Query 035122
Match_columns 72
No_of_seqs 100 out of 141
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 09:23:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035122.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035122hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0009 Ubiquitin-like/40S rib 100.0 1.2E-31 2.6E-36 168.2 2.2 57 1-57 1-57 (62)
2 PTZ00467 40S ribosomal protein 100.0 3.3E-31 7.2E-36 167.6 1.6 55 1-55 1-55 (66)
3 PF04758 Ribosomal_S30: Riboso 99.9 2.2E-30 4.9E-35 160.7 -3.0 54 3-56 1-54 (59)
4 PRK09336 30S ribosomal protein 99.9 5.1E-27 1.1E-31 141.9 1.5 48 1-50 1-48 (50)
5 COG4919 Ribosomal protein S30 99.7 2.8E-18 6E-23 105.5 0.9 46 4-50 3-48 (54)
6 PF09368 Sas10: Sas10 C-termin 30.6 30 0.00066 22.2 1.2 28 15-46 17-44 (76)
7 PF15364 PAXIP1_C: PAXIP1-asso 22.4 32 0.00068 24.4 0.2 31 14-55 101-131 (141)
8 PF05760 IER: Immediate early 22.3 24 0.00052 27.7 -0.4 21 41-62 246-266 (300)
9 PF03818 MadM: Malonate/sodium 21.6 32 0.0007 21.6 0.1 6 2-7 37-42 (60)
10 KOG0635 Adenosine 5'-phosphosu 19.5 43 0.00093 25.4 0.4 19 7-25 152-170 (207)
No 1
>KOG0009 consensus Ubiquitin-like/40S ribosomal S30 protein fusion [Translation, ribosomal structure and biogenesis; Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=1.2e-31 Score=168.22 Aligned_cols=57 Identities=70% Similarity=0.940 Sum_probs=54.9
Q ss_pred CCceecccccCCcccCCCCCcccccccCCCChhhhhhhhhchheeecchhhhhcccc
Q 035122 1 MGKVHGSLARAGKVRGQTPKVAKQDKKKRPRGRAYKRMQYNRRFVTAGQLIISHRFS 57 (72)
Q Consensus 1 mGKvHGSLarAGKVR~QTPKV~KqeKkk~~~GRak~R~qYnrRfvnv~~t~~~~r~~ 57 (72)
|||||||||+|||||+||||||+|||+|+++|||++|+|||+||+|++..|+..|+-
T Consensus 1 ~gkvhgslarAGKVr~QTPKv~kqeK~kkk~GRa~~Rlqy~rR~vn~~~~~g~Kr~~ 57 (62)
T KOG0009|consen 1 MGKVHGSLARAGKVRGQTPKVEKQEKKKKKRGRAKKRLQYNRRFVNVVFGVGGKRGP 57 (62)
T ss_pred CCceeeehhhcccccccCCcchhhhhcccccchHHHHhhhheeeEEeeeccccccCC
Confidence 899999999999999999999999999999999999999999999999999988763
No 2
>PTZ00467 40S ribosomal protein S30; Provisional
Probab=99.96 E-value=3.3e-31 Score=167.62 Aligned_cols=55 Identities=62% Similarity=0.917 Sum_probs=52.9
Q ss_pred CCceecccccCCcccCCCCCcccccccCCCChhhhhhhhhchheeecchhhhhcc
Q 035122 1 MGKVHGSLARAGKVRGQTPKVAKQDKKKRPRGRAYKRMQYNRRFVTAGQLIISHR 55 (72)
Q Consensus 1 mGKvHGSLarAGKVR~QTPKV~KqeKkk~~~GRak~R~qYnrRfvnv~~t~~~~r 55 (72)
|||||||||+||||++||||||++||+|.++|||++|+|||+||+|++.+++..|
T Consensus 1 mgKvHGSLarAGKVr~QTPkv~k~eKkk~~~gRA~~R~qYnrRfv~~~~~~g~kr 55 (66)
T PTZ00467 1 MGKIHGSLARAGKVKNQTPKVAKQEKPKQPRGRALKRLKYTRRFLAKTVKPGEKV 55 (66)
T ss_pred CcchhhhhhhcccccCCCCCchhhhcccCCCchHHHHHHHHhhhhhccccCCccc
Confidence 9999999999999999999999999999999999999999999999999988665
No 3
>PF04758 Ribosomal_S30: Ribosomal protein S30; InterPro: IPR006846 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 is for the ribosomal protein S30.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_X 2XZM_X 3IZB_Z 3U5G_e 3U5C_e 3J16_E 3IZ6_Z.
Probab=99.95 E-value=2.2e-30 Score=160.69 Aligned_cols=54 Identities=69% Similarity=0.948 Sum_probs=49.4
Q ss_pred ceecccccCCcccCCCCCcccccccCCCChhhhhhhhhchheeecchhhhhccc
Q 035122 3 KVHGSLARAGKVRGQTPKVAKQDKKKRPRGRAYKRMQYNRRFVTAGQLIISHRF 56 (72)
Q Consensus 3 KvHGSLarAGKVR~QTPKV~KqeKkk~~~GRak~R~qYnrRfvnv~~t~~~~r~ 56 (72)
|||||||+|||||+||||||++||++.++|||++|++||+||++++++|+.+++
T Consensus 1 KvHGSLarAGKVR~QTPKV~k~~k~k~~~gRak~R~~Y~rRfv~~~~~~g~k~~ 54 (59)
T PF04758_consen 1 KVHGSLARAGKVRGQTPKVEKQEKKKKPTGRAKKRIQYNRRFVNVVPTFGKKKG 54 (59)
T ss_dssp HHCCCCTTTTHHHHHSSSSS--HHHHHHHCHHHHHHHHHHHCSTTHHHSCTTTT
T ss_pred CcccchhhcccccccCCCcCccccccCCchhHHHHHhhhhheeeecccCCCccC
Confidence 799999999999999999999999888999999999999999999999997665
No 4
>PRK09336 30S ribosomal protein S30e; Provisional
Probab=99.93 E-value=5.1e-27 Score=141.93 Aligned_cols=48 Identities=48% Similarity=0.689 Sum_probs=44.0
Q ss_pred CCceecccccCCcccCCCCCcccccccCCCChhhhhhhhhchheeecchh
Q 035122 1 MGKVHGSLARAGKVRGQTPKVAKQDKKKRPRGRAYKRMQYNRRFVTAGQL 50 (72)
Q Consensus 1 mGKvHGSLarAGKVR~QTPKV~KqeKkk~~~GRak~R~qYnrRfvnv~~t 50 (72)
|+ +|||||+||||++||||||++||+++ +|||++|++||+||+|+.++
T Consensus 1 m~-~HGSLarAGKVr~qTPkv~k~ekkk~-~gra~~R~qynrRf~~~~~~ 48 (50)
T PRK09336 1 MP-SHGSLTKAGKVRSQTPKIPPKPKKNE-VPRVRNRREYERRVLKARQQ 48 (50)
T ss_pred CC-cchhhhhcccccCCCCCcchhhhccC-CchhHHHHHHHHHHhhhhcc
Confidence 44 89999999999999999999998765 79999999999999999864
No 5
>COG4919 Ribosomal protein S30 [Translation, ribosomal structure and biogenesis]
Probab=99.70 E-value=2.8e-18 Score=105.45 Aligned_cols=46 Identities=43% Similarity=0.622 Sum_probs=43.0
Q ss_pred eecccccCCcccCCCCCcccccccCCCChhhhhhhhhchheeecchh
Q 035122 4 VHGSLARAGKVRGQTPKVAKQDKKKRPRGRAYKRMQYNRRFVTAGQL 50 (72)
Q Consensus 4 vHGSLarAGKVR~QTPKV~KqeKkk~~~GRak~R~qYnrRfvnv~~t 50 (72)
+|||||+|||||+||||++.++|++ .++|.+||.+|.+|++.+.++
T Consensus 3 sHGSLTKAGKVR~QTPkipaK~kkn-~~PR~rNr~~Y~~Rv~ka~sq 48 (54)
T COG4919 3 SHGSLTKAGKVRKQTPKIPAKQKKN-YPPRLRNRLKYQVRVEKAASQ 48 (54)
T ss_pred CccccccccchhccCCCCCcccccc-CChhHHHHHHHHHHHHHHHhc
Confidence 6999999999999999999999988 589999999999999988765
No 6
>PF09368 Sas10: Sas10 C-terminal domain; InterPro: IPR018972 This entry represents the C-terminal domain of the Something about silencing protein 10 (Sas10), which is essential for gene silencing and has a role in the structure of silenced chromatin [, ]. Sas10 plays a role in the developing brain, and may bind RNA. SAS10 from Saccharomyces cerevisiae (Baker's yeast) is primarily required at the G2/M phase and is essential for viability, being involved in nucleolar processing of pre-18S ribosomal RNA as part of the ribosomal small subunit (SSU) processome [].; GO: 0016458 gene silencing, 0005634 nucleus
Probab=30.55 E-value=30 Score=22.17 Aligned_cols=28 Identities=36% Similarity=0.582 Sum_probs=19.1
Q ss_pred cCCCCCcccccccCCCChhhhhhhhhchheee
Q 035122 15 RGQTPKVAKQDKKKRPRGRAYKRMQYNRRFVT 46 (72)
Q Consensus 15 R~QTPKV~KqeKkk~~~GRak~R~qYnrRfvn 46 (72)
++-||+=.|. ...+|.++|+.|.+-...
T Consensus 17 kGLt~~RkK~----~rNpRvk~R~Ky~ka~kk 44 (76)
T PF09368_consen 17 KGLTPKRKKE----NRNPRVKKRMKYEKAMKK 44 (76)
T ss_pred cCccccCCcc----CCCcchHHHHHHHHHHHH
Confidence 5567766333 347899999999875443
No 7
>PF15364 PAXIP1_C: PAXIP1-associated-protein-1 C term PTIP binding protein
Probab=22.39 E-value=32 Score=24.44 Aligned_cols=31 Identities=39% Similarity=0.478 Sum_probs=19.5
Q ss_pred ccCCCCCcccccccCCCChhhhhhhhhchheeecchhhhhcc
Q 035122 14 VRGQTPKVAKQDKKKRPRGRAYKRMQYNRRFVTAGQLIISHR 55 (72)
Q Consensus 14 VR~QTPKV~KqeKkk~~~GRak~R~qYnrRfvnv~~t~~~~r 55 (72)
||.|||.-.+...+| | .-||.+|.+.+-+||
T Consensus 101 ~Rr~tp~~~~~S~kK--------r---~A~~dkVLsdmkRhr 131 (141)
T PF15364_consen 101 VRRRTPGSPKRSAKK--------R---TARFDKVLSDMKRHR 131 (141)
T ss_pred ccccCCCCCCCCccc--------c---hhhHHHHHHHHHHHH
Confidence 667777664333322 2 237888888888876
No 8
>PF05760 IER: Immediate early response protein (IER); InterPro: IPR008653 This family consists of several eukaryotic immediate early response (IER) 2 and 5 proteins. The role of IER5 is unclear although it play an important role in mediating the cellular response to mitogenic signals. Again, little is known about the function of IER2 although it is thought to play a role in mediating the cellular responses to a variety of extracellular signals [, ].
Probab=22.28 E-value=24 Score=27.67 Aligned_cols=21 Identities=29% Similarity=0.284 Sum_probs=18.1
Q ss_pred chheeecchhhhhcccccceee
Q 035122 41 NRRFVTAGQLIISHRFSGLLNI 62 (72)
Q Consensus 41 nrRfvnv~~t~~~~r~~~~~~~ 62 (72)
.-.|-|.+.-|+|. |||||+-
T Consensus 246 t~NvsnLIsIfgSs-FSGLls~ 266 (300)
T PF05760_consen 246 TGNVSNLISIFGSS-FSGLLSK 266 (300)
T ss_pred ccchhHHHHHHhhh-hhhhhcC
Confidence 56888999999998 9999974
No 9
>PF03818 MadM: Malonate/sodium symporter MadM subunit; InterPro: IPR018402 The MSS family includes the monobasic malonate:Na+ symporter of Malonomonas rubra. It consists of two integral membrane proteins, MadL and MadM.The transporter is believed to catalyze the electroneutral reversible uptake of H+-malonate with one Na+, and both subunits have been shown to be essential for activity.
Probab=21.63 E-value=32 Score=21.60 Aligned_cols=6 Identities=67% Similarity=1.509 Sum_probs=5.3
Q ss_pred Cceecc
Q 035122 2 GKVHGS 7 (72)
Q Consensus 2 GKvHGS 7 (72)
|++|||
T Consensus 37 GrihGS 42 (60)
T PF03818_consen 37 GRIHGS 42 (60)
T ss_pred CCcchH
Confidence 789998
No 10
>KOG0635 consensus Adenosine 5'-phosphosulfate kinase [Inorganic ion transport and metabolism]
Probab=19.55 E-value=43 Score=25.39 Aligned_cols=19 Identities=42% Similarity=0.513 Sum_probs=14.2
Q ss_pred ccccCCcccCCCCCccccc
Q 035122 7 SLARAGKVRGQTPKVAKQD 25 (72)
Q Consensus 7 SLarAGKVR~QTPKV~Kqe 25 (72)
.+|||||+++.|-=-++=|
T Consensus 152 K~ARaGkIKgFTGIddPYE 170 (207)
T KOG0635|consen 152 KLARAGKIKGFTGIDDPYE 170 (207)
T ss_pred HHHhcccccccccCCCccc
Confidence 3799999999996554443
Done!