Query 028910
Match_columns 202
No_of_seqs 136 out of 248
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 04:28:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028910.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028910hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0829 60S ribosomal protein 100.0 8.8E-94 1.9E-98 591.0 11.9 169 31-202 1-169 (169)
2 PF01775 Ribosomal_L18ae: Ribo 100.0 3.1E-71 6.7E-76 442.3 12.3 124 30-153 1-124 (124)
3 PRK00773 rplX 50S ribosomal pr 100.0 1.4E-33 3E-38 208.9 6.3 73 98-170 2-74 (76)
4 COG2157 RPL20A Ribosomal prote 100.0 6.7E-30 1.4E-34 193.2 6.0 84 93-176 2-85 (85)
5 PRK00773 rplX 50S ribosomal pr 51.1 33 0.00071 25.6 4.3 60 30-92 2-61 (76)
6 KOG0149 Predicted RNA-binding 36.4 27 0.00058 31.7 2.2 24 81-104 36-59 (247)
7 KOG0126 Predicted RNA-binding 32.2 52 0.0011 29.3 3.3 28 82-110 60-87 (219)
8 COG5347 GTPase-activating prot 31.3 24 0.00053 32.7 1.2 35 79-114 15-50 (319)
9 PHA03066 Hypothetical protein; 28.3 39 0.00085 27.3 1.7 22 94-115 60-81 (110)
10 COG3500 Phage protein D [Gener 24.7 33 0.00072 32.5 0.9 40 130-178 122-161 (350)
11 COG0509 GcvH Glycine cleavage 24.5 30 0.00065 28.6 0.5 27 80-106 75-104 (131)
12 COG1727 RPL18A Ribosomal prote 23.2 17 0.00038 29.7 -1.1 25 72-96 90-114 (122)
13 COG2157 RPL20A Ribosomal prote 20.0 67 0.0015 24.8 1.5 65 28-92 2-66 (85)
No 1
>KOG0829 consensus 60S ribosomal protein L18A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.8e-94 Score=590.98 Aligned_cols=169 Identities=64% Similarity=1.059 Sum_probs=165.8
Q ss_pred eEEEEEeecCCCCCCCCCceEEEEeeecCceeeehhhHHHHHHHhhhhccCcceEEEEEeccCCCceeeEeeEEEEEecC
Q 028910 31 HQYQVVGRALPTEKDEHPKIYRMKLWATNEVRAKSKFWYFLRKLKKVKKSNGQMLAINEIFEKNPTKIKNYGIWLRYQSR 110 (202)
Q Consensus 31 keY~VvGr~lPtek~p~P~lyrM~IFApN~VvAKSrFWyfl~~l~K~Kkt~GeIv~~~eI~Ek~p~~VKNfGIwlrYdSr 110 (202)
+||+||||+||||++|+|+||+|+|||||||+|||||||||++|+||||++||||+|+||+|++|+.|||||||||||||
T Consensus 1 kEY~VvGr~lPTe~~p~p~l~~m~ifa~N~V~AKsrfwyfl~~l~KvKks~Geiv~i~qi~E~~p~~vkNfGIwlrYdSR 80 (169)
T KOG0829|consen 1 KEYQVVGRALPTEKEPTPKLYRMRIFAPNHVVAKSRFWYFLSKLKKVKKSSGEIVAINQIFEKSPLKVKNFGIWLRYDSR 80 (169)
T ss_pred CceEEeeeecCCCCCCCCceEEEEEeccceeehhHHHHHHHHHHHHHhhcCceEEEeceecCCCCceeeeeEEEEEEccC
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceecceeeccCChhhHHHHHHHHhhhccccCCCCceEEEeeeeCCCccCCccccccccCCCcCcccccccCCCCcccC
Q 028910 111 TGYHNMYKEYRDTTLNGAVEQMYTEMASRHRVRSPCIQIIRTATIPAKLCKRESTKQFHNSKIKFPLVFKKVRPPTRKLK 190 (202)
Q Consensus 111 sgthNmyKEyRdlt~~gAVeq~YsemgsRHRar~~sIqIikVeeI~~~e~rrp~vkQf~~~kikFPl~~r~~~~~~k~~~ 190 (202)
||||||||||||+|.+|||||||+|||+|||||+++||||+|+||++++|+|+.+|||||++|+||||||++.. +.+
T Consensus 81 sG~HNmYkEyRd~t~~gAV~q~y~dMaaRhRar~~~I~Iikv~~v~a~~~kR~~vkqFhd~kikFPL~~rv~~~---k~~ 157 (169)
T KOG0829|consen 81 SGTHNMYKEYRDTTRVGAVEQCYRDMAARHRARFRSIQIIKVAEVPAEDCKRAYVKQFHDSKIKFPLPHRVVNR---KSK 157 (169)
T ss_pred CcchHHHHHHHHhhhhhHHHHHHHHHHHHhhhcccceeEEEEeeeeHHHhchHHHHHhhccCcccccccccccc---ccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998866 557
Q ss_pred CceeecCCCCCC
Q 028910 191 TTYKASRPNLFM 202 (202)
Q Consensus 191 ~~F~~~rP~t~~ 202 (202)
++|++.||||||
T Consensus 158 ~~fs~~rP~tf~ 169 (169)
T KOG0829|consen 158 KTFSTKRPSTFF 169 (169)
T ss_pred cccccCCCcccC
Confidence 899999999997
No 2
>PF01775 Ribosomal_L18ae: Ribosomal L18ae/LX protein domain; InterPro: IPR023573 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 entry represents the eukaryotic 60S ribosomal protein L18ae [] and the archaea 50S ribosomal protein LX. Rat ribosomal protein L18 is homologous to Xenopus laevis L14 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 4A1D_X 4A1B_X 4A18_X 4A19_X 2JXT_A 3IZR_S 3IZS_S.
Probab=100.00 E-value=3.1e-71 Score=442.27 Aligned_cols=124 Identities=64% Similarity=1.131 Sum_probs=112.4
Q ss_pred eeEEEEEeecCCCCCCCCCceEEEEeeecCceeeehhhHHHHHHHhhhhccCcceEEEEEeccCCCceeeEeeEEEEEec
Q 028910 30 FHQYQVVGRALPTEKDEHPKIYRMKLWATNEVRAKSKFWYFLRKLKKVKKSNGQMLAINEIFEKNPTKIKNYGIWLRYQS 109 (202)
Q Consensus 30 lkeY~VvGr~lPtek~p~P~lyrM~IFApN~VvAKSrFWyfl~~l~K~Kkt~GeIv~~~eI~Ek~p~~VKNfGIwlrYdS 109 (202)
|+||+|+||+||||++|+|+||+|+|||||+|+|||||||||++|+|+||++||||+|++|+|++|+.||||||||+|||
T Consensus 1 l~ey~vvgr~lpt~k~~~p~iy~m~ifa~n~vvAkSrfwy~~~~~~K~Kk~~geiv~~~~i~ek~p~~VKnfgI~lry~s 80 (124)
T PF01775_consen 1 LKEYQVVGRKLPTEKEPNPPIYRMRIFAPNHVVAKSRFWYFLRKLKKMKKTSGEIVSCKEIFEKNPTKVKNFGIWLRYDS 80 (124)
T ss_dssp -EEEEEEEEETT-STTS---EEEEEEEESSHHHHHHHHHHHHHHCTS--STTEEEEEEEEE-SSSTTS-EEEEEEEEEEE
T ss_pred CeEEEEEEecCCCCCCCCCCeEEEEEecCCcEEEEhhHHHHHHHHHhhhcccceEEEeEcccCCCCcceeEEEEEEEEec
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcceecceeeccCChhhHHHHHHHHhhhccccCCCCceEEEee
Q 028910 110 RTGYHNMYKEYRDTTLNGAVEQMYTEMASRHRVRSPCIQIIRTA 153 (202)
Q Consensus 110 rsgthNmyKEyRdlt~~gAVeq~YsemgsRHRar~~sIqIikVe 153 (202)
|+|+|||||||||+|++|||||||+|||||||+|+++|||++|+
T Consensus 81 r~g~~nfyKEyra~s~~~Aveq~YsdmGSrHrvkr~~I~I~~Ve 124 (124)
T PF01775_consen 81 RSGTHNFYKEYRALSENGAVEQVYSDMGSRHRVKRSSIQIIKVE 124 (124)
T ss_dssp SSCEEEEEEEEEESCHHHHHHHHHHHHHHTTT--GGGEEEEEEE
T ss_pred CCccEEEEEEeccCCHHHHHHHHHHHhhhhhCCCccceEEEEeC
Confidence 99999999999999999999999999999999999999999996
No 3
>PRK00773 rplX 50S ribosomal protein LX; Validated
Probab=100.00 E-value=1.4e-33 Score=208.86 Aligned_cols=73 Identities=19% Similarity=0.348 Sum_probs=71.8
Q ss_pred eeEeeEEEEEecCCcceecceeeccCChhhHHHHHHHHhhhccccCCCCceEEEeeeeCCCccCCcccccccc
Q 028910 98 IKNYGIWLRYQSRTGYHNMYKEYRDTTLNGAVEQMYTEMASRHRVRSPCIQIIRTATIPAKLCKRESTKQFHN 170 (202)
Q Consensus 98 VKNfGIwlrYdSrsgthNmyKEyRdlt~~gAVeq~YsemgsRHRar~~sIqIikVeeI~~~e~rrp~vkQf~~ 170 (202)
+||||||++|+||+|+|||||||||++++|||||||+||||||++++++|+|++|+||+++||+||+++||+.
T Consensus 2 ~k~f~V~g~~~~~~~~~~f~Ke~ra~~~~~Ave~~Ys~~gSrH~~kr~~I~I~~V~ei~~~e~~~~~vkq~~~ 74 (76)
T PRK00773 2 MKIYRVKGTFLAGDEWQKFTKEVRALNEKDALEKVYSLFGSKHKVKRTQIKIEEVSEISPEEAEDPRVRELAK 74 (76)
T ss_pred ceEEEEEEEEEcCCCeEEEEEEEecCCHHHHHHHHHHHHHhhcCCCcccEEEEEEEEeCHHHcCCHHHHHHhh
Confidence 7999999999999999999999999999999999999999999999999999999999999999999999974
No 4
>COG2157 RPL20A Ribosomal protein L20A (L18A) [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=6.7e-30 Score=193.19 Aligned_cols=84 Identities=31% Similarity=0.597 Sum_probs=81.7
Q ss_pred CCCceeeEeeEEEEEecCCcceecceeeccCChhhHHHHHHHHhhhccccCCCCceEEEeeeeCCCccCCccccccccCC
Q 028910 93 KNPTKIKNYGIWLRYQSRTGYHNMYKEYRDTTLNGAVEQMYTEMASRHRVRSPCIQIIRTATIPAKLCKRESTKQFHNSK 172 (202)
Q Consensus 93 k~p~~VKNfGIwlrYdSrsgthNmyKEyRdlt~~gAVeq~YsemgsRHRar~~sIqIikVeeI~~~e~rrp~vkQf~~~k 172 (202)
..|..++|+|||+.|||++|+||||||+||+++++|+|.+||||||||++++++|+|++|+||+++|+.|+.|++|++.+
T Consensus 2 ~~~K~f~V~G~~~~~~~~~~~~kf~Kevra~~e~~AiE~vYS~~gsrhkvkR~~I~I~~V~Ei~pedv~d~~vk~L~~~~ 81 (85)
T COG2157 2 PMPKIFRVKGIWIFYDSRSGWHKFTKEVRALKEEDAIEKVYSDFGSRHKVKRSSIKIEEVEEIEPEDVEDPVVKRLLTED 81 (85)
T ss_pred CcceEEEEeeEEEEecCCCcceehhHHhhhcCHHHHHHHHHHHhhhhccccccceeEEEEEecChhhcccHHHHHHhccc
Confidence 35778999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcCc
Q 028910 173 IKFP 176 (202)
Q Consensus 173 ikFP 176 (202)
++||
T Consensus 82 ~~~~ 85 (85)
T COG2157 82 LKFP 85 (85)
T ss_pred ccCC
Confidence 9998
No 5
>PRK00773 rplX 50S ribosomal protein LX; Validated
Probab=51.14 E-value=33 Score=25.56 Aligned_cols=60 Identities=23% Similarity=0.306 Sum_probs=50.8
Q ss_pred eeEEEEEeecCCCCCCCCCceEEEEeeecCceeeehhhHHHHHHHhhhhccCcceEEEEEecc
Q 028910 30 FHQYQVVGRALPTEKDEHPKIYRMKLWATNEVRAKSKFWYFLRKLKKVKKSNGQMLAINEIFE 92 (202)
Q Consensus 30 lkeY~VvGr~lPtek~p~P~lyrM~IFApN~VvAKSrFWyfl~~l~K~Kkt~GeIv~~~eI~E 92 (202)
++.|.|.|+-.... .+.=|.=-+=|+|+..|-.+-.--|--.+++|.++=+|+.+.+|.+
T Consensus 2 ~k~f~V~g~~~~~~---~~~~f~Ke~ra~~~~~Ave~~Ys~~gSrH~~kr~~I~I~~V~ei~~ 61 (76)
T PRK00773 2 MKIYRVKGTFLAGD---EWQKFTKEVRALNEKDALEKVYSLFGSKHKVKRTQIKIEEVSEISP 61 (76)
T ss_pred ceEEEEEEEEEcCC---CeEEEEEEEecCCHHHHHHHHHHHHHhhcCCCcccEEEEEEEEeCH
Confidence 68899999966433 3455666777999999999999999999999999999999999954
No 6
>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]
Probab=36.42 E-value=27 Score=31.73 Aligned_cols=24 Identities=29% Similarity=0.451 Sum_probs=22.3
Q ss_pred CcceEEEEEeccCCCceeeEeeEE
Q 028910 81 NGQMLAINEIFEKNPTKIKNYGIW 104 (202)
Q Consensus 81 ~GeIv~~~eI~Ek~p~~VKNfGIw 104 (202)
=||||...-|-+|++.+-|+||-.
T Consensus 36 fGeI~eavvitd~~t~rskGyGfV 59 (247)
T KOG0149|consen 36 FGEIVEAVVITDKNTGRSKGYGFV 59 (247)
T ss_pred hCceEEEEEEeccCCccccceeeE
Confidence 499999999999999999999965
No 7
>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=32.24 E-value=52 Score=29.27 Aligned_cols=28 Identities=32% Similarity=0.611 Sum_probs=24.5
Q ss_pred cceEEEEEeccCCCceeeEeeEEEEEecC
Q 028910 82 GQMLAINEIFEKNPTKIKNYGIWLRYQSR 110 (202)
Q Consensus 82 GeIv~~~eI~Ek~p~~VKNfGIwlrYdSr 110 (202)
||||.++-|.+++.++-|+|. +|+|.-.
T Consensus 60 Ge~vdinLiRDk~TGKSKGFa-FLcYEDQ 87 (219)
T KOG0126|consen 60 GEIVDINLIRDKKTGKSKGFA-FLCYEDQ 87 (219)
T ss_pred CceEEEEEEecCCCCcccceE-EEEecCc
Confidence 999999999999999999996 6777643
No 8
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=31.32 E-value=24 Score=32.74 Aligned_cols=35 Identities=29% Similarity=0.333 Sum_probs=22.5
Q ss_pred ccCcceEEEEEeccCCCcee-eEeeEEEEEecCCcce
Q 028910 79 KSNGQMLAINEIFEKNPTKI-KNYGIWLRYQSRTGYH 114 (202)
Q Consensus 79 kt~GeIv~~~eI~Ek~p~~V-KNfGIwlrYdSrsgth 114 (202)
+...+=-.|-+.--.+|.=+ =||||+||-| ++|.|
T Consensus 15 ~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~-CagvH 50 (319)
T COG5347 15 KSDSSNKKCADCGAPNPTWASVNLGVFLCID-CAGVH 50 (319)
T ss_pred hhccccCccccCCCCCCceEecccCeEEEee-cchhh
Confidence 33344345555555666653 5999999998 45666
No 9
>PHA03066 Hypothetical protein; Provisional
Probab=28.29 E-value=39 Score=27.28 Aligned_cols=22 Identities=18% Similarity=0.279 Sum_probs=16.6
Q ss_pred CCceeeEeeEEEEEecCCccee
Q 028910 94 NPTKIKNYGIWLRYQSRTGYHN 115 (202)
Q Consensus 94 ~p~~VKNfGIwlrYdSrsgthN 115 (202)
+|...-.=-||+.|||++|+.-
T Consensus 60 ~~~~~~~~~v~~~Yds~~~~Vt 81 (110)
T PHA03066 60 DPETVISTQVNTYYNSSIGTVT 81 (110)
T ss_pred CCCCcccceEEEEEcCcCCeEE
Confidence 4455555579999999999863
No 10
>COG3500 Phage protein D [General function prediction only]
Probab=24.73 E-value=33 Score=32.52 Aligned_cols=40 Identities=23% Similarity=0.382 Sum_probs=32.6
Q ss_pred HHHHHHhhhccccCCCCceEEEeeeeCCCccCCccccccccCCCcCccc
Q 028910 130 EQMYTEMASRHRVRSPCIQIIRTATIPAKLCKRESTKQFHNSKIKFPLV 178 (202)
Q Consensus 130 eq~YsemgsRHRar~~sIqIikVeeI~~~e~rrp~vkQf~~~kikFPl~ 178 (202)
..+-+|||++|.... .|++.++.-|+|-|.-.|++.|.+-
T Consensus 122 sdi~~eIAa~hgLt~---------av~~t~~~~~~idQ~~ESD~~FL~r 161 (350)
T COG3500 122 SDIASEIAAEHGLTA---------AVSATQVAHPHIDQYYESDINFLLR 161 (350)
T ss_pred HHHHHHHHHHcCCcc---------ccccccccchhhhhcccccHHHHHH
Confidence 345589999999954 4566888899999999999999763
No 11
>COG0509 GcvH Glycine cleavage system H protein (lipoate-binding) [Amino acid transport and metabolism]
Probab=24.53 E-value=30 Score=28.58 Aligned_cols=27 Identities=30% Similarity=0.726 Sum_probs=23.7
Q ss_pred cCcceEEEEEeccCCCceeeE--ee-EEEE
Q 028910 80 SNGQMLAINEIFEKNPTKIKN--YG-IWLR 106 (202)
Q Consensus 80 t~GeIv~~~eI~Ek~p~~VKN--fG-Iwlr 106 (202)
-+||||.+|+-.+++|..|.. || =||.
T Consensus 75 vsGeVvevN~~l~~~PeliN~dPyg~gWi~ 104 (131)
T COG0509 75 VSGEVVEVNEALVDSPELINSDPYGEGWIV 104 (131)
T ss_pred CceeEEEechhhhcChhhhccCCCCCceEE
Confidence 579999999999999999987 88 4865
No 12
>COG1727 RPL18A Ribosomal protein L18E [Translation, ribosomal structure and biogenesis]
Probab=23.20 E-value=17 Score=29.72 Aligned_cols=25 Identities=28% Similarity=0.616 Sum_probs=22.3
Q ss_pred HHHhhhhccCcceEEEEEeccCCCc
Q 028910 72 RKLKKVKKSNGQMLAINEIFEKNPT 96 (202)
Q Consensus 72 ~~l~K~Kkt~GeIv~~~eI~Ek~p~ 96 (202)
.-..||.++.||++.+.|+.|++|.
T Consensus 90 ~A~~KI~~aGGe~~tl~el~e~nPk 114 (122)
T COG1727 90 TAREKIEEAGGECLTLEELAERNPK 114 (122)
T ss_pred HHHHHHHHcCCeEeeHHHHHHHCCC
Confidence 3467999999999999999999995
No 13
>COG2157 RPL20A Ribosomal protein L20A (L18A) [Translation, ribosomal structure and biogenesis]
Probab=20.02 E-value=67 Score=24.84 Aligned_cols=65 Identities=18% Similarity=0.099 Sum_probs=49.9
Q ss_pred cceeEEEEEeecCCCCCCCCCceEEEEeeecCceeeehhhHHHHHHHhhhhccCcceEEEEEecc
Q 028910 28 FRFHQYQVVGRALPTEKDEHPKIYRMKLWATNEVRAKSKFWYFLRKLKKVKKSNGQMLAINEIFE 92 (202)
Q Consensus 28 ~~lkeY~VvGr~lPtek~p~P~lyrM~IFApN~VvAKSrFWyfl~~l~K~Kkt~GeIv~~~eI~E 92 (202)
+..+.|+|.|--.=....+.+.=|.-.+=|-|+.-|--+-..-|---+|+|.++-.|+++.||..
T Consensus 2 ~~~K~f~V~G~~~~~~~~~~~~kf~Kevra~~e~~AiE~vYS~~gsrhkvkR~~I~I~~V~Ei~p 66 (85)
T COG2157 2 PMPKIFRVKGIWIFYDSRSGWHKFTKEVRALKEEDAIEKVYSDFGSRHKVKRSSIKIEEVEEIEP 66 (85)
T ss_pred CcceEEEEeeEEEEecCCCcceehhHHhhhcCHHHHHHHHHHHhhhhccccccceeEEEEEecCh
Confidence 45789999995544444444455566667888888888888888888999999999999999865
Done!