Query 035394
Match_columns 51
No_of_seqs 106 out of 191
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 02:41:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035394.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035394hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK01242 rpl39e 50S ribosomal 100.0 4.2E-35 9.1E-40 164.8 5.0 50 2-51 1-50 (50)
2 COG2167 RPL39 Ribosomal protei 100.0 1.4E-32 3E-37 155.4 4.2 51 1-51 1-51 (51)
3 KOG0002 60s ribosomal protein 100.0 9.6E-32 2.1E-36 150.4 0.8 48 4-51 1-48 (48)
4 PF00832 Ribosomal_L39: Riboso 100.0 1.1E-31 2.3E-36 147.3 0.7 43 9-51 1-43 (43)
5 PF04700 Baculo_gp41: Structur 34.7 23 0.00049 24.5 1.2 23 3-25 60-82 (186)
6 KOG2781 U3 small nucleolar rib 31.2 41 0.00089 24.7 2.1 18 8-25 27-44 (290)
7 PF14475 Mso1_Sec1_bdg: Sec1-b 29.9 28 0.00061 18.7 0.8 12 16-27 30-41 (41)
8 PRK13719 conjugal transfer tra 23.7 52 0.0011 22.9 1.5 23 17-39 24-46 (217)
9 cd08767 Cdt1_c The C-terminal 20.0 42 0.00091 20.9 0.4 15 23-37 95-109 (126)
10 COG2027 DacB D-alanyl-D-alanin 19.6 64 0.0014 24.6 1.3 12 22-33 406-417 (470)
No 1
>PRK01242 rpl39e 50S ribosomal protein L39e; Validated
Probab=100.00 E-value=4.2e-35 Score=164.83 Aligned_cols=50 Identities=42% Similarity=0.789 Sum_probs=48.4
Q ss_pred CCCchHHHHHHHHHHHhhcCCCCceEEEecCCceeecCcccccccccCCC
Q 035394 2 PSHKTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRTKLGF 51 (51)
Q Consensus 2 ~s~K~~~~K~rLaK~~kqNrpiP~Wv~~KT~~kiryn~kRRhWRRtkL~~ 51 (51)
+|||||++|++||||++||+||||||+||||++|+|||||||||||+|+.
T Consensus 1 ~s~Kt~~~K~rLaK~~kQNrpvP~Wv~~KT~~kvr~n~kRRhWRRtkL~~ 50 (50)
T PRK01242 1 MRNKPLGKKLRLAKALKQNRRVPAWVIVKTNRRVRRHPKRRHWRRSKLKV 50 (50)
T ss_pred CCcchHHHHHHHHHHHhccCCCCeEEEEEcCCceecCCccccccccccCC
Confidence 58999999999999999999999999999999999999999999999973
No 2
>COG2167 RPL39 Ribosomal protein L39E [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.4e-32 Score=155.41 Aligned_cols=51 Identities=51% Similarity=0.937 Sum_probs=50.2
Q ss_pred CCCCchHHHHHHHHHHHhhcCCCCceEEEecCCceeecCcccccccccCCC
Q 035394 1 MPSHKTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRTKLGF 51 (51)
Q Consensus 1 M~s~K~~~~K~rLaK~~kqNrpiP~Wv~~KT~~kiryn~kRRhWRRtkL~~ 51 (51)
||++|+++.|++||||.|||++||+||+|+|+++|+|||+||||||++|++
T Consensus 1 M~~~K~~~~K~RLaKA~KqNrrvP~Wv~~kT~~~v~~npkRRhWRR~kLki 51 (51)
T COG2167 1 MGRNKPLGKKLRLAKALKQNRRVPVWVRVKTNRRVRYNPKRRHWRRTKLKI 51 (51)
T ss_pred CCccchHHHHHHHHHHHHcCCCCCeEEEEecCCccccChhhhhhhhhccCC
Confidence 999999999999999999999999999999999999999999999999985
No 3
>KOG0002 consensus 60s ribosomal protein L39 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=9.6e-32 Score=150.44 Aligned_cols=48 Identities=83% Similarity=1.399 Sum_probs=46.9
Q ss_pred CchHHHHHHHHHHHhhcCCCCceEEEecCCceeecCcccccccccCCC
Q 035394 4 HKTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRTKLGF 51 (51)
Q Consensus 4 ~K~~~~K~rLaK~~kqNrpiP~Wv~~KT~~kiryn~kRRhWRRtkL~~ 51 (51)
+|+|.+|++|||+++||+||||||+|+|||+|+||+||||||||||+|
T Consensus 1 ~ks~~ik~kl~k~~kqnr~iP~WiRm~~gn~iryN~kRRHWRrtKL~l 48 (48)
T KOG0002|consen 1 HKSFRIKQKLAKKLKQNRPIPQWIRMRTGNTIRYNAKRRHWRRTKLGL 48 (48)
T ss_pred CchhHHHHHHHHHHHccCCccHHHhhccCCccchhHHHHHHHHhhcCC
Confidence 689999999999999999999999999999999999999999999987
No 4
>PF00832 Ribosomal_L39: Ribosomal L39 protein; InterPro: IPR000077 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 are very basic. About 50 residues long, they are the smallest proteins of eukaryotic-type ribosomes.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3CCJ_2 3CME_2 3OW2_1 1YI2_2 1KD1_3 3CXC_1 3G6E_2 1VQ4_2 3CCU_2 3CC7_2 ....
Probab=99.96 E-value=1.1e-31 Score=147.34 Aligned_cols=43 Identities=67% Similarity=1.211 Sum_probs=32.4
Q ss_pred HHHHHHHHHhhcCCCCceEEEecCCceeecCcccccccccCCC
Q 035394 9 IKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRTKLGF 51 (51)
Q Consensus 9 ~K~rLaK~~kqNrpiP~Wv~~KT~~kiryn~kRRhWRRtkL~~ 51 (51)
+|++||||++||+||||||+||||++|+|||+|||||||+|++
T Consensus 1 ~K~rLaKa~kqNrpvP~Wv~~kT~~kiryn~kRRhWRRtkLkv 43 (43)
T PF00832_consen 1 IKLRLAKAQKQNRPVPQWVRMKTGNKIRYNPKRRHWRRTKLKV 43 (43)
T ss_dssp HHHHHHHHHHHTS---HHGHHCTTSS-SSGTT---TTTS-S--
T ss_pred CcHHHHHHHhccCCCCcEEEEeCCCceeeCCCcccccccccCC
Confidence 5899999999999999999999999999999999999999986
No 5
>PF04700 Baculo_gp41: Structural glycoprotein p40/gp41 conserved region; InterPro: IPR006790 This is a family of viral structural glycoproteins [] from the baculoviridae.; GO: 0005198 structural molecule activity, 0019012 virion
Probab=34.70 E-value=23 Score=24.53 Aligned_cols=23 Identities=35% Similarity=0.608 Sum_probs=19.2
Q ss_pred CCchHHHHHHHHHHHhhcCCCCc
Q 035394 3 SHKTFMIKKKLAKKMRQNRPIPH 25 (51)
Q Consensus 3 s~K~~~~K~rLaK~~kqNrpiP~ 25 (51)
+|=+...|--.|-+.-||.|||-
T Consensus 60 ~hLs~~vkYQiA~AVT~n~PiPl 82 (186)
T PF04700_consen 60 RHLSDVVKYQIAEAVTQNKPIPL 82 (186)
T ss_pred HHHHHHHHHHHHHHHHcCCCcCc
Confidence 34566788889999999999996
No 6
>KOG2781 consensus U3 small nucleolar ribonucleoprotein (snoRNP) component [RNA processing and modification]
Probab=31.23 E-value=41 Score=24.74 Aligned_cols=18 Identities=28% Similarity=0.588 Sum_probs=15.9
Q ss_pred HHHHHHHHHHhhcCCCCc
Q 035394 8 MIKKKLAKKMRQNRPIPH 25 (51)
Q Consensus 8 ~~K~rLaK~~kqNrpiP~ 25 (51)
-+|.+|.+|+.+|.+||.
T Consensus 27 ekk~~lr~ALe~nk~ip~ 44 (290)
T KOG2781|consen 27 EKKRRLREALEENKKIPK 44 (290)
T ss_pred HHHHHHHHHHhcCCCCCh
Confidence 467889999999999995
No 7
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=29.94 E-value=28 Score=18.73 Aligned_cols=12 Identities=33% Similarity=1.002 Sum_probs=9.4
Q ss_pred HHhhcCCCCceE
Q 035394 16 KMRQNRPIPHWI 27 (51)
Q Consensus 16 ~~kqNrpiP~Wv 27 (51)
-..|.+|.|.|.
T Consensus 30 Y~~k~~~~P~WL 41 (41)
T PF14475_consen 30 YTEKGRPFPGWL 41 (41)
T ss_pred HHHcCCCCCCcC
Confidence 346799999994
No 8
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=23.73 E-value=52 Score=22.91 Aligned_cols=23 Identities=26% Similarity=0.379 Sum_probs=20.3
Q ss_pred HhhcCCCCceEEEecCCceeecC
Q 035394 17 MRQNRPIPHWIRMRTDNTIRYNA 39 (51)
Q Consensus 17 ~kqNrpiP~Wv~~KT~~kiryn~ 39 (51)
.=++-|+|++|+-.+|.=|-||+
T Consensus 24 ~i~~~~~P~CiR~~~g~fi~~N~ 46 (217)
T PRK13719 24 FIDDYSYPACIRNESGKFIFYNT 46 (217)
T ss_pred HHHcCCCCeEEECCCCCeeecch
Confidence 45789999999999999888886
No 9
>cd08767 Cdt1_c The C-terminal fold of replication licensing factor Cdt1 is essential for Cdt1 activity and directly interacts with MCM2-7 helicase. Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the Origin Recognition Complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region (Cdt1_n) binds DNA in a sequence-, strand-, and conformation-independent manner; the middle winged helix fold (Cdt1_m) binds geminin to inhibit both binding of the MCM complex to origins of replication and DNA; and the C-terminal region (Cdt1_c) is essential for Cdt1 activity and directly interacts with the MCM2-7 helicase. Precise duplication of chromosomal DNA is required for genomic stability during replication. Assembly of replication factors to start DNA replication in eukaryotes must occur only once per cell cycle. To form a pre-replicative complex on replicat
Probab=20.00 E-value=42 Score=20.87 Aligned_cols=15 Identities=27% Similarity=0.596 Sum_probs=11.7
Q ss_pred CCceEEEecCCceee
Q 035394 23 IPHWIRMRTDNTIRY 37 (51)
Q Consensus 23 iP~Wv~~KT~~kiry 37 (51)
+|.|+..++.+...|
T Consensus 95 ~P~Wis~~~~~~~~~ 109 (126)
T cd08767 95 APDWISEKSLRKGDY 109 (126)
T ss_pred ChHHheeeeeCCceE
Confidence 599999998776554
No 10
>COG2027 DacB D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]
Probab=19.64 E-value=64 Score=24.61 Aligned_cols=12 Identities=17% Similarity=0.166 Sum_probs=11.1
Q ss_pred CCCceEEEecCC
Q 035394 22 PIPHWIRMRTDN 33 (51)
Q Consensus 22 piP~Wv~~KT~~ 33 (51)
+++.|+++|||.
T Consensus 406 ~~~G~v~aKTGT 417 (470)
T COG2027 406 GAAGKVRAKTGT 417 (470)
T ss_pred CCCCcEEEeecc
Confidence 999999999984
Done!