Query 019383
Match_columns 342
No_of_seqs 32 out of 34
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 09:00:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019383.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019383hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0779 Protease, Ulp1 family 97.7 2.5E-05 5.4E-10 82.2 3.1 302 8-342 10-379 (595)
2 PLN03189 Protease specific for 96.7 0.00028 6.1E-09 73.0 -0.9 31 312-342 284-314 (490)
3 COG5160 ULP1 Protease, Ulp1 fa 95.9 0.0015 3.3E-08 68.2 -1.0 36 306-342 372-407 (578)
4 KOG0778 Protease, Ulp1 family 95.2 0.0033 7.1E-08 65.6 -1.5 27 315-341 317-343 (511)
5 PF15328 GCOM2: Putative GRINL 92.6 0.11 2.5E-06 48.6 3.4 35 73-107 3-39 (223)
6 KOG4439 RNA polymerase II tran 65.1 7.3 0.00016 43.3 4.0 31 81-111 209-239 (901)
7 PRK00306 50S ribosomal protein 37.2 81 0.0018 24.3 4.7 53 58-111 5-64 (66)
8 PF00831 Ribosomal_L29: Riboso 27.4 1E+02 0.0022 23.2 3.8 49 57-106 2-57 (58)
9 PRK14549 50S ribosomal protein 24.4 1.7E+02 0.0036 23.1 4.6 51 57-108 7-65 (69)
10 PF15463 ECM11: Extracellular 24.0 1.2E+02 0.0025 26.6 4.0 50 58-107 64-113 (139)
11 TIGR00012 L29 ribosomal protei 21.0 1.4E+02 0.0031 22.3 3.5 42 61-102 3-51 (55)
No 1
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=97.67 E-value=2.5e-05 Score=82.17 Aligned_cols=302 Identities=11% Similarity=-0.054 Sum_probs=170.1
Q ss_pred ccCCCccccccccCCCCCCCCCceeeeccCCCCCCCCCCCCCCCCCCChhhhccCCCchHHHHHHHHhhhhhhhcccCCC
Q 019383 8 RNKRKLNIDWEEVLPGRNDDVPAELIVKKSGPPTPAQKSVPMSDDPGSGEELDRQIPDQELGVRIARMKDTYSKVRHCLP 87 (342)
Q Consensus 8 ~~k~~l~idW~~~~~~~dd~~p~~~iv~~t~~~~p~~~t~~~~dD~~~~~el~~~lsD~eL~E~I~R~k~~L~gl~~rLP 87 (342)
+.++...|.|+.++. +....+.+.+|-++++- +|+++ .|. ...+...+.+..|.+.-.|..+.+..++.+++
T Consensus 10 ~~~~~~~~~~~~~~~-~~~~~~~~~~v~~~~~~---~~~~~-~~i---~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (595)
T KOG0779|consen 10 SEVKSSSIMVESADV-KELLIRRLEFVVLIKKS---RPNYL-NDI---IIDLVLLKDDNTLNDEYTRELSILFILAVKKG 81 (595)
T ss_pred cccccceeEeccCCC-ccceeeccccccccccC---Ccccc-ccc---ccchheeccccCCCccccceeeecccCCcccc
Confidence 668899999999888 56677777777766643 35555 333 23457889999999999999999988999999
Q ss_pred cchHhHHHHHHHHHHHHHHHHhhCCCCc---------------ccccccccccccCC----------------------C
Q 019383 88 DKGKKILATVTRLEKECERRRLAGAVPV---------------CLDIDGCDKLTQSP----------------------S 130 (342)
Q Consensus 88 DkG~Klr~~I~~le~E~dRRkarr~~~~---------------~~Dv~~cek~vqS~----------------------S 130 (342)
+.|.+-+..|..++.+..+|+..+- .. -+|.- +.+...-. .
T Consensus 82 ~~~~~~~~ki~~~~~~~~~~~~~~~-~~~~~~~~~t~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (595)
T KOG0779|consen 82 LTSLTEPLKIAVLEEQKPHAVVPKK-IISVSELRNTNLTEGTFYSDYL-NRIKNIFESVRKFFNQVSYPKFMPNVTSFMP 159 (595)
T ss_pred ccccccccccccccccCCccccccc-cccchhccccCCcccceecccc-cccccccchhcchhhhcccccccchhhcccC
Confidence 9999999999999999999977651 00 01111 11111111 0
Q ss_pred CCccccCC----CCCcccccccchhhhhhhhccccccccchhhhHHHhhhccccccccccCCcccccccccccc--CCcc
Q 019383 131 SDCFTQRT----PSPQIQSKSSFTSVFREKMEENRDCREANAFDKELSILAHCDRRKMRSDGDLSQRGRQNVRS--SSRK 204 (342)
Q Consensus 131 Sd~~~q~~----~sSk~~S~S~Fts~F~~~~E~ntd~~~~~Af~kElS~lg~cd~~~~k~ng~~~~~~k~n~~s--Ssrq 204 (342)
+.++++.. +..=..++..|..+|.+. ..++-....++..++...+ ++....+ -+...-+...+..- +.-.
T Consensus 160 ~~~~~~q~~~~~~~~i~i~~~~~~~~fi~~--~~~~~~~~~~~~~~~~~~l-~~~~~~~-~~~~~~~~~~~~k~~~~~~~ 235 (595)
T KOG0779|consen 160 SPLEKCQLQRVFTWTINITRKLFKKLFIKI--FKNEPFHFKAVKFLLPSAL-TKSDVCD-IADLEVIFLNSRKDSHSLVI 235 (595)
T ss_pred CcccccccccccceeeeeeecchhhhcccC--cccCchhhhhhhcccchhc-cchhhhh-hhcccccchhcccchhhhhh
Confidence 11111000 000012334444444321 0122233445555665554 2222111 11111111111111 1111
Q ss_pred Cccc-----cCCCcc----------cCCCCCCCCCCCCCCCCCCCCCCC--------CCCCcccccccccCCCCcccccc
Q 019383 205 WPFH-----KGDKSF----------NSNGSQKDRASLTCPSHQSGENSS--------SCLPKKKESFEVLPSKNPRLRKE 261 (342)
Q Consensus 205 ~~~~-----s~D~~~----------~~ng~~~g~~S~~~~~~~~~en~~--------i~s~Kr~~~f~~~~s~~~r~rk~ 261 (342)
.++. ....+. ...+.-.++.+.++.+++..+..- .-..++.|.....++....++..
T Consensus 236 ~~~~~~~~~~~~s~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~dd~~~~~~~~~~~~~~~~~~~~~~~s~~q~~s~~~~ 315 (595)
T KOG0779|consen 236 SSINSPNIKTFFSKEVKSRPTPASYFIFSSFLPGLDPPAELHQNDDIDDIGIILNESPLDKPFEWLLANSPNQSESRSRD 315 (595)
T ss_pred cccccccchhhhccccccCCCcccccccccccCCCCccccccccchhhhhhhcccccccccchhhhhhcCcccchhcccc
Confidence 1111 111111 022333444666777666655222 22588889988888888777774
Q ss_pred cce-Ee-ccCCCCCCcccccccccccccchhhhhHHHHhhhccceeeccCCCCCCceeeecccccccCccccccCcccce
Q 019383 262 QNL-VL-LDEDESPVEDASEESEGSLHIETTEQADEFAECMIDAKIYYPSRVDPESVEICYTDINHLAPAAYLTSPIMNF 339 (342)
Q Consensus 262 ~~~-vl-ldd~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~ki~YPSr~dpe~vei~~~Di~cL~P~~~L~spiinF 339 (342)
... ++ +.+.+-.. ..+.+... .--..+-|+-.+ ..+.|+..|+.||++.+||+++||+|
T Consensus 316 ~~~~~~~~~~~~~~~------------~l~~~~~~------el~~~~~p~~~~-~~~~v~~~Dl~cl~~~e~L~d~i~df 376 (595)
T KOG0779|consen 316 SLDNWFPVKEADKQR------------TLIVKLAI------ELLEVRVPQICN-QSHQVNNNDLVCLEEGEFLNDTIKDF 376 (595)
T ss_pred ccccccccccccccc------------chHHHhhc------cccccCCccccc-cccceeccchhhccccchhhhhhhhh
Confidence 322 33 54444322 11223332 233344555455 58899999999999999999999999
Q ss_pred ecC
Q 019383 340 YIR 342 (342)
Q Consensus 340 Yi~ 342 (342)
|++
T Consensus 377 yl~ 379 (595)
T KOG0779|consen 377 YLE 379 (595)
T ss_pred hhH
Confidence 974
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=96.73 E-value=0.00028 Score=72.97 Aligned_cols=31 Identities=23% Similarity=0.551 Sum_probs=29.0
Q ss_pred CCCceeeecccccccCccccccCcccceecC
Q 019383 312 DPESVEICYTDINHLAPAAYLTSPIMNFYIR 342 (342)
Q Consensus 312 dpe~vei~~~Di~cL~P~~~L~spiinFYi~ 342 (342)
++..|+|++.||.||.|..+||+.||||||+
T Consensus 284 ~~~~i~IT~~DL~~L~Pg~WLNDeVINfYm~ 314 (490)
T PLN03189 284 ENSNIDITGEILRCLKPGAWLNDEVINLYLE 314 (490)
T ss_pred CCCceEEEHHHhhccCCCCccCHHHHHHHHH
Confidence 5678999999999999999999999999984
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=95.88 E-value=0.0015 Score=68.16 Aligned_cols=36 Identities=33% Similarity=0.695 Sum_probs=32.5
Q ss_pred eccCCCCCCceeeecccccccCccccccCcccceecC
Q 019383 306 YYPSRVDPESVEICYTDINHLAPAAYLTSPIMNFYIR 342 (342)
Q Consensus 306 ~YPSr~dpe~vei~~~Di~cL~P~~~L~spiinFYi~ 342 (342)
+||=- +-+.+||+..|++||.++++||++|||||++
T Consensus 372 ~~~~~-~~~~i~IT~~D~~~L~~~~wLNDtIIdFy~k 407 (578)
T COG5160 372 CYPFN-DRSSIEITNQDFKRLRNGDWLNDTIIDFYMK 407 (578)
T ss_pred ccccc-CcCcceeehHhhhhhccccchhhHHHHHHHH
Confidence 77754 5689999999999999999999999999984
No 4
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=95.19 E-value=0.0033 Score=65.61 Aligned_cols=27 Identities=30% Similarity=0.749 Sum_probs=26.0
Q ss_pred ceeeecccccccCccccccCcccceec
Q 019383 315 SVEICYTDINHLAPAAYLTSPIMNFYI 341 (342)
Q Consensus 315 ~vei~~~Di~cL~P~~~L~spiinFYi 341 (342)
.++|+..||.||.|..+||+.|||||+
T Consensus 317 ~i~It~~dl~tl~~~~WLNDevINfYm 343 (511)
T KOG0778|consen 317 NIDITGKDLQTLRPGNWLNDEVINFYM 343 (511)
T ss_pred cccccHHHHhhccCccchhHHHHHHHH
Confidence 399999999999999999999999997
No 5
>PF15328 GCOM2: Putative GRINL1B complex locus protein 2
Probab=92.57 E-value=0.11 Score=48.58 Aligned_cols=35 Identities=37% Similarity=0.452 Sum_probs=29.9
Q ss_pred HHhhhhhh--hcccCCCcchHhHHHHHHHHHHHHHHH
Q 019383 73 ARMKDTYS--KVRHCLPDKGKKILATVTRLEKECERR 107 (342)
Q Consensus 73 ~R~k~~L~--gl~~rLPDkG~Klr~~I~~le~E~dRR 107 (342)
+|+..+|. .+-.+|||||+||...+..|..++.+|
T Consensus 3 ~rq~klL~nkkfi~kLpDKGkKI~~~~~kL~~ai~~r 39 (223)
T PF15328_consen 3 RRQEKLLRNKKFICKLPDKGKKIQDFVEKLKAAIAER 39 (223)
T ss_pred hHHHHHhcchhhhhcCCchhHHHHHHHHHHHHHHHHH
Confidence 45666665 466899999999999999999999998
No 6
>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=65.09 E-value=7.3 Score=43.32 Aligned_cols=31 Identities=39% Similarity=0.637 Sum_probs=27.9
Q ss_pred hcccCCCcchHhHHHHHHHHHHHHHHHHhhC
Q 019383 81 KVRHCLPDKGKKILATVTRLEKECERRRLAG 111 (342)
Q Consensus 81 gl~~rLPDkG~Klr~~I~~le~E~dRRkarr 111 (342)
.+...|||+|.++...|+.|.+|+.||..-+
T Consensus 209 ~~~~~Lpd~g~~~~kr~~el~~~~~~~~~~~ 239 (901)
T KOG4439|consen 209 KAIDDLPDKGARLIKRLQELDRELERRMQFG 239 (901)
T ss_pred hhhhhCCccHHHHHHHHHHHHHHHHHHHhhh
Confidence 3567999999999999999999999998765
No 7
>PRK00306 50S ribosomal protein L29; Reviewed
Probab=37.17 E-value=81 Score=24.33 Aligned_cols=53 Identities=19% Similarity=0.354 Sum_probs=39.2
Q ss_pred hhccCCCchHHHHHHHHhhhhhhhc-----ccCC--CcchHhHHHHHHHHHHHHHHHHhhC
Q 019383 58 ELDRQIPDQELGVRIARMKDTYSKV-----RHCL--PDKGKKILATVTRLEKECERRRLAG 111 (342)
Q Consensus 58 el~~~lsD~eL~E~I~R~k~~L~gl-----~~rL--PDkG~Klr~~I~~le~E~dRRkarr 111 (342)
|| +.+|+.+|++.|...+..|-.+ ...+ |-.-..+|+.|.+|.=.+..|..+.
T Consensus 5 el-r~ls~~eL~~~l~~lkkeL~~lR~~~~~~~~~n~~~i~~~rk~IARi~Tvl~er~~~~ 64 (66)
T PRK00306 5 EL-RELSVEELNEKLLELKKELFNLRFQKATGQLENTHRLREVRRDIARIKTVLRERELGA 64 (66)
T ss_pred HH-hhCCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCcHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 45 9999999999999998876421 1223 3344677889999998888887653
No 8
>PF00831 Ribosomal_L29: Ribosomal L29 protein; InterPro: IPR001854 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 L29 is one of the proteins from the large ribosomal subunit. L29 belongs to a family of ribosomal proteins of 63 to 138 amino-acid residues which, on the basis of sequence similarities [], groups: Red algal L29. Bacterial L29. Mammalian L35 Caenorhabditis elegans L35 (ZK652.4). Yeast L35. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1VSP_W 3MS1_Y 3MRZ_Y 3F1H_2 3PYT_Y 3PYO_Y 3D5D_2 3D5B_2 3PYR_Y 1VSA_W ....
Probab=27.43 E-value=1e+02 Score=23.24 Aligned_cols=49 Identities=22% Similarity=0.390 Sum_probs=33.4
Q ss_pred hhhccCCCchHHHHHHHHhhhhhhh-----cccCC--CcchHhHHHHHHHHHHHHHH
Q 019383 57 EELDRQIPDQELGVRIARMKDTYSK-----VRHCL--PDKGKKILATVTRLEKECER 106 (342)
Q Consensus 57 ~el~~~lsD~eL~E~I~R~k~~L~g-----l~~rL--PDkG~Klr~~I~~le~E~dR 106 (342)
.|| +.+|+.||.++|...+..|.. ....| |-.=..+|+.|.+|.=.+..
T Consensus 2 ~el-r~ls~~eL~~~l~elk~eL~~Lr~q~~~~~l~n~~~ir~~Rr~IARi~Tvl~e 57 (58)
T PF00831_consen 2 KEL-RELSDEELQEKLEELKKELFNLRFQKATGQLENPHRIREIRRDIARILTVLRE 57 (58)
T ss_dssp HHH-CHSHHHHHHHHHHHHHHHHHHHHHHHHHSSSSCCHHHHHHHHHHHHHHHHHHH
T ss_pred HHH-HhCCHHHHHHHHHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHHHhc
Confidence 356 899999999999999887642 11222 44445667778777665543
No 9
>PRK14549 50S ribosomal protein L29P; Provisional
Probab=24.43 E-value=1.7e+02 Score=23.06 Aligned_cols=51 Identities=18% Similarity=0.273 Sum_probs=36.5
Q ss_pred hhhccCCCchHHHHHHHHhhhhhhhc------ccCC--CcchHhHHHHHHHHHHHHHHHH
Q 019383 57 EELDRQIPDQELGVRIARMKDTYSKV------RHCL--PDKGKKILATVTRLEKECERRR 108 (342)
Q Consensus 57 ~el~~~lsD~eL~E~I~R~k~~L~gl------~~rL--PDkG~Klr~~I~~le~E~dRRk 108 (342)
.|| +.+|..||.++|...+..|-.| +..| |-.=..+|+.|.+|.=.+..|+
T Consensus 7 ~el-r~ls~~eL~~~l~elk~eLf~LR~q~~~~~~l~n~~~ir~~Rk~IARi~Tvl~ek~ 65 (69)
T PRK14549 7 SEI-REMSPEEREEKLEELKLELLKERAQAAMGGAPENPGRIREIRRTIARILTIQREKK 65 (69)
T ss_pred HHH-HhCCHHHHHHHHHHHHHHHHHHHHHHHhCcCccccHHHHHHHHHHHHHHHHHHHHH
Confidence 355 9999999999999999887532 2212 3344567888888887776664
No 10
>PF15463 ECM11: Extracellular mutant protein 11
Probab=24.02 E-value=1.2e+02 Score=26.58 Aligned_cols=50 Identities=18% Similarity=0.216 Sum_probs=37.2
Q ss_pred hhccCCCchHHHHHHHHhhhhhhhcccCCCcchHhHHHHHHHHHHHHHHH
Q 019383 58 ELDRQIPDQELGVRIARMKDTYSKVRHCLPDKGKKILATVTRLEKECERR 107 (342)
Q Consensus 58 el~~~lsD~eL~E~I~R~k~~L~gl~~rLPDkG~Klr~~I~~le~E~dRR 107 (342)
.+|..+|..+-.+.-..+-.....|-.+|-+.=.++|.++..++.|+.+|
T Consensus 64 ~~fs~ls~~eWe~~Gd~~l~qf~~l~~kl~~~R~~~r~~~~~fe~eI~~R 113 (139)
T PF15463_consen 64 EFFSNLSFDEWEEAGDWFLEQFSELMQKLKEARRKLRKKFAVFEDEINRR 113 (139)
T ss_pred HHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46777887766655444443333455778888889999999999999999
No 11
>TIGR00012 L29 ribosomal protein L29. called L29 in prokaryotic (50S) large subunits and L35 in eukaryotic (60S) large subunits.
Probab=21.03 E-value=1.4e+02 Score=22.26 Aligned_cols=42 Identities=19% Similarity=0.379 Sum_probs=28.1
Q ss_pred cCCCchHHHHHHHHhhhhhhhcc-----c--CCCcchHhHHHHHHHHHH
Q 019383 61 RQIPDQELGVRIARMKDTYSKVR-----H--CLPDKGKKILATVTRLEK 102 (342)
Q Consensus 61 ~~lsD~eL~E~I~R~k~~L~gl~-----~--rLPDkG~Klr~~I~~le~ 102 (342)
+.+|+.||.+.|...+..|-.+- . .=|-.-..+|+.|.+|.=
T Consensus 3 r~~s~~EL~~~l~~lr~eLf~Lr~~~~~~~~~~~~~i~~~Rk~IARi~T 51 (55)
T TIGR00012 3 REKSKEELAKKLDELKKELFELRFQKATGQLAKPHRIRQVRRDIARLLT 51 (55)
T ss_pred hhCCHHHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHHH
Confidence 88999999999998887764211 1 124445566677776653
Done!