Query 033375
Match_columns 120
No_of_seqs 109 out of 411
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 13:07:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033375.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033375hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00193 60S ribosomal protein 100.0 9.6E-54 2.1E-58 330.0 12.4 113 4-118 75-188 (188)
2 KOG0893 60S ribosomal protein 100.0 8.8E-45 1.9E-49 267.2 7.0 113 2-116 9-121 (125)
3 PF01198 Ribosomal_L31e: Ribos 100.0 2E-40 4.4E-45 229.1 7.5 83 10-93 1-83 (83)
4 PRK01192 50S ribosomal protein 100.0 6.5E-36 1.4E-40 209.1 9.5 74 10-84 3-78 (89)
5 COG2097 RPL31A Ribosomal prote 100.0 1.3E-31 2.7E-36 187.6 8.9 72 11-83 5-76 (89)
6 PTZ00181 60S ribosomal protein 72.2 11 0.00023 26.4 4.7 37 35-82 2-40 (82)
7 KOG3499 60S ribosomal protein 55.3 29 0.00062 23.4 4.1 44 35-99 2-47 (69)
8 PF01781 Ribosomal_L38e: Ribos 49.1 21 0.00045 24.1 2.7 23 35-57 1-25 (69)
9 COG2066 GlsA Glutaminase [Amin 33.0 58 0.0013 27.8 3.6 38 34-71 132-169 (309)
10 KOG3086 Predicted dioxygenase 32.6 23 0.0005 29.8 1.2 49 12-71 68-118 (296)
11 PF02501 T2SI: Type II secreti 26.3 1.3E+02 0.0029 19.5 3.8 23 74-101 57-79 (81)
No 1
>PTZ00193 60S ribosomal protein L31; Provisional
Probab=100.00 E-value=9.6e-54 Score=330.05 Aligned_cols=113 Identities=41% Similarity=0.680 Sum_probs=110.2
Q ss_pred ccccccccceeeEEEEecCccccCCCCCcchHHHHHHHHHHHHHHcCCCCeEeCchhhHHHHhCCCCCCCceeEEEEEee
Q 033375 4 KTKGRKEEVVTREFTINLHKRLHGCTFKKKAPKAIKEIRKFAEKAMGTKDVRVDVKLNKQIWSRGIRSVPKRVRVRIARR 83 (120)
Q Consensus 4 ~~~~~~~~~vtreyTInL~K~~~~~~~kkRAp~Aik~Irkfa~K~m~t~dV~ID~~LNk~IWsrGi~~~P~rIRVr~sRk 83 (120)
|+++++.+++|+||||||||++||++|++|||+||++||+||+|||||+||+|||+||++||++||+|||++|||+++|+
T Consensus 75 ~~~~~~~e~VTREyTINLHKriHgv~fKKRAPrAIKeIRkFA~K~MgT~DVRIDtrLNkaIWsrGIRnvP~RIRVRlsRK 154 (188)
T PTZ00193 75 KRTGRKPDNISMEATIHLSKLLKKKTFHKRAPIAIKRIKAFVGRLMKTKDNRIDASLNTYIWHKGVKGVPGRVRVLVERK 154 (188)
T ss_pred HhhccCCCcceeEEEEeeeehhcCCCccccCHHHHHHHHHHHHHhcCCCcEEECHHHHHHHHHccCcCCCceEEEEEEee
Confidence 55788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eCCCCCCccc-ceEEEEEEecCCCCccCceeEEccc
Q 033375 84 RNDDEDAKEE-LYSLVTVAEIPPEGLRGLGTKVIED 118 (120)
Q Consensus 84 ~~eded~~~k-~y~~v~~v~v~~~~fk~l~t~~~~~ 118 (120)
+|||||+++| |||||+||||+ +||||||++|+|
T Consensus 155 rNedEDs~~KklYTlVtyVpV~--sFKgLqT~~Vdq 188 (188)
T PTZ00193 155 SETLEGGKRKHFYTVISNVPVA--SFKNLTTKVVEQ 188 (188)
T ss_pred cCccccCcccceEEEEEEEEcC--CccCceEEeccC
Confidence 9999999997 99999999999 999999999986
No 2
>KOG0893 consensus 60S ribosomal protein L31 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.8e-45 Score=267.19 Aligned_cols=113 Identities=52% Similarity=0.859 Sum_probs=107.6
Q ss_pred ccccccccccceeeEEEEecCccccCCCCCcchHHHHHHHHHHHHHHcCCCCeEeCchhhHHHHhCCCCCCCceeEEEEE
Q 033375 2 VEKTKGRKEEVVTREFTINLHKRLHGCTFKKKAPKAIKEIRKFAEKAMGTKDVRVDVKLNKQIWSRGIRSVPKRVRVRIA 81 (120)
Q Consensus 2 ~~~~~~~~~~~vtreyTInL~K~~~~~~~kkRAp~Aik~Irkfa~K~m~t~dV~ID~~LNk~IWsrGi~~~P~rIRVr~s 81 (120)
.+|+.++|++++|+||||||||++|+++|+|+||+|+++|++|||++|||+||++|++||++||++||+|+|++||||++
T Consensus 9 ~~k~~s~ine~vtre~tinihk~~h~v~fkK~ap~alkeI~kFA~keMgt~dv~~Dt~lnkavwakgirnv~~~irvrls 88 (125)
T KOG0893|consen 9 KKKGHSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIWKFAMKEMGTPDVHVDTRLNKAVWEKGIRNVPYRIRVRLS 88 (125)
T ss_pred cccCccchhhhhhhheecccccchhccchhhhhHHHHHHHHHHHHHHhCCccceecchhhHHHHHhcccCCcchhhcccc
Confidence 34678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeCCCCCCcccceEEEEEEecCCCCccCceeEEc
Q 033375 82 RRRNDDEDAKEELYSLVTVAEIPPEGLRGLGTKVI 116 (120)
Q Consensus 82 Rk~~eded~~~k~y~~v~~v~v~~~~fk~l~t~~~ 116 (120)
|++|+|||++++|||+++|+||+ +|++++...+
T Consensus 89 rk~n~~e~~~~~l~t~~t~v~~~--~~~~~~~~~~ 121 (125)
T KOG0893|consen 89 RKRNEDEDSPNKLYTQVTYVPVS--HGKNPQGKTV 121 (125)
T ss_pred cccccccccchhheeeEEEEeec--ccccccceEE
Confidence 99999999999999999999999 9999655443
No 3
>PF01198 Ribosomal_L31e: Ribosomal protein L31e; InterPro: IPR000054 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 archaebacterial large subunit ribosomal proteins can be grouped on the basis of sequence similarities. These proteins have 87 to 128 amino-acid residues. This family consists of: Yeast L34 Archaeal L31 [] Plants L31 Mammalian L31 [] ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3G6E_X 3I56_X 1YIT_X 1NJI_Y 3CC4_X 1VQM_X 1KC8_Y 1VQ9_X 1VQN_X 1M1K_Y ....
Probab=100.00 E-value=2e-40 Score=229.09 Aligned_cols=83 Identities=65% Similarity=1.072 Sum_probs=77.3
Q ss_pred ccceeeEEEEecCccccCCCCCcchHHHHHHHHHHHHHHcCCCCeEeCchhhHHHHhCCCCCCCceeEEEEEeeeCCCCC
Q 033375 10 EEVVTREFTINLHKRLHGCTFKKKAPKAIKEIRKFAEKAMGTKDVRVDVKLNKQIWSRGIRSVPKRVRVRIARRRNDDED 89 (120)
Q Consensus 10 ~~~vtreyTInL~K~~~~~~~kkRAp~Aik~Irkfa~K~m~t~dV~ID~~LNk~IWsrGi~~~P~rIRVr~sRk~~eded 89 (120)
++++|||||||||++ ++++|++|||+||++|++||+||||++||+|||+||++||++|+++||++|||+++|++++|||
T Consensus 1 ~~~v~re~TInL~k~-~~~~~~kRA~rAvk~Ir~f~~k~mkt~dV~iD~~lN~~IWsrGi~~pP~rIRVr~~r~~~~~e~ 79 (83)
T PF01198_consen 1 KEVVTREYTINLRKV-HGVPFKKRAPRAVKEIRKFAQKHMKTEDVKIDPELNKAIWSRGIRKPPRRIRVRVSRKEEEDED 79 (83)
T ss_dssp TSSEEEEEEEECHHH-CCSSGGGHHHHHHHHHHHHHHHHHTTSCEEE-HHHHHHHHTTTSSS--SEEEEEEEEETTTTEE
T ss_pred CCceeEEEEEechhh-cCCCCcccCHHHHHHHHHHHHHHhCCCceEEchHHHHHHHhcccCCCCceEEEEEEEcccCCCC
Confidence 478999999999998 9999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Cccc
Q 033375 90 AKEE 93 (120)
Q Consensus 90 ~~~k 93 (120)
+++|
T Consensus 80 ~~~~ 83 (83)
T PF01198_consen 80 AKEK 83 (83)
T ss_dssp EEEE
T ss_pred CCCC
Confidence 8865
No 4
>PRK01192 50S ribosomal protein L31e; Reviewed
Probab=100.00 E-value=6.5e-36 Score=209.12 Aligned_cols=74 Identities=34% Similarity=0.620 Sum_probs=71.2
Q ss_pred ccceeeEEEEecCccccCCCCCcchHHHHHHHHHHHHHHcCCC--CeEeCchhhHHHHhCCCCCCCceeEEEEEeee
Q 033375 10 EEVVTREFTINLHKRLHGCTFKKKAPKAIKEIRKFAEKAMGTK--DVRVDVKLNKQIWSRGIRSVPKRVRVRIARRR 84 (120)
Q Consensus 10 ~~~vtreyTInL~K~~~~~~~kkRAp~Aik~Irkfa~K~m~t~--dV~ID~~LNk~IWsrGi~~~P~rIRVr~sRk~ 84 (120)
.+++|++|||||||+ |+++|++|||+||++||+||+|||||+ ||+|||+||++||++|++|||+||||+++++.
T Consensus 3 ~~~~~r~yTInLrk~-~~~~~~kRA~rAik~Ir~f~~k~mkt~~~~V~iD~~lN~~IW~rGi~~~P~riRVr~~rk~ 78 (89)
T PRK01192 3 KEVEERIYTIPLRDV-KKVPRTKRADRAVKLVREFLARHFKADEDKVKIDPSINEKIWERGREKPPSKVRVRVAKKG 78 (89)
T ss_pred CcceEEEEEEeCeec-cCCCccccCHHHHHHHHHHHHHHhCCCCCcEEEChHHHHHHHHccCCCCCceEEEEEEEec
Confidence 468899999999998 999999999999999999999999998 99999999999999999999999999999974
No 5
>COG2097 RPL31A Ribosomal protein L31E [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.3e-31 Score=187.58 Aligned_cols=72 Identities=42% Similarity=0.737 Sum_probs=69.9
Q ss_pred cceeeEEEEecCccccCCCCCcchHHHHHHHHHHHHHHcCCCCeEeCchhhHHHHhCCCCCCCceeEEEEEee
Q 033375 11 EVVTREFTINLHKRLHGCTFKKKAPKAIKEIRKFAEKAMGTKDVRVDVKLNKQIWSRGIRSVPKRVRVRIARR 83 (120)
Q Consensus 11 ~~vtreyTInL~K~~~~~~~kkRAp~Aik~Irkfa~K~m~t~dV~ID~~LNk~IWsrGi~~~P~rIRVr~sRk 83 (120)
++.+++||||||+ ++++++++|||+|+++||+|++|||++++|+|||+||++||+||+++||++|||++++.
T Consensus 5 ~~~er~ytI~LR~-~~~v~r~kRA~rAVk~ir~fv~rHmk~e~V~id~~lNe~iW~rG~ekpP~klRVrv~k~ 76 (89)
T COG2097 5 VVVERIYTIPLRR-AKKVPRTKRAPRAVKIIRKFVARHMKAEEVRIDPSLNEKIWERGIEKPPSKLRVRVSKF 76 (89)
T ss_pred ccceEEEEEEchh-hccCCccccchHHHHHHHHHHHHHhCCceEEECHHHhHHHHHhhccCCCceEEEEEEEe
Confidence 6889999999995 69999999999999999999999999999999999999999999999999999999997
No 6
>PTZ00181 60S ribosomal protein L38; Provisional
Probab=72.17 E-value=11 Score=26.42 Aligned_cols=37 Identities=24% Similarity=0.494 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHcC--CCCeEeCchhhHHHHhCCCCCCCceeEEEEEe
Q 033375 35 PKAIKEIRKFAEKAMG--TKDVRVDVKLNKQIWSRGIRSVPKRVRVRIAR 82 (120)
Q Consensus 35 p~Aik~Irkfa~K~m~--t~dV~ID~~LNk~IWsrGi~~~P~rIRVr~sR 82 (120)
|+-|.+|++|+...-+ +..|+| -++ .--.+..||.||
T Consensus 2 PkeI~dIK~FL~~arrkDAksvkI---------Kkn--~~~tKFKvRcsr 40 (82)
T PTZ00181 2 PREIKTLKEFLAICSRKDARCVKV---------KHN--PSATKFKVRCSR 40 (82)
T ss_pred chhHHHHHHHHHHhhccCceEEEe---------ecC--CcceEEEEEecc
Confidence 6789999999887666 445888 111 234567777777
No 7
>KOG3499 consensus 60S ribosomal protein L38 [Translation, ribosomal structure and biogenesis]
Probab=55.30 E-value=29 Score=23.40 Aligned_cols=44 Identities=36% Similarity=0.575 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHcCC--CCeEeCchhhHHHHhCCCCCCCceeEEEEEeeeCCCCCCcccceEEEE
Q 033375 35 PKAIKEIRKFAEKAMGT--KDVRVDVKLNKQIWSRGIRSVPKRVRVRIARRRNDDEDAKEELYSLVT 99 (120)
Q Consensus 35 p~Aik~Irkfa~K~m~t--~dV~ID~~LNk~IWsrGi~~~P~rIRVr~sRk~~eded~~~k~y~~v~ 99 (120)
|+-|.+|+.|+...-.. ..|+|--.-| --+..||.|| -|||||-
T Consensus 2 pr~i~eiK~FL~~arR~Da~s~kiKkn~~-----------~~KFKvRcsr----------yLYTLvv 47 (69)
T KOG3499|consen 2 PRQITEIKDFLLTARRKDAKSVKIKKNKN-----------NVKFKVRCSR----------YLYTLVV 47 (69)
T ss_pred cchHHHHHHHHHHHHhcccceeEEEecCC-----------ceeEEEEeee----------eeeeeee
Confidence 67899999998776543 2355543322 3456677777 3677663
No 8
>PF01781 Ribosomal_L38e: Ribosomal L38e protein family; InterPro: IPR002675 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 L38e forms part of the 60S ribosomal subunit []. This family is found in eukaryotes.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_n 3IZR_n 4A1D_P 4A19_P 4A18_P 4A1B_P.
Probab=49.05 E-value=21 Score=24.15 Aligned_cols=23 Identities=39% Similarity=0.692 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHcCCC--CeEeC
Q 033375 35 PKAIKEIRKFAEKAMGTK--DVRVD 57 (120)
Q Consensus 35 p~Aik~Irkfa~K~m~t~--dV~ID 57 (120)
|+-|.+|++|+....+.+ .|+|-
T Consensus 1 Pkqi~~iK~FL~~arrkDAksv~iK 25 (69)
T PF01781_consen 1 PKQIKDIKDFLETARRKDAKSVKIK 25 (69)
T ss_dssp -THHHHHHHHHHHHCSS-EEEEEEE
T ss_pred CcchhhHHHHHHHHhhCCCceEEEE
Confidence 567899999998877643 35554
No 9
>COG2066 GlsA Glutaminase [Amino acid transport and metabolism]
Probab=32.97 E-value=58 Score=27.78 Aligned_cols=38 Identities=16% Similarity=0.282 Sum_probs=32.7
Q ss_pred hHHHHHHHHHHHHHHcCCCCeEeCchhhHHHHhCCCCC
Q 033375 34 APKAIKEIRKFAEKAMGTKDVRVDVKLNKQIWSRGIRS 71 (120)
Q Consensus 34 Ap~Aik~Irkfa~K~m~t~dV~ID~~LNk~IWsrGi~~ 71 (120)
++.....|.+|+.+..|-+.+.+|.+++..-|+.+-||
T Consensus 132 ~~~r~~~il~~~~~lag~~~i~~d~~Va~Se~~t~~rN 169 (309)
T COG2066 132 ADERWERILEFVRGLAGDRRLTLDEEVAQSERETAFRN 169 (309)
T ss_pred cHHHHHHHHHHHHHhcCCCceeecHHHHHHHhccchhh
Confidence 44445669999999988889999999999999988887
No 10
>KOG3086 consensus Predicted dioxygenase [General function prediction only]
Probab=32.63 E-value=23 Score=29.80 Aligned_cols=49 Identities=27% Similarity=0.407 Sum_probs=34.8
Q ss_pred ceeeEEEEecCccccCCCCCcchHHHHHHHHHHHHHHcCCC--CeEeCchhhHHHHhCCCCC
Q 033375 12 VVTREFTINLHKRLHGCTFKKKAPKAIKEIRKFAEKAMGTK--DVRVDVKLNKQIWSRGIRS 71 (120)
Q Consensus 12 ~vtreyTInL~K~~~~~~~kkRAp~Aik~Irkfa~K~m~t~--dV~ID~~LNk~IWsrGi~~ 71 (120)
.+.|++..-...+ +.+.++|-.+... ..|| |.+||.++|+.+|+.|.-.
T Consensus 68 ~v~RIFILGPSHH---v~l~~CalS~~s~--------yrTPLgdLkVD~~i~~eL~~tg~F~ 118 (296)
T KOG3086|consen 68 NVQRIFILGPSHH---VYLSKCALSSASI--------YRTPLGDLKVDQKICKELWATGMFE 118 (296)
T ss_pred HeeEEEEecCcce---eeecchhhhhhhh--------hcCccccccccHHHHHHHHHcCCcc
Confidence 5677777655433 4556666655443 4576 9999999999999999544
No 11
>PF02501 T2SI: Type II secretion system (T2SS), protein I; InterPro: IPR003413 The bacterial general secretion pathway (GSP) is involved in the export of proteins (also called the type II pathway). This family includes GSPI and GSPJ, which contain the pre-pilin signal sequence [].; GO: 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex; PDB: 2RET_G 3CFI_G 3CI0_I.
Probab=26.35 E-value=1.3e+02 Score=19.51 Aligned_cols=23 Identities=43% Similarity=0.655 Sum_probs=16.2
Q ss_pred ceeEEEEEeeeCCCCCCcccceEEEEEE
Q 033375 74 KRVRVRIARRRNDDEDAKEELYSLVTVA 101 (120)
Q Consensus 74 ~rIRVr~sRk~~eded~~~k~y~~v~~v 101 (120)
.+|.|.++ +++....+++|++|+
T Consensus 57 ~rv~v~V~-----~~~~~~~l~~L~~~~ 79 (81)
T PF02501_consen 57 RRVEVQVS-----DEDQEQPLASLSTFV 79 (81)
T ss_dssp EEEEEEEE-----STTSSSECEEEEEEE
T ss_pred EEEEEEEe-----cCCCCceEEEEEEEE
Confidence 56777776 345566689998886
Done!