Query 029217
Match_columns 197
No_of_seqs 162 out of 359
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 09:23:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029217.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029217hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1646 40S ribosomal protein 100.0 9.6E-86 2.1E-90 562.4 14.1 183 1-188 53-236 (237)
2 PTZ00028 40S ribosomal protein 100.0 6.3E-78 1.4E-82 515.6 16.7 165 1-172 53-217 (218)
3 PF01092 Ribosomal_S6e: Riboso 100.0 4.5E-37 9.7E-42 245.8 2.8 75 1-77 53-127 (127)
4 PRK04290 30S ribosomal protein 100.0 1.7E-31 3.8E-36 210.8 6.7 63 1-66 53-115 (115)
5 COG2125 RPS6A Ribosomal protei 100.0 7.8E-30 1.7E-34 202.4 6.6 67 1-70 54-120 (120)
6 PF11208 DUF2992: Protein of u 47.6 92 0.002 25.4 6.8 51 128-178 61-112 (132)
7 PRK08406 transcription elongat 36.0 53 0.0012 26.6 3.7 53 46-111 23-82 (140)
8 TIGR01952 nusA_arch NusA famil 32.8 77 0.0017 26.0 4.2 54 46-111 23-83 (141)
9 PRK00247 putative inner membra 27.7 3.4E+02 0.0073 26.4 8.1 46 127-172 312-358 (429)
10 PRK06569 F0F1 ATP synthase sub 19.8 5.4E+02 0.012 21.6 8.2 44 135-178 37-80 (155)
No 1
>KOG1646 consensus 40S ribosomal protein S6 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.6e-86 Score=562.45 Aligned_cols=183 Identities=70% Similarity=1.024 Sum_probs=178.6
Q ss_pred CCCCCCCCCCcCCCCCCCCeEEEeecCCCccccCCCCCCCcceeeeecceeecCCcceEEEEEEeeCCcCCCCCCCCCCC
Q 029217 1 MGGCDKQGFPMKQGVLTPGRVRLLLHRGTPCFRGYGRRDGERRRKSVRGCIVSPDLSVLNLVIVKKGEHDLPGLTDTEKP 80 (197)
Q Consensus 1 tGGnDkqGFPMkqgVlt~~RvrlLLskG~sgyrg~prr~GeRkRKSVRGciV~~~is~LNlvIvkkGek~I~gLTd~~~p 80 (197)
|||||+|||||+|||||++||++||++|||||| |||+|||+||||||||||+|+|+||||||++||+|||||||+++|
T Consensus 53 ~GGndkQGFPMkqGvLt~~RvrlLL~kg~scyR--pRr~GeRkRKSVRGcIV~anlsvLnLvIvKkGekdipGLTdt~~P 130 (237)
T KOG1646|consen 53 TGGNDKQGFPMKQGVLTPGRVRLLLSKGHSCYR--PRRTGERKRKSVRGCIVSANLSVLNLVIVKKGEKDIPGLTDTTVP 130 (237)
T ss_pred cCCccccCCcccccccccchhhhhhhcCccccc--cccccccccccccceeecccceeeeeeEeccCcccCCCccccccc
Confidence 799999999999999999999999999999999 999999999999999999999999999999999999999999999
Q ss_pred CcCCCCchhhHHHHhCCCCcchHhHhhhhhhcccc-ccCCcccccCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029217 81 RMRGPKRASKIRKLFNLSKEDDVRKYVNTYRRTFT-TKSGKKVSKAPKIQRLVTPLTLQRKRARIAEKKQRIAKAKAEAA 159 (197)
Q Consensus 81 ~~lgPKRaskIrKlFnLsk~ddV~kyV~~~irr~~-k~~kk~~~KapKIQrLvTp~~lqrK~~~~a~kk~~~~k~keea~ 159 (197)
++|||||||+||||||||+||||++|| |++++ ++|++|+||||||||||||.+||||+++||+|++++++++|+||
T Consensus 131 ~rlGPkRaskIrKlfnLskEddvr~~v---ir~~~~~~~~k~~tkaPKIqrlvtp~~lqrk~~~~alkk~~~~k~re~aa 207 (237)
T KOG1646|consen 131 RRLGPKRASKIRKLFNLSKEDDVRQYV---IRRPLTKEGKKPKTKAPKIQRLVTPRRLQRKRQRIALKKKQIKKNREEAA 207 (237)
T ss_pred cccCchhhHHHHHHhCCCccccceeeE---EeccccccCCCccccCcchhhccchHHHHhhhhHHHHHHHHHHHhHHHHH
Confidence 999999999999999999999999999 99999 89999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHhhhhhh
Q 029217 160 EYQKLLATRLKEQRERRSESLAKKRSRLS 188 (197)
Q Consensus 160 eY~kllakr~ke~k~~~~~~~~~~~~s~~ 188 (197)
||++||++|++|+++++.+..+++.+|++
T Consensus 208 ey~kLLakr~kE~k~kr~e~~~rr~ss~~ 236 (237)
T KOG1646|consen 208 EYAKLLAKRLKEAKEKRFEVKRRRASSLR 236 (237)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 99999999999999999887777777654
No 2
>PTZ00028 40S ribosomal protein S6e; Provisional
Probab=100.00 E-value=6.3e-78 Score=515.63 Aligned_cols=165 Identities=64% Similarity=0.959 Sum_probs=161.1
Q ss_pred CCCCCCCCCCcCCCCCCCCeEEEeecCCCccccCCCCCCCcceeeeecceeecCCcceEEEEEEeeCCcCCCCCCCCCCC
Q 029217 1 MGGCDKQGFPMKQGVLTPGRVRLLLHRGTPCFRGYGRRDGERRRKSVRGCIVSPDLSVLNLVIVKKGEHDLPGLTDTEKP 80 (197)
Q Consensus 1 tGGnDkqGFPMkqgVlt~~RvrlLLskG~sgyrg~prr~GeRkRKSVRGciV~~~is~LNlvIvkkGek~I~gLTd~~~p 80 (197)
|||||+|||||+|||+|++||+|||++||+||| |+++|||+||||||||||+||||||++||++||++||||||+++|
T Consensus 53 TGGsDkqGfPMkqgV~~~~RvrlLL~kG~~gyr--prr~GeRkRKsVRGciVs~dis~lNlvIvk~Ge~~i~gLtd~~~p 130 (218)
T PTZ00028 53 SGGNDKQGFPMMQGVLTNNRVRLLFRKGMKCYR--PRRTGEMKRKSVRGCIVGHDLSVLNLVLVKKGPQEIPGLTDGERP 130 (218)
T ss_pred ecccCCCCcccCCCccCCceEEEEecCCCCCCC--cCCCCcceeeeeeeeeecCCceEEEEEEEecCCccChhhccCcCC
Confidence 799999999999999999999999999999999 999999999999999999999999999999999999999999999
Q ss_pred CcCCCCchhhHHHHhCCCCcchHhHhhhhhhccccccCCcccccCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029217 81 RMRGPKRASKIRKLFNLSKEDDVRKYVNTYRRTFTTKSGKKVSKAPKIQRLVTPLTLQRKRARIAEKKQRIAKAKAEAAE 160 (197)
Q Consensus 81 ~~lgPKRaskIrKlFnLsk~ddV~kyV~~~irr~~k~~kk~~~KapKIQrLvTp~~lqrK~~~~a~kk~~~~k~keea~e 160 (197)
++|||||||+||||||||++|||++|| |++++ +|+++ +|||||||||||.+||||++++++|+++..++++|++|
T Consensus 131 rrlgPkraskirklfnlsk~ddvrk~v---irr~~-~gkk~-~KapKIQRLiTp~~lqrKr~~~~~k~~r~~~~k~~~~e 205 (218)
T PTZ00028 131 RRLGPKRASKIRKLFNLSKSDDVRKFV---VRRKI-EGKNK-TKAPKIQRLVTPQRLQRKRRYRKTLKKKVLQSREEAKE 205 (218)
T ss_pred ccCCCcchhhhHHHhCCCccCChhhce---ecccc-CCCCC-CcCCceeecCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999 99999 66654 99999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHH
Q 029217 161 YQKLLATRLKEQ 172 (197)
Q Consensus 161 Y~kllakr~ke~ 172 (197)
|++||++|++|.
T Consensus 206 y~kll~~~~~e~ 217 (218)
T PTZ00028 206 YQKLLEEYKNEK 217 (218)
T ss_pred HHHHHHHHHhhc
Confidence 999999998874
No 3
>PF01092 Ribosomal_S6e: Ribosomal protein S6e; InterPro: IPR001377 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins have been grouped on the basis of sequence similarities. Ribosomal protein S6 is the major substrate of protein kinases in eukaryotic ribosomes [] and may play an important role in controlling cell growth and proliferation through the selective translation of particular classes of mRNA.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZM_Y 2XZN_Y 3U5C_G 3U5G_G 3J16_C.
Probab=100.00 E-value=4.5e-37 Score=245.79 Aligned_cols=75 Identities=73% Similarity=1.184 Sum_probs=56.4
Q ss_pred CCCCCCCCCCcCCCCCCCCeEEEeecCCCccccCCCCCCCcceeeeecceeecCCcceEEEEEEeeCCcCCCCCCCC
Q 029217 1 MGGCDKQGFPMKQGVLTPGRVRLLLHRGTPCFRGYGRRDGERRRKSVRGCIVSPDLSVLNLVIVKKGEHDLPGLTDT 77 (197)
Q Consensus 1 tGGnDkqGFPMkqgVlt~~RvrlLLskG~sgyrg~prr~GeRkRKSVRGciV~~~is~LNlvIvkkGek~I~gLTd~ 77 (197)
|||||+|||||+|||++++||++||++|++||| |+++||||||||||||||+||||||++||++||++||||||+
T Consensus 53 tGGsD~~GfPMr~~v~~~~rvr~Ll~~G~~gyr--p~r~GeRrRKsVRG~~is~di~qiN~~Iv~~G~k~i~glt~~ 127 (127)
T PF01092_consen 53 TGGSDKQGFPMRQGVLGPGRVRLLLSKGGPGYR--PRRKGERRRKSVRGNIISADISQINLVIVKKGEKPIPGLTDT 127 (127)
T ss_dssp EEEEECCC-BB-TT---SSEEEEEE-TTBTTB----SSTT--EEEEEE-SC--TTEEEEEEEEEE--SS--HHHHT-
T ss_pred ecccCCCCceeecCCCCcceEEEEEeCCCcccc--cCcCCeEeeeeeeccEecCCeeeEEEEEEEecCccCccccCC
Confidence 699999999999999999999999999999999 999999999999999999999999999999999999999996
No 4
>PRK04290 30S ribosomal protein S6e; Validated
Probab=99.97 E-value=1.7e-31 Score=210.80 Aligned_cols=63 Identities=49% Similarity=0.827 Sum_probs=61.4
Q ss_pred CCCCCCCCCCcCCCCCCCCeEEEeecCCCccccCCCCCCCcceeeeecceeecCCcceEEEEEEee
Q 029217 1 MGGCDKQGFPMKQGVLTPGRVRLLLHRGTPCFRGYGRRDGERRRKSVRGCIVSPDLSVLNLVIVKK 66 (197)
Q Consensus 1 tGGnDkqGFPMkqgVlt~~RvrlLLskG~sgyrg~prr~GeRkRKSVRGciV~~~is~LNlvIvkk 66 (197)
|||||+|||||+|||+|++|++|||++| +||+ |+++||||||||||||||+||+|||++||++
T Consensus 53 tGGsDk~GfPM~~~v~~~~r~rlLl~~g-~gyr--p~r~GeRrRKsVRG~~vs~di~qiN~~iv~~ 115 (115)
T PRK04290 53 TGGSDKSGFPMRPDVPGPVRRRILLSGG-PGFR--PKEKGERRRKTVRGNTISDDIVQINAKVVEY 115 (115)
T ss_pred ecccCCCCccccCCccCCceEEEEecCC-CCCC--cCCCCcEEEEEEEccEEcCCeeEEEEEEEcC
Confidence 7999999999999999999999999999 7999 9999999999999999999999999999974
No 5
>COG2125 RPS6A Ribosomal protein S6E (S10) [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=7.8e-30 Score=202.39 Aligned_cols=67 Identities=57% Similarity=0.962 Sum_probs=64.8
Q ss_pred CCCCCCCCCCcCCCCCCCCeEEEeecCCCccccCCCCCCCcceeeeecceeecCCcceEEEEEEeeCCcC
Q 029217 1 MGGCDKQGFPMKQGVLTPGRVRLLLHRGTPCFRGYGRRDGERRRKSVRGCIVSPDLSVLNLVIVKKGEHD 70 (197)
Q Consensus 1 tGGnDkqGFPMkqgVlt~~RvrlLLskG~sgyrg~prr~GeRkRKSVRGciV~~~is~LNlvIvkkGek~ 70 (197)
|||||++||||++||++++|+++|||+ ++||+ |+++||||||||||||||+||+|||++||++|+++
T Consensus 54 tGGsD~~GfPMr~dv~g~~r~riLls~-~~Gyr--P~~~GeRrRKtVRG~~Is~dI~QiN~~Iv~~ge~~ 120 (120)
T COG2125 54 TGGSDKDGFPMRPDVPGPRRVRILLSG-GPGYR--PRRKGERKRKTVRGNIISPDIVQINLVIVEYGEKP 120 (120)
T ss_pred eCCcCCCCCcccCCCCCcceEEEEecc-CCCcC--CCCCCceeeeeecccccchhheeeEEEEEecCCCC
Confidence 799999999999999999999999997 58999 99999999999999999999999999999999874
No 6
>PF11208 DUF2992: Protein of unknown function (DUF2992); InterPro: IPR016787 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=47.63 E-value=92 Score=25.44 Aligned_cols=51 Identities=22% Similarity=0.268 Sum_probs=26.3
Q ss_pred cccCcchHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 029217 128 IQRLVTPLTLQRKRARIAEKK-QRIAKAKAEAAEYQKLLATRLKEQRERRSE 178 (197)
Q Consensus 128 IQrLvTp~~lqrK~~~~a~kk-~~~~k~keea~eY~kllakr~ke~k~~~~~ 178 (197)
...-+.|-+|||.-.....+. -.|+....-..+|......+....++.+.+
T Consensus 61 ~~~~~NPKR~qR~a~ke~~~~g~~TkAQ~ALk~q~E~~K~~rk~~~k~~re~ 112 (132)
T PF11208_consen 61 KEKKINPKRLQREAKKEMKKKGISTKAQQALKLQREQRKKERKKRSKEQREA 112 (132)
T ss_pred cccCCChhHHHHHHHHhhhccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455678888887543332221 124444444455555555555555555433
No 7
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=36.03 E-value=53 Score=26.63 Aligned_cols=53 Identities=19% Similarity=0.427 Sum_probs=33.6
Q ss_pred eecceeecCCcceEEEEEEeeCCcCCCCCCCCCCCCcCCC--CchhhHHHHhCC-----CCcchHhHhhhhhh
Q 029217 46 SVRGCIVSPDLSVLNLVIVKKGEHDLPGLTDTEKPRMRGP--KRASKIRKLFNL-----SKEDDVRKYVNTYR 111 (197)
Q Consensus 46 SVRGciV~~~is~LNlvIvkkGek~I~gLTd~~~p~~lgP--KRaskIrKlFnL-----sk~ddV~kyV~~~i 111 (197)
+++-|++++|.. ..+|+.| .+....|+ .|...|..+.|- .-.+|..+|+.+++
T Consensus 23 ~~~dc~~d~~~v---i~vV~~~----------~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d~~~fI~n~l 82 (140)
T PRK08406 23 TVKDCIIDDDRI---IFVVKEG----------DMGLAIGKGGENVKRLEEKLGKDIELVEYSDDPEEFIKNIF 82 (140)
T ss_pred CceEEEEeCCEE---EEEEeCC----------CccccCCcCchHHHHHHHHhCCceEEEEcCCCHHHHHHHHc
Confidence 578899999644 2355554 35667776 555666666552 12278899997754
No 8
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=32.78 E-value=77 Score=26.02 Aligned_cols=54 Identities=17% Similarity=0.359 Sum_probs=36.0
Q ss_pred eecceeecCCcceEEEEEEeeCCcCCCCCCCCCCCCcCCC--CchhhHHHHhCC-----CCcchHhHhhhhhh
Q 029217 46 SVRGCIVSPDLSVLNLVIVKKGEHDLPGLTDTEKPRMRGP--KRASKIRKLFNL-----SKEDDVRKYVNTYR 111 (197)
Q Consensus 46 SVRGciV~~~is~LNlvIvkkGek~I~gLTd~~~p~~lgP--KRaskIrKlFnL-----sk~ddV~kyV~~~i 111 (197)
+++-|+++++- -=+.+|+.| .+....|+ .|..+|+.++|- .-.+|..+||.+.+
T Consensus 23 ~~~dc~~d~~~--riifvV~~g----------~vG~~IG~~G~rIk~i~el~gekIdVVeys~D~~~fI~N~l 83 (141)
T TIGR01952 23 TVVDCLIDDRN--RVVFVVKEG----------EMGAAIGKGGENVKRLEELIGKSIELIEYSENLEEFVANKL 83 (141)
T ss_pred ceEEEEecCCc--EEEEEEcCC----------CccccCCCCchHHHHHHHhcCCeeEEEEcCCCHHHHHHHcC
Confidence 57889999985 224466666 34556676 677777777772 22378899986633
No 9
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=27.70 E-value=3.4e+02 Score=26.36 Aligned_cols=46 Identities=20% Similarity=0.277 Sum_probs=27.6
Q ss_pred CcccCcchHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 029217 127 KIQRLVTPLTLQRKRARI-AEKKQRIAKAKAEAAEYQKLLATRLKEQ 172 (197)
Q Consensus 127 KIQrLvTp~~lqrK~~~~-a~kk~~~~k~keea~eY~kllakr~ke~ 172 (197)
..+-||+|-.+..=+..+ ++|+.+++..+|+.++-..+-++|.+..
T Consensus 312 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~k~~~k~~~~~~~~~~ 358 (429)
T PRK00247 312 RLRMIITPWRAPELHAENAEIKKTRTAEKNEAKARKKEIAQKRRAAE 358 (429)
T ss_pred cccccCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356689997665554444 4566566555666666655555555444
No 10
>PRK06569 F0F1 ATP synthase subunit B'; Validated
Probab=19.76 E-value=5.4e+02 Score=21.59 Aligned_cols=44 Identities=7% Similarity=0.160 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 029217 135 LTLQRKRARIAEKKQRIAKAKAEAAEYQKLLATRLKEQRERRSE 178 (197)
Q Consensus 135 ~~lqrK~~~~a~kk~~~~k~keea~eY~kllakr~ke~k~~~~~ 178 (197)
.+|.-+...|+--....+..++|++++.+-....+.+++.+.++
T Consensus 37 ~iLe~R~~~I~~~L~~Ae~~k~eAe~l~a~ye~~L~~Ar~eA~~ 80 (155)
T PRK06569 37 EIFNNRQTNIQDNITQADTLTIEVEKLNKYYNEEIDKTNTEIDR 80 (155)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46667777888877788888887766555555555555555444
Done!