Query 034124
Match_columns 103
No_of_seqs 104 out of 173
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 10:02:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034124.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034124hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08293 MRP-S33: Mitochondria 100.0 5.2E-36 1.1E-40 201.7 7.5 78 15-92 2-87 (87)
2 KOG4844 Mitochondrial ribosoma 100.0 5.9E-31 1.3E-35 180.6 6.7 91 13-103 5-102 (102)
3 KOG4104 Ganglioside-induced di 100.0 1.6E-29 3.5E-34 175.5 5.3 98 4-102 4-113 (113)
4 PF12752 SUZ: SUZ domain; Int 61.1 8.5 0.00018 23.7 2.2 16 14-29 42-57 (59)
5 PF04844 Ovate: Transcriptiona 32.3 54 0.0012 20.7 2.5 19 68-86 2-20 (59)
6 TIGR03398 plc_access_R phospho 29.2 69 0.0015 23.6 3.0 29 6-35 106-139 (141)
7 PF06904 Extensin-like_C: Exte 26.1 67 0.0014 24.2 2.6 27 11-37 131-157 (178)
8 PF07874 DUF1660: Prophage pro 24.7 23 0.00049 22.9 -0.1 13 21-33 2-14 (64)
9 PF14907 NTP_transf_5: Unchara 24.1 38 0.00083 24.9 0.9 27 47-73 77-106 (249)
10 TIGR01568 A_thal_3678 uncharac 20.5 1.1E+02 0.0025 19.7 2.5 19 68-86 8-26 (66)
11 PRK13868 type IV secretion sys 20.3 64 0.0014 28.0 1.6 31 5-60 134-164 (556)
No 1
>PF08293 MRP-S33: Mitochondrial ribosomal subunit S27; InterPro: IPR013219 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 represents a mitochondrial ribosomal subunit annotated as S27 in yeast and S33 in humans [, ]. It is a small 106 residue protein. The evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, reveals an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome [].
Probab=100.00 E-value=5.2e-36 Score=201.74 Aligned_cols=78 Identities=47% Similarity=0.728 Sum_probs=73.2
Q ss_pred HHHHHHHHHHhhhcccCCCCCCCchhHHhhhccccccccccCCCCCC--------ccCCCCCChHHHHHHHHHHHHHhcC
Q 034124 15 VTTGLTEARAKIFGHVLNPAGQRSPHKILRKKLIGDKVAGWYPYDIK--------KDDPLVMARQQQERLSKLEMLKRRG 86 (103)
Q Consensus 15 r~~~l~~ls~rIFg~~~nPt~~Rsg~kvlr~~lkG~~v~~YYP~~~~--------r~~g~~~De~e~~R~~~~~~rk~RG 86 (103)
|+++|++|||+||||++|||++|||+||||++|+|++|++|||+++. +.+++|+||||++|+++++++++||
T Consensus 2 r~~~l~~ls~rIFg~~~nP~~~Rsg~Kilr~~lkg~~~~~YYP~~~~~~~~l~~l~~~~~~~De~e~~R~e~~~~rk~RG 81 (87)
T PF08293_consen 2 RLLRLARLSARIFGTVYNPTGSRSGNKILRKRLKGPKLASYYPPHIVTFKLLKRLRPDGLFRDEHEDFREEMVELRKRRG 81 (87)
T ss_pred HHHHHHHHHHHHhCCCCCCccchHHHHHHhhcCCCchHhHhCCCcchHHHHHHHHccccCcCChhHHHHHHHHHHHHhCC
Confidence 78999999999999999999999999999999999999999999763 3455699999999999999999999
Q ss_pred CCCCCC
Q 034124 87 KGPPKK 92 (103)
Q Consensus 87 Kg~PKK 92 (103)
||+|||
T Consensus 82 Kg~PKK 87 (87)
T PF08293_consen 82 KGPPKK 87 (87)
T ss_pred CCCCCC
Confidence 999997
No 2
>KOG4844 consensus Mitochondrial ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=5.9e-31 Score=180.60 Aligned_cols=91 Identities=63% Similarity=0.887 Sum_probs=84.4
Q ss_pred HHHHHHHHHHHHhhhcccCCCCCCCchhHHhhhccccccccccCCCCC-CccCC------CCCChHHHHHHHHHHHHHhc
Q 034124 13 TVVTTGLTEARAKIFGHVLNPAGQRSPHKILRKKLIGDKVAGWYPYDI-KKDDP------LVMARQQQERLSKLEMLKRR 85 (103)
Q Consensus 13 ~~r~~~l~~ls~rIFg~~~nPt~~Rsg~kvlr~~lkG~~v~~YYP~~~-~r~~g------~~~De~e~~R~~~~~~rk~R 85 (103)
+|++..++.||++||||.|||||+|||+|||+++|+|+.|++|||+.+ ++.++ .|.|-+|+.|+++++.+++|
T Consensus 5 kAvl~~v~elsakIFg~~~np~g~Rtg~Kil~~~LkG~kvasyYp~~~~~r~l~tll~d~ef~d~~e~~R~s~~e~~kRr 84 (102)
T KOG4844|consen 5 KAVLRGVTELSAKIFGHMLNPTGQRTGHKILRKKLKGDKVASYYPPYDIKRELPTLLADEEFDDIAEWGRISKLEMLKRR 84 (102)
T ss_pred HHHHHHHHHHHHHHHhcccCCCCCcchhHHHHHHhccchHhhhcchHHhhhhhhhhhcccccccHHHHHHHHHHHHHHHc
Confidence 899999999999999999999999999999999999999999999954 46555 28899999999999999999
Q ss_pred CCCCCCCCCChhHhhhcC
Q 034124 86 GKGPPKKGQGKRAAKRSK 103 (103)
Q Consensus 86 GKg~PKKg~gkra~kkk~ 103 (103)
|||+|||++++++++.++
T Consensus 85 gKGapKk~kk~~aa~~~~ 102 (102)
T KOG4844|consen 85 GKGAPKKGKKKRAAKRNK 102 (102)
T ss_pred cCCCCcccchhhhhhccC
Confidence 999999999999988764
No 3
>KOG4104 consensus Ganglioside-induced differentiation associated protein 3 [Signal transduction mechanisms]
Probab=99.96 E-value=1.6e-29 Score=175.49 Aligned_cols=98 Identities=28% Similarity=0.443 Sum_probs=88.1
Q ss_pred chhhhhhhhHHHHHHHHHHHHhhhcccCCCCCCCchhHH--hhhcc--ccccccccCCCCCC--------ccCCCCCChH
Q 034124 4 GGRLKNILATVVTTGLTEARAKIFGHVLNPAGQRSPHKI--LRKKL--IGDKVAGWYPYDIK--------KDDPLVMARQ 71 (103)
Q Consensus 4 ~~~~~~~~s~~r~~~l~~ls~rIFg~~~nPt~~Rsg~kv--lr~~l--kG~~v~~YYP~~~~--------r~~g~~~De~ 71 (103)
+|.+-+.||. +..+|++||++|||+|.+|||.+|+++| ||+.| +-+++.+|||++.. |++|+|+|||
T Consensus 4 ~~~~is~~t~-ya~RM~rLSnRvfGEV~rpTn~KSmKVVr~fSeeP~~kk~~~~~wYPnh~~~h~Lmk~LRf~GLfrDeH 82 (113)
T KOG4104|consen 4 AGRGISQPTP-YAKRMDRLSNRVFGEVVRPTNTKSMKVVRVFSEEPYEKKEQLSKWYPNHPMFHYLMKMLRFHGLFRDEH 82 (113)
T ss_pred cccccCCccH-HHHHHHHHHHHHHhhccccCCCcceehhhhccccchhhHHHHHHhccCchHHHHHHHHHHHhhhhhhhH
Confidence 4445556665 8899999999999999999999999976 99999 56889999999653 8999999999
Q ss_pred HHHHHHHHHHHHhcCCCCCCCCCChhHhhhc
Q 034124 72 QQERLSKLEMLKRRGKGPPKKGQGKRAAKRS 102 (103)
Q Consensus 72 e~~R~~~~~~rk~RGKg~PKKg~gkra~kkk 102 (103)
++|++++.+++++|||.+||||+||||++++
T Consensus 83 qdF~deqkrLkklRGK~~PkkGeGKRA~kr~ 113 (113)
T KOG4104|consen 83 QDFRDEQKRLKKLRGKVVPKKGEGKRAQKRG 113 (113)
T ss_pred HHHHHHHHHHHHhcCCCCCCCCcchhhhhcC
Confidence 9999999999999999999999999999864
No 4
>PF12752 SUZ: SUZ domain; InterPro: IPR024771 The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterised in the Caenorhabditis elegans protein SZY-20 where it has been shown to bind RNA and allow their localization to the centrosome [].
Probab=61.10 E-value=8.5 Score=23.74 Aligned_cols=16 Identities=44% Similarity=0.617 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHhhhcc
Q 034124 14 VVTTGLTEARAKIFGH 29 (103)
Q Consensus 14 ~r~~~l~~ls~rIFg~ 29 (103)
+|-..-+++++||||.
T Consensus 42 ERE~eY~~AR~RIFg~ 57 (59)
T PF12752_consen 42 EREAEYAEARARIFGS 57 (59)
T ss_pred HHHHHHHHHHHHHhCC
Confidence 5666778999999996
No 5
>PF04844 Ovate: Transcriptional repressor, ovate; InterPro: IPR006458 This group of sequences contain an uncharacterised domain of about 70 residues found exclusively in plants, generally toward the C terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana (Mouse-ear cress). Other regions of these proteins tend to consist largely of low-complexity sequence. Function is not known.
Probab=32.26 E-value=54 Score=20.69 Aligned_cols=19 Identities=26% Similarity=0.319 Sum_probs=16.1
Q ss_pred CChHHHHHHHHHHHHHhcC
Q 034124 68 MARQQQERLSKLEMLKRRG 86 (103)
Q Consensus 68 ~De~e~~R~~~~~~rk~RG 86 (103)
.||.+|||..|+++-..+|
T Consensus 2 ~DP~~DFr~SM~EMI~~~~ 20 (59)
T PF04844_consen 2 SDPYEDFRESMVEMIEENG 20 (59)
T ss_pred CCHHHHHHHHHHHHHHHcC
Confidence 4899999999999877665
No 6
>TIGR03398 plc_access_R phospholipase C accessory protein PlcR. The class of microbial phosphocholine-preferring phospholipase C enzymes described by model TIGR03396 has two members in Pseudomonas aeruginosa, one of which (PlcH) is hemolytic and can hydrolyzes sphingomyelin as well as phosphatidylcholine. This model describes PlcR, an accessory protein for PlcH with which it forms a heterodimer. The member of the family from P. aeruginosa, although not the members from various Burkholderia species, is encoded immediately downstream of phospholipase C.
Probab=29.21 E-value=69 Score=23.58 Aligned_cols=29 Identities=21% Similarity=0.355 Sum_probs=19.9
Q ss_pred hhhhhhhH-----HHHHHHHHHHHhhhcccCCCCC
Q 034124 6 RLKNILAT-----VVTTGLTEARAKIFGHVLNPAG 35 (103)
Q Consensus 6 ~~~~~~s~-----~r~~~l~~ls~rIFg~~~nPt~ 35 (103)
++..+|.+ ++-++|..|+-.|||+ -+|..
T Consensus 106 V~asVpD~eQq~aaid~RL~aLR~Qifg~-~sp~~ 139 (141)
T TIGR03398 106 VQASVPDPEQQQAAIDQRLQALRVQIFGE-ASPSL 139 (141)
T ss_pred HHhcCCCHHHHHHHHHHHHHHHHHHHhcC-cCccc
Confidence 34455544 4567899999999997 44443
No 7
>PF06904 Extensin-like_C: Extensin-like protein C-terminus; InterPro: IPR009683 This entry represents the C terminus (approx. 120 residues) of a number of bacterial extensin-like proteins. Extensins are cell wall glycoproteins normally associated with plants, where they strengthen the cell wall in response to mechanical stress []. Many proteins in this entry are hypothetical.
Probab=26.06 E-value=67 Score=24.23 Aligned_cols=27 Identities=19% Similarity=0.255 Sum_probs=22.0
Q ss_pred hhHHHHHHHHHHHHhhhcccCCCCCCC
Q 034124 11 LATVVTTGLTEARAKIFGHVLNPAGQR 37 (103)
Q Consensus 11 ~s~~r~~~l~~ls~rIFg~~~nPt~~R 37 (103)
+..+-+..|..-.|..|++|..|..-.
T Consensus 131 ~~~~fl~~v~~~AC~~F~tVLgP~~na 157 (178)
T PF06904_consen 131 PEAAFLRAVRAGACGRFGTVLGPDYNA 157 (178)
T ss_pred hHHHHHHHHHHHHHhcCCcccCCCCch
Confidence 345678888999999999999987643
No 8
>PF07874 DUF1660: Prophage protein (DUF1660); InterPro: IPR012455 This entry is represented by Bacteriophage bIL285, Orf33. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=24.72 E-value=23 Score=22.92 Aligned_cols=13 Identities=31% Similarity=0.480 Sum_probs=11.0
Q ss_pred HHHHhhhcccCCC
Q 034124 21 EARAKIFGHVLNP 33 (103)
Q Consensus 21 ~ls~rIFg~~~nP 33 (103)
+|-|+||||.+-+
T Consensus 2 KL~CKLFGHKw~~ 14 (64)
T PF07874_consen 2 KLMCKLFGHKWTF 14 (64)
T ss_pred cchhhhcCCCCCC
Confidence 5789999998874
No 9
>PF14907 NTP_transf_5: Uncharacterised nucleotidyltransferase
Probab=24.07 E-value=38 Score=24.89 Aligned_cols=27 Identities=19% Similarity=0.160 Sum_probs=19.4
Q ss_pred cccccccccCCCCCCccCCC---CCChHHH
Q 034124 47 LIGDKVAGWYPYDIKKDDPL---VMARQQQ 73 (103)
Q Consensus 47 lkG~~v~~YYP~~~~r~~g~---~~De~e~ 73 (103)
+||..++.+||..-.|..++ ++.+++.
T Consensus 77 lKG~~l~~~Y~~~~~R~~~DiDlLV~~~d~ 106 (249)
T PF14907_consen 77 LKGAALAQLYPDPGLRPMGDIDLLVPPEDL 106 (249)
T ss_pred EchHHHHHhCCCCCCCCCCCeEEEEeCCcH
Confidence 48999999999876677764 5554443
No 10
>TIGR01568 A_thal_3678 uncharacterized plant-specific domain TIGR01568. This model describes an uncharacterized domain of about 70 residues found exclusively in plants, generally toward the C-terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana. Other regions of these proteins tend to consist largely of low-complexity sequence.
Probab=20.55 E-value=1.1e+02 Score=19.67 Aligned_cols=19 Identities=26% Similarity=0.169 Sum_probs=16.7
Q ss_pred CChHHHHHHHHHHHHHhcC
Q 034124 68 MARQQQERLSKLEMLKRRG 86 (103)
Q Consensus 68 ~De~e~~R~~~~~~rk~RG 86 (103)
.||.+|||..|+++-..+|
T Consensus 8 ~DPy~DFr~SM~EMI~~~~ 26 (66)
T TIGR01568 8 DDPYEDFRRSMEEMIEERE 26 (66)
T ss_pred CChHHHHHHHHHHHHHHcC
Confidence 5999999999999888775
No 11
>PRK13868 type IV secretion system single-stranded DNA binding protein VirE2; Provisional
Probab=20.34 E-value=64 Score=28.04 Aligned_cols=31 Identities=16% Similarity=0.427 Sum_probs=23.1
Q ss_pred hhhhhhhhHHHHHHHHHHHHhhhcccCCCCCCCchhHHhhhccccccccccCCCCC
Q 034124 5 GRLKNILATVVTTGLTEARAKIFGHVLNPAGQRSPHKILRKKLIGDKVAGWYPYDI 60 (103)
Q Consensus 5 ~~~~~~~s~~r~~~l~~ls~rIFg~~~nPt~~Rsg~kvlr~~lkG~~v~~YYP~~~ 60 (103)
|-|-.||+++- --++|+++-.- +-+||||+.
T Consensus 134 GnL~~lPTkaE----FNasCRLYRDG---------------------aGNYyPPPl 164 (556)
T PRK13868 134 GNLDHLPTKAE----FNASCRLYRDG---------------------AGNYYPPPL 164 (556)
T ss_pred cccccCCcHHH----hhhhhhheecC---------------------CCCcCCCch
Confidence 77888999976 45788877643 449999975
Done!