHHH
Confidence 999999 9997 8999997776 7799999999986
No 7
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=99.91 E-value=3.2e-25 Score=178.85 Aligned_cols=101 Identities=23% Similarity=0.184 Sum_probs=90.1
Q ss_pred HHHHHHhCCCCCCCCcceEEEEecCCcEEEEEEeeccCCCEEEEEEecccccccccccCCCcHHHHHHHHHHHHHHHHhh
Q 025449 33 RIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKM 112 (252)
Q Consensus 33 R~rLi~qdKnKynspKpRLVVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k~gltN~aAAYltGlLlArRAL~k 112 (252)
|.|..+.| ++.+|||+|++||+|||||||++ ..++|||||||.|++.++|..+++|++|||++|+++|+|++++
T Consensus 4 r~r~ki~g----~~~rpRL~V~rSnkhiyaQvidd--~~g~tlasaST~ek~~~~~~~~~~n~~aA~~vG~lla~ra~~~ 77 (109)
T CHL00139 4 RVRKKIKG----TAERPRLSVFRSNKHIYAQIIDD--TNGKTLVACSTLEPDVKSSLSSTSTCDASKLVGQKLAKKSLKK 77 (109)
T ss_pred eeeeeecC----CCCCCEEEEEEeCCeEEEEEEEC--CCCCEEEEEecCchhhhccccCCCCHHHHHHHHHHHHHHHHHC
Confidence 44455556 67899999999999999999996 3569999999999998898878999999999999999999999
Q ss_pred hccccccCCceeecCcccccccCCCCCcceEEEeecccccccCcceeeeeccccc
Q 025449 113 LEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKVIFK 167 (252)
Q Consensus 113 ~~~d~~y~Gi~eV~g~~~~ve~~d~~~~f~~~LDiGL~rtt~G~rVFaalKGavD 167 (252)
||++ +++|.|..+ -++||++.++||.|
T Consensus 78 --------gi~~------------------vvfDrgg~~--yhGrV~a~a~~are 104 (109)
T CHL00139 78 --------GITK------------------VVFDRGGKL--YHGRIKALAEAARE 104 (109)
T ss_pred --------CCCE------------------EEEcCCCCc--cchHHHHHHHHHHH
Confidence 9987 899999766 67999999999986
No 8
>cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.
Probab=99.91 E-value=1.4e-24 Score=170.44 Aligned_cols=93 Identities=39% Similarity=0.393 Sum_probs=87.1
Q ss_pred CCCcceEEEEecCCcEEEEEEeeccCCCEEEEEEecccccccccccCCCcHHHHHHHHHHHHHHHHhhhccccccCCcee
Q 025449 45 NTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVE 124 (252)
Q Consensus 45 nspKpRLVVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k~gltN~aAAYltGlLlArRAL~k~~~d~~y~Gi~e 124 (252)
+.++|||+|++||+|||||||++. +|+|||+|||+|++.+++..+++|++|||++|.++|+|++++ |+++
T Consensus 8 ~~~~~RL~v~~Sn~~i~aqvi~~~--~~~vl~sast~e~~~~~~~~~~~n~~aA~~vG~~la~r~~~~--------gi~~ 77 (103)
T cd00432 8 TQERPRLVVRKSNKHIYAQIIDDS--GDKTLVSASTLELAIKGVLGSGNNVEAAYLVGRLLAKRALEK--------GIKK 77 (103)
T ss_pred cCCCCEEEEEEeCCEEEEEEEEeC--cCeEEEEEecCchhhcccccCCCcHHHHHHHHHHHHHHHHHC--------CCCE
Confidence 456999999999999999999994 999999999999998888778999999999999999999999 8887
Q ss_pred ecCcccccccCCCCCcceEEEeecccccccCcceeeeeccccc
Q 025449 125 ATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKVIFK 167 (252)
Q Consensus 125 V~g~~~~ve~~d~~~~f~~~LDiGL~rtt~G~rVFaalKGavD 167 (252)
+++|.|..+. ++||+|+++|+.|
T Consensus 78 ------------------vv~D~~~~~~--~grv~a~~~~~r~ 100 (103)
T cd00432 78 ------------------VVFDRGGYRY--HGRVKALAKGARE 100 (103)
T ss_pred ------------------EEEeCCCccc--ccHHHHHHHHHHH
Confidence 8999999999 9999999999986
No 9
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=99.88 E-value=1.6e-22 Score=164.71 Aligned_cols=101 Identities=29% Similarity=0.242 Sum_probs=86.3
Q ss_pred hHHHHHHHHHhCCCCCCC--CcceEEEEecCCcEEEEEEeeccCCCEEEEEEecccccccccccCCCcHHHHHHHHHHHH
Q 025449 29 DYRARIRLINQDKNKYNT--PKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLA 106 (252)
Q Consensus 29 DY~~R~rLi~qdKnKyns--pKpRLVVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k~gltN~aAAYltGlLlA 106 (252)
..+.|.|..+.| ++ .+|||+|++||+|||||||++ ++|+|||||||.|++ ++ +++|++|||++|+++|
T Consensus 7 ~r~~r~r~ki~g----t~~~~rpRL~V~rSnk~iyaQiIdd--~~~~tlasaST~ek~-~~---~~~n~~aA~~vG~~la 76 (114)
T TIGR00060 7 RRHKRIRRKLRE----TGEANRPRLVVFRSNRHIYAQVIDD--SKSEVLASASTLEKK-LK---YTGNKDAAKKVGKLVA 76 (114)
T ss_pred HHHHHHHHHhcC----CCCCCCcEEEEEEeCCeEEEEEEEC--CCCEEEEEEecchhh-hc---CCCCHHHHHHHHHHHH
Confidence 345667777776 45 599999999999999999988 699999999999986 32 6789999999999999
Q ss_pred HHHHhhhccccccCCceeecCcccccccCCCCCcceEEEeecccccccCcceeeeeccccc
Q 025449 107 RRVLKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKVIFK 167 (252)
Q Consensus 107 rRAL~k~~~d~~y~Gi~eV~g~~~~ve~~d~~~~f~~~LDiGL~rtt~G~rVFaalKGavD 167 (252)
+|++++ ||++ +++|.| ...-.+||.|.+.|+.|
T Consensus 77 ~ra~~~--------gi~~------------------vvfDrg--g~~YhGrv~A~a~~aRe 109 (114)
T TIGR00060 77 ERLKEK--------GIKD------------------VVFDRG--GYKYHGRVAALAEAARE 109 (114)
T ss_pred HHHHHC--------CCCE------------------EEEeCC--CCcchHHHHHHHHHHHH
Confidence 999999 9987 899998 44447899999888875
No 10
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=99.64 E-value=5.7e-16 Score=137.42 Aligned_cols=74 Identities=23% Similarity=0.201 Sum_probs=62.8
Q ss_pred HHhCCCCCCCCcceEEEEecCCcEEEEEEeeccCCCEEEEEEecccccccccc------------cCCCcHHHHHHHHHH
Q 025449 37 INQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLE------------VGLTNYAAAYCTGLL 104 (252)
Q Consensus 37 i~qdKnKynspKpRLVVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k------------~gltN~aAAYltGlL 104 (252)
|+||| .+|||+|++||+||||||||| ..++|||||||.+..-.+.- .+++|.+||+.+|.+
T Consensus 99 i~~gk-----rrPRLsV~RSnkHIYAQIIDD--~~~~TLasaSTlek~l~~~~~~~~~~~~n~~~~~g~nieaA~~VGk~ 171 (211)
T PTZ00032 99 IIKGK-----RRPRLTLKNTNNQMYATIVDD--YTRHVLCFSCTNFKYLSHIFGTYPTKTTNRVRNNGGTIKAAYELGKL 171 (211)
T ss_pred HHcCC-----CcceEEEEecCCeEEEEEEEC--CCCCEEEEecCCCHHHHhhhcccccccccccccCCCcHHHHHHHHHH
Confidence 56675 479999999999999999998 58899999999887532221 147899999999999
Q ss_pred HHHHHHhhhccccccCCceee
Q 025449 105 LARRVLKMLEMDAEYEGHVEA 125 (252)
Q Consensus 105 lArRAL~k~~~d~~y~Gi~eV 125 (252)
||+||+++ ||++|
T Consensus 172 IAerAl~k--------GI~kV 184 (211)
T PTZ00032 172 IGRKALSK--------GISKV 184 (211)
T ss_pred HHHHHHHC--------CCCEE
Confidence 99999999 99984
No 11
>KOG3333 consensus Mitochondrial/chloroplast ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=95.46 E-value=0.038 Score=48.77 Aligned_cols=66 Identities=23% Similarity=0.158 Sum_probs=55.0
Q ss_pred ceEEEEecCCcEEEEEEeeccCCCEEEEEEecccccc-cccccCCCcHHHHHHHHHHHHHHHHhhhccccccCCceeec
Q 025449 49 YRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPR-YGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEAT 126 (252)
Q Consensus 49 pRLVVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~k-yG~k~gltN~aAAYltGlLlArRAL~k~~~d~~y~Gi~eV~ 126 (252)
+||=|-+|.+|+..-+... .|.|+.|||+.|... ..+ -+++|+.|+--+|..||.|.|+. ||....
T Consensus 61 h~lev~~~~~hveg~v~H~---~~gvvvSAST~EwaIk~qL-Yst~dtsA~~niGRVLAqRCLqs--------GI~fm~ 127 (188)
T KOG3333|consen 61 HRLEVIRTQHHVEGLVEHQ---NGGVVVSASTREWAIKKQL-YSTRDTSACENIGRVLAQRCLQS--------GINFMV 127 (188)
T ss_pred eEEEEeecccceeeeeeEe---cCCEEEEecccchHHHHHH-hhccchHHHHHHHHHHHHHHHHh--------Ccceec
Confidence 6888999999999999886 445888999999862 222 26789999999999999999999 998743
No 12
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=94.31 E-value=0.26 Score=45.39 Aligned_cols=67 Identities=18% Similarity=0.399 Sum_probs=52.3
Q ss_pred CCcceEEEEecCCcEEEEEEeeccCCCE-EEEEEecccccccccccCCCc-HHHHHHHHHHHHHHHHhhhccccccCCce
Q 025449 46 TPKYRFVVRFTNKDITAQIISASIAGDI-VLASAYAHELPRYGLEVGLTN-YAAAYCTGLLLARRVLKMLEMDAEYEGHV 123 (252)
Q Consensus 46 spKpRLVVrrTNrhIiaQII~~~~eGD~-tLaSAsS~EL~kyG~k~gltN-~aAAYltGlLlArRAL~k~~~d~~y~Gi~ 123 (252)
+.+.++||.-|-+++++|+.|. .|.. ||+-+|+-.. |.++...+ --||+.++.-+|+++.+. |+.
T Consensus 116 ~~~f~~vI~aSfNNTIVTlTD~--~GNv~tl~WSSAG~~---GFKGsKKsTpfAAQ~aae~aakka~~~--------GIk 182 (233)
T PTZ00090 116 TDRFMLVITTSKNNVHAQVVNK--SKNYKTVFGSFAGNV---GFRKKLQQSERCAYRIGENIAKKCRRL--------GIF 182 (233)
T ss_pred CCcEEEEEEeccCcEEEEEEeC--CCCEEEEEEEccccc---CcccCccCCHHHHHHHHHHHHHHHHHc--------CCe
Confidence 4678999999999999999997 5875 7888877555 34433333 347899999999999998 887
Q ss_pred ee
Q 025449 124 EA 125 (252)
Q Consensus 124 eV 125 (252)
+|
T Consensus 183 ~V 184 (233)
T PTZ00090 183 AV 184 (233)
T ss_pred EE
Confidence 64
No 13
>PF00411 Ribosomal_S11: Ribosomal protein S11; InterPro: IPR001971 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 S11 [] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. On the basis of sequence similarities, S11 belongs to a family of bacterial, archaeal and eukaryotic ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_K 3U5C_O 3O2Z_H 3IZB_K 3U5G_O 3O30_H 1S1H_K 3BBN_K 2XZN_K 2XZM_K ....
Probab=88.30 E-value=4.2 Score=32.81 Aligned_cols=62 Identities=15% Similarity=0.059 Sum_probs=45.9
Q ss_pred EEEEecCCcEEEEEEeeccCCCEEEEEEecccccccccccCCCcHHHHHHHHHHHHHHHHhhhccccccCCceee
Q 025449 51 FVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEA 125 (252)
Q Consensus 51 LVVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k~gltN~aAAYltGlLlArRAL~k~~~d~~y~Gi~eV 125 (252)
+-|+-|.+++++.+.|. .+.++++.|+-.+.-.|- ......||+.++.-+++++.+. |++.|
T Consensus 3 ihI~~s~NNt~vtlTd~---~G~~~~~~S~G~~gfK~~--rk~t~~Aa~~~a~~~~~~~~~~--------gi~~v 64 (110)
T PF00411_consen 3 IHIKSSFNNTIVTLTDL---KGNVLFWSSAGSLGFKGA--RKSTPYAAQQAAEKIAKKAKEL--------GIKTV 64 (110)
T ss_dssp EEEEEESSEEEEEEEET---TSEEEEEEETTTSSTTTT--CGSSHHHHHHHHHHHHHHHHCT--------TEEEE
T ss_pred EEEEecCCCEEEEEECC---CCCEEEEEeccccccccc--cccCHHHHHHHHHHHHHHHHHc--------CCeEE
Confidence 34777899999999997 457888888865532222 1356788999999999999988 87764
No 14
>CHL00041 rps11 ribosomal protein S11
Probab=87.51 E-value=4.3 Score=33.32 Aligned_cols=71 Identities=18% Similarity=0.118 Sum_probs=51.6
Q ss_pred CCCCCCCcceEEEEecCCcEEEEEEeeccCCCEEEEEEecccccccccccCC-CcHHHHHHHHHHHHHHHHhhhcccccc
Q 025449 41 KNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGL-TNYAAAYCTGLLLARRVLKMLEMDAEY 119 (252)
Q Consensus 41 KnKynspKpRLVVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k~gl-tN~aAAYltGlLlArRAL~k~~~d~~y 119 (252)
|+|.+.+.--+-|+-|-+++++-+.|. .| .+++.+|+-.+. .++.. ...-||+.++.-+++++++.
T Consensus 6 ~~~~~~~~gi~hI~~t~NNTiiTlTd~--~G-~~l~~~S~G~~g---fKg~rK~T~~Aa~~~a~~~~~~~~~~------- 72 (116)
T CHL00041 6 KSKRKIPKGVIHIQASFNNTIVTVTDV--RG-RVISWSSAGACG---FKGARKGTPFAAQTAAENAIRTVIDQ------- 72 (116)
T ss_pred cccccceeEEEEEEcccCCEEEEEEcC--CC-CEEEEEecCcee---eCCCccCCHHHHHHHHHHHHHHHHHc-------
Confidence 445555556677888999999999987 45 589988886553 33322 34558889999999999988
Q ss_pred CCceee
Q 025449 120 EGHVEA 125 (252)
Q Consensus 120 ~Gi~eV 125 (252)
|+.++
T Consensus 73 -gi~~v 77 (116)
T CHL00041 73 -GMKRA 77 (116)
T ss_pred -CCcEE
Confidence 77764
No 15
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=86.22 E-value=4.7 Score=32.59 Aligned_cols=61 Identities=20% Similarity=0.124 Sum_probs=44.2
Q ss_pred EEEecCCcEEEEEEeeccCCCEEEEEEecccccccccccCCCcHHHHHHHHHHHHHHHHhhhccccccCCceee
Q 025449 52 VVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEA 125 (252)
Q Consensus 52 VVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k~gltN~aAAYltGlLlArRAL~k~~~d~~y~Gi~eV 125 (252)
-|.-|.+++++-+.|. .|+ +++.+|+-.+...|-+ ....-||+.++..+++++++. |+..+
T Consensus 4 hI~~s~NNT~itlTd~--~g~-~~~~~S~G~~gfkg~r--k~t~~Aa~~~a~~~~~~~~~~--------gi~~v 64 (108)
T TIGR03632 4 HIHATFNNTIVTITDP--QGN-VLSWASAGAVGFKGSK--KSTPYAAQLAAEDAAKKAKEF--------GMKTV 64 (108)
T ss_pred EEEccCCCEEEEEEcC--CCC-EEEEEecCceeeCCCc--cCCHHHHHHHHHHHHHHHHHc--------CCcEE
Confidence 3667889999999997 465 7888877655433332 234556899999999999998 77664
No 16
>PRK05309 30S ribosomal protein S11; Validated
Probab=86.16 E-value=5 Score=33.52 Aligned_cols=61 Identities=20% Similarity=0.058 Sum_probs=44.1
Q ss_pred CcceEEEEecCCcEEEEEEeeccCCCEEEEEEecccccccccccCCCcHHHHHHHHHHHHHHHHhh
Q 025449 47 PKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKM 112 (252)
Q Consensus 47 pKpRLVVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k~gltN~aAAYltGlLlArRAL~k 112 (252)
+.--+-|+-|.+++++-+.|. .| .+++.+|+-.+.-.|-+ ....-||+.++.-+++.+++.
T Consensus 16 ~~gi~hI~~t~NNTiitlTd~--~G-~~~~~~S~G~~gfKg~r--K~T~~Aa~~aa~~~~~~~~~~ 76 (128)
T PRK05309 16 PSGVAHIHATFNNTIVTITDR--QG-NVISWASAGGLGFKGSR--KSTPYAAQVAAEDAAKKAKEH 76 (128)
T ss_pred ceeEEEEEccCCCEEEEEEcC--CC-CEEEEEecCccEeCCCc--cCCHHHHHHHHHHHHHHHHHc
Confidence 345677888999999999996 45 57787777544322222 234558999999999999987
No 17
>PF02109 DAD: DAD family; InterPro: IPR003038 Members of this family are thought to be integral membrane proteins. Some members of this family have been shown to cause apoptosis if mutated [], these proteins are known as DAD for defender against death. The family also includes the epsilon subunit of the oligosaccharyltransferase that is involved in N-linked glycosylation [].; GO: 0016021 integral to membrane
Probab=78.73 E-value=1.5 Score=36.45 Aligned_cols=34 Identities=24% Similarity=0.460 Sum_probs=31.9
Q ss_pred ccCCCccCCCCCCcChhhHHHHHHHhhhhhhhhh
Q 025449 170 QTSYDYINGFSTTLDLSDYLLSILTVLFVFVNFL 203 (252)
Q Consensus 170 Phs~~~fpg~d~~~~~~~~~~~~~~~~~~~~~~~ 203 (252)
|.+.+.||+.++|..+.||+.+-+.+-|+.+||+
T Consensus 78 p~n~~~f~~is~eRafaDfv~~slvLh~~v~nFi 111 (112)
T PF02109_consen 78 PENKSEFPGISPERAFADFVFCSLVLHFVVFNFI 111 (112)
T ss_pred cccccccCCCChhhhhHHHHHHHHHHHHheeecc
Confidence 8889999999999999999999999999999986
No 18
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=78.61 E-value=12 Score=32.54 Aligned_cols=59 Identities=12% Similarity=0.055 Sum_probs=41.0
Q ss_pred EEecCCcEEEEEEeeccCCCEEEEEEecccccccccccCC-CcH-HHHHHHHHHHHHHHHhhhccccccCCceee
Q 025449 53 VRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGL-TNY-AAAYCTGLLLARRVLKMLEMDAEYEGHVEA 125 (252)
Q Consensus 53 VrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k~gl-tN~-aAAYltGlLlArRAL~k~~~d~~y~Gi~eV 125 (252)
|+-|-++.+..|.|. .|. +++.++|-.. |.|+.. .+. -||..+..-+|+++++. |+..+
T Consensus 33 I~as~NNTiItiTD~--~G~-~~~w~SsG~~---gfKg~r~KsTpyAAq~aa~~~a~k~~~~--------Gi~~v 93 (149)
T PTZ00129 33 IFASFNDTFIHVTDL--SGR-ETLVRVTGGM---KVKADRDESSPYAAMMAAQDVAARCKEL--------GINAL 93 (149)
T ss_pred EEcccCCeEEEEEcc--cCC-EEEEEecCcc---eecccccCCCHHHHHHHHHHHHHHHHHc--------CCeEE
Confidence 555778899999986 465 5565665443 344333 333 37888899999999998 88774
No 19
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=76.58 E-value=17 Score=30.94 Aligned_cols=62 Identities=11% Similarity=0.011 Sum_probs=46.0
Q ss_pred EEEEecCCcEEEEEEeeccCCCEEEEEEecccccccccccCCCcH-HHHHHHHHHHHHHHHhhhccccccCCceee
Q 025449 51 FVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNY-AAAYCTGLLLARRVLKMLEMDAEYEGHVEA 125 (252)
Q Consensus 51 LVVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k~gltN~-aAAYltGlLlArRAL~k~~~d~~y~Gi~eV 125 (252)
+-|+-|-++.+..+.|. .|..|++.+|+-...+.|-+ .+. -||..++.-+|+++++. |+..|
T Consensus 12 ~hI~as~NNTivtvTD~--~G~~~~~~~S~G~~g~kg~k---K~TpyAAq~aae~~~~~~~~~--------Gi~~v 74 (132)
T PRK09607 12 AHIYASFNNTIITITDL--TGAETIAKSSGGMVVKADRD---ESSPYAAMQAAEKAAEDAKEK--------GITGV 74 (132)
T ss_pred EEEEcccCCeEEEEEcC--CCCEEEEEecCcceeeCCCc---cCCHHHHHHHHHHHHHHHHHc--------CCcEE
Confidence 33556888899999986 57789998888766544433 233 37889999999999988 77764
No 20
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=76.30 E-value=16 Score=30.36 Aligned_cols=61 Identities=11% Similarity=0.009 Sum_probs=45.6
Q ss_pred EEecCCcEEEEEEeeccCCCEEEEEEecccccccccccCCCcHHHHHHHHHHHHHHHHhhhccccccCCceee
Q 025449 53 VRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEA 125 (252)
Q Consensus 53 VrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k~gltN~aAAYltGlLlArRAL~k~~~d~~y~Gi~eV 125 (252)
|+-|-++.+..+.|. .|..+++-+|+-...+.|-+ .. .--||..+..-+++++++. |+..|
T Consensus 7 I~as~NNTiitvTD~--~G~~~~~~~S~G~~g~kg~k-k~-TpyAAq~aa~~~~~~~~~~--------Gi~~v 67 (114)
T TIGR03628 7 IYSSFNNTIITITDI--TGAETIARSSGGMVVKADRD-ES-SPYAAMQAAGRAAEKAKER--------GITGL 67 (114)
T ss_pred EEccCCCeEEEEEcC--CCCEEEEEecCcceEeCCCc-cC-CHHHHHHHHHHHHHHHHHc--------CCcEE
Confidence 566788899999986 68789998888776554443 12 2337788889999999988 77764
No 21
>KOG1746 consensus Defender against cell death protein/oligosaccharyltransferase, epsilon subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=63.94 E-value=4.9 Score=33.59 Aligned_cols=34 Identities=29% Similarity=0.514 Sum_probs=31.3
Q ss_pred ccCCCccCCCCCCcChhhHHHHHHHhhhhhhhhh
Q 025449 170 QTSYDYINGFSTTLDLSDYLLSILTVLFVFVNFL 203 (252)
Q Consensus 170 Phs~~~fpg~d~~~~~~~~~~~~~~~~~~~~~~~ 203 (252)
|.+...|||.+.|..|.|++.+-+.+=||.+||+
T Consensus 81 ~qn~~~f~~iSpeRAFadFifasliLHlvv~nFl 114 (115)
T KOG1746|consen 81 QQNKSEFKGISPERAFADFIFASLILHLVVVNFL 114 (115)
T ss_pred ccccccccCCChhHHHHHHHHHHHHHHHHHhhcc
Confidence 6667799999999999999999999999999996
No 22
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=47.97 E-value=79 Score=27.01 Aligned_cols=101 Identities=18% Similarity=0.076 Sum_probs=58.0
Q ss_pred EEEEecCCcEEEEEEeeccCCCEEEEEEecccccccccccCCCcHH-HHHHHHHHHHHHHHhhhccccccCCceeecCcc
Q 025449 51 FVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYA-AAYCTGLLLARRVLKMLEMDAEYEGHVEATGED 129 (252)
Q Consensus 51 LVVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k~gltN~a-AAYltGlLlArRAL~k~~~d~~y~Gi~eV~g~~ 129 (252)
.=|+-|-++.+.-|.|. .| .+++.++|=-+ |++++...+| ||-..+.-+|+.+++. |++++.
T Consensus 21 ahI~asfNNTivtitD~--~G-n~i~wassG~~---gfk~~rk~tpyAA~~aa~~aa~~a~e~--------Gi~~v~--- 83 (129)
T COG0100 21 AHIHASFNNTIVTITDL--TG-NVIIWASSGGM---GFKGSRKSTPYAAQLAAEDAAKKAKEH--------GIKSVE--- 83 (129)
T ss_pred EEEEcccCCcEEEecCC--CC-CEEEEEecCCc---eEcCCCCCCHHHHHHHHHHHHHHHHHh--------CccEEE---
Confidence 33555777777777765 45 67777777554 4554444444 4555677778888886 777642
Q ss_pred cccccCC-C-CCcceEEEeecccccccCcceeeeeccccc--ccccCCCccCCC
Q 025449 130 YSVEPTE-N-RRPFRALLDVGLVKTTTGNRVFGALKVIFK--FIQTSYDYINGF 179 (252)
Q Consensus 130 ~~ve~~d-~-~~~f~~~LDiGL~rtt~G~rVFaalKGavD--~IPhs~~~fpg~ 179 (252)
-.|.... + +.+.+|+.-+||.-+. ..| .|||+-.|=|+-
T Consensus 84 v~vkgpG~GreaAiraL~~ag~~i~~-----------I~DvTPiphnG~Rppk~ 126 (129)
T COG0100 84 VKVKGPGPGREAAIRALAAAGLKITR-----------IEDVTPIPHNGCRPPKR 126 (129)
T ss_pred EEEECCCCcHHHHHHHHHHccceEEE-----------EEEcCCCCCCCCCCCCC
Confidence 1111111 1 2234555544443221 345 899998887764
No 23
>PRK05337 beta-hexosaminidase; Provisional
Probab=42.26 E-value=29 Score=33.08 Aligned_cols=64 Identities=19% Similarity=0.227 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHHHHhhhccccccCCceeecCcccccccCCCCCcceEEEeecccccc-cCcceee------------e
Q 025449 95 YAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDVGLVKTT-TGNRVFG------------A 161 (252)
Q Consensus 95 ~aAAYltGlLlArRAL~k~~~d~~y~Gi~eV~g~~~~ve~~d~~~~f~~~LDiGL~rtt-~G~rVFa------------a 161 (252)
.+.|+..|..+|+.+.+. |+.- -|.-++|+. .++. .|.|-|| .
T Consensus 96 ~~la~~~g~~~a~Elra~--------Gin~---------------~~aPvlDv~-~~~~~ig~RsfgeDp~lv~~~a~a~ 151 (337)
T PRK05337 96 LKLAEEAGWLMAAELRAC--------GIDL---------------SFAPVLDLD-GISAVIGDRAFHRDPQVVAALASAF 151 (337)
T ss_pred HHHHHHHHHHHHHHHHHh--------CCCc---------------cccCccCCC-CCCCeeeccCCCCCHHHHHHHHHHH
Confidence 788999999999999887 6642 133467776 2322 4667776 4
Q ss_pred eccccc-ccccCCCccCCCCCC
Q 025449 162 LKVIFK-FIQTSYDYINGFSTT 182 (252)
Q Consensus 162 lKGavD-~IPhs~~~fpg~d~~ 182 (252)
++|.-+ .|-..-|-|||++.+
T Consensus 152 i~Glq~~gv~~~~KHFpG~G~~ 173 (337)
T PRK05337 152 IDGMHAAGMAATGKHFPGHGAV 173 (337)
T ss_pred HHHHHHCCCEEEecccCCCCCC
Confidence 566666 777888999999654
No 24
>KOG0408 consensus Mitochondrial/chloroplast ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=35.27 E-value=1.8e+02 Score=26.34 Aligned_cols=63 Identities=14% Similarity=0.088 Sum_probs=42.7
Q ss_pred cceEEEEecCCcEEEEEEeeccCCCEEEEEEeccccccccccc--CCCcHHHHHHHHHHHHHHHHhhhccccccCCceee
Q 025449 48 KYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEV--GLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEA 125 (252)
Q Consensus 48 KpRLVVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k~--gltN~aAAYltGlLlArRAL~k~~~d~~y~Gi~eV 125 (252)
-|=.-|+-|-++.+.|+.|. .++++..+|-- ++ |++. .+|++ ||..+|--+++|+..+ |+..|
T Consensus 79 iPi~hIraS~NNTivtVtd~---kg~vi~~~Scg-te--GFrntrkgT~i-AaQtaavaa~~r~v~~--------G~~~v 143 (190)
T KOG0408|consen 79 IPIIHIRASFNNTIVTVTDV---KGEVISWSSCG-TE--GFRNTRKGTPI-AAQTAAVAAIRRAVDQ--------GMQTV 143 (190)
T ss_pred cceEEEEecCCCeEEEEEcc---CCcEEEEeecc-cc--cccccccCCch-hHHHHHHHHHHHHHHh--------cceEE
Confidence 35444788999999999997 44666655542 22 2221 23454 6678888999999999 88764
No 25
>PF13069 DUF3933: Protein of unknown function (DUF3933)
Probab=29.21 E-value=15 Score=26.69 Aligned_cols=9 Identities=33% Similarity=0.479 Sum_probs=7.3
Q ss_pred CcEEEEEEe
Q 025449 58 KDITAQIIS 66 (252)
Q Consensus 58 rhIiaQII~ 66 (252)
..+|||||+
T Consensus 3 qyvicqii~ 11 (53)
T PF13069_consen 3 QYVICQIID 11 (53)
T ss_pred eEEEEEEec
Confidence 458999987
No 26
>PF13216 DUF4024: Protein of unknown function (DUF4024)
Probab=28.73 E-value=16 Score=24.55 Aligned_cols=10 Identities=60% Similarity=1.414 Sum_probs=8.3
Q ss_pred hhhhhcccce
Q 025449 200 VNFLLCLDFR 209 (252)
Q Consensus 200 ~~~~~~~~~~ 209 (252)
||||.|+.|-
T Consensus 17 vnflfcief~ 26 (35)
T PF13216_consen 17 VNFLFCIEFM 26 (35)
T ss_pred ccEEEEehhh
Confidence 7999998773
No 27
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=27.60 E-value=4.2e+02 Score=23.16 Aligned_cols=54 Identities=15% Similarity=0.272 Sum_probs=32.4
Q ss_pred CCCCCCcce-EEEEecCCcEEEEEEeeccCCCEEEEEEecccccccccccCCCcHHHHHHHHHHHHHHHHhh
Q 025449 42 NKYNTPKYR-FVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKM 112 (252)
Q Consensus 42 nKynspKpR-LVVrrTNrhIiaQII~~~~eGD~tLaSAsS~EL~kyG~k~gltN~aAAYltGlLlArRAL~k 112 (252)
..|+.++.. +++|..+-...+-|.. .|+++|+ |..+.+.|+.....+++.+.+.
T Consensus 29 ~eY~P~~fpgli~Rl~~Pk~t~lIF~----SGKiv~t-------------Gaks~~~a~~a~~~~~~~L~~~ 83 (174)
T cd04518 29 AEYNPDQFPGLVYRLEDPKIAALIFR----SGKMVCT-------------GAKSVEDLHRAVKEIIKKLKDY 83 (174)
T ss_pred cEECCCcCcEEEEEccCCcEEEEEEC----CCeEEEE-------------ccCCHHHHHHHHHHHHHHHHhc
Confidence 478887744 6666666566666555 3466664 3345566666666666665444
No 28
>COG5329 Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
Probab=21.79 E-value=3.2e+02 Score=28.73 Aligned_cols=104 Identities=15% Similarity=0.260 Sum_probs=66.4
Q ss_pred CcceEEEEecCCc-EEEEEEeeccCCCEEEEEEecccc---cccccccCCCcHHHHHHHHHHHHHHHHhhhccccccCCc
Q 025449 47 PKYRFVVRFTNKD-ITAQIISASIAGDIVLASAYAHEL---PRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGH 122 (252)
Q Consensus 47 pKpRLVVrrTNrh-IiaQII~~~~eGD~tLaSAsS~EL---~kyG~k~gltN~aAAYltGlLlArRAL~k~~~d~~y~Gi 122 (252)
++||+++..||++ +.-|.+.. ..++.++|++-..-. +..+.. ...|. ......+ |.
T Consensus 7 ~~~r~i~~~sn~~~~~fr~~~~-~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~-----------------~~i~g~~-Gl 66 (570)
T COG5329 7 EKPRSIAIVSNNYALSFRRLGV-KNSERILCATELVGVRFEPDEGFS-SLSSA-----------------HKIYGVI-GL 66 (570)
T ss_pred cCceeEEEEeccceEEEEecCC-CccceEEEeeccceeecccCccch-hhccc-----------------eeEEeEE-EE
Confidence 4789999999999 77888843 467788887766533 233322 11121 2222333 55
Q ss_pred eeecCcccccccCCCCCcceEEEeecccccccCcceeeeecccccccccCCCccCCCCCC
Q 025449 123 VEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALKVIFKFIQTSYDYINGFSTT 182 (252)
Q Consensus 123 ~eV~g~~~~ve~~d~~~~f~~~LDiGL~rtt~G~rVFaalKGavD~IPhs~~~fpg~d~~ 182 (252)
-+.+|+.|.. ++=+.-+++.-.|+.|+-.++ +|.||-..+.++..+.|
T Consensus 67 i~l~~~~yl~----------~it~~s~v~~~~g~~IykI~~--vdfi~l~~~~~d~~~~~ 114 (570)
T COG5329 67 IKLKGDIYLI----------VITGASLVGVIPGHSIYKILD--VDFISLNNNKWDDELEE 114 (570)
T ss_pred EEecCcEEEE----------EEecceEEeeeCCcceEEEee--eEEEEccccccchhhhh
Confidence 6788887763 334455556777787777663 66788888888777554
Done!