Query 044565
Match_columns 99
No_of_seqs 104 out of 173
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 04:32:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044565.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044565hhsearch_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 2.4E-36 5.2E-41 201.5 7.6 79 10-88 1-87 (87)
2 KOG4844 Mitochondrial ribosoma 100.0 2.5E-31 5.5E-36 180.4 6.9 93 7-99 2-102 (102)
3 KOG4104 Ganglioside-induced di 100.0 7.6E-29 1.6E-33 170.2 5.9 92 6-98 10-113 (113)
4 PF12752 SUZ: SUZ domain; Int 61.7 8.2 0.00018 23.5 2.2 16 10-25 42-57 (59)
5 PF04844 Ovate: Transcriptiona 36.4 43 0.00093 20.9 2.6 19 64-82 2-20 (59)
6 PF07874 DUF1660: Prophage pro 29.5 17 0.00036 23.3 -0.1 13 17-29 2-14 (64)
7 PF14907 NTP_transf_5: Unchara 29.0 34 0.00073 24.9 1.4 27 43-69 77-106 (249)
8 PF06904 Extensin-like_C: Exte 27.4 59 0.0013 24.2 2.5 26 8-33 132-157 (178)
9 TIGR01568 A_thal_3678 uncharac 24.3 89 0.0019 19.9 2.5 20 63-82 7-26 (66)
10 TIGR02682 cas_csx11 CRISPR-ass 17.3 75 0.0016 29.5 1.5 26 3-28 481-506 (918)
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=2.4e-36 Score=201.47 Aligned_cols=79 Identities=47% Similarity=0.654 Sum_probs=73.6
Q ss_pred HHHHHHHHHHHhhhCcCCCCCCCCchhhHhhccccchhhhccCCCCCc--------ccCCCCcChHHHHHHHHHHHHHhc
Q 044565 10 IVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDIK--------KDDPLVMARQEQERLSKLEILKRR 81 (99)
Q Consensus 10 ~r~~~l~~ls~rIFg~~~nPt~~Rsg~kvlr~~lkg~~~~~YYP~~~~--------r~~g~~~De~e~~R~~~~~~~k~R 81 (99)
.|+++|++|||+|||+++|||++|||+|||+++|+|++|++|||+++. ..+++|+||||++|+++++++++|
T Consensus 1 ~r~~~l~~ls~rIFg~~~nP~~~Rsg~Kilr~~lkg~~~~~YYP~~~~~~~~l~~l~~~~~~~De~e~~R~e~~~~rk~R 80 (87)
T PF08293_consen 1 NRLLRLARLSARIFGTVYNPTGSRSGNKILRKRLKGPKLASYYPPHIVTFKLLKRLRPDGLFRDEHEDFREEMVELRKRR 80 (87)
T ss_pred CHHHHHHHHHHHHhCCCCCCccchHHHHHHhhcCCCchHhHhCCCcchHHHHHHHHccccCcCChhHHHHHHHHHHHHhC
Confidence 378999999999999999999999999999999999999999998763 344569999999999999999999
Q ss_pred CCCCCCC
Q 044565 82 GKGPPKK 88 (99)
Q Consensus 82 GKg~PKK 88 (99)
|||+|||
T Consensus 81 GKg~PKK 87 (87)
T PF08293_consen 81 GKGPPKK 87 (87)
T ss_pred CCCCCCC
Confidence 9999997
No 2
>KOG4844 consensus Mitochondrial ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=2.5e-31 Score=180.41 Aligned_cols=93 Identities=59% Similarity=0.807 Sum_probs=85.3
Q ss_pred ch-HHHHHHHHHHHHhhhCcCCCCCCCCchhhHhhccccchhhhccCCCCC-cccCC------CCcChHHHHHHHHHHHH
Q 044565 7 FA-TIVTTGLTEARAKIFGHVLNLTGQRSPHKILRKKLIDDKVAGWYPYDI-KKDDP------LVMARQEQERLSKLEIL 78 (99)
Q Consensus 7 ~s-~~r~~~l~~ls~rIFg~~~nPt~~Rsg~kvlr~~lkg~~~~~YYP~~~-~r~~g------~~~De~e~~R~~~~~~~ 78 (99)
.| +|+++.++.||++||||.||||++|||+|||+++|+|+.|++|||+.+ ++.++ .|.|-+|+.|+++++++
T Consensus 2 as~kAvl~~v~elsakIFg~~~np~g~Rtg~Kil~~~LkG~kvasyYp~~~~~r~l~tll~d~ef~d~~e~~R~s~~e~~ 81 (102)
T KOG4844|consen 2 ASGKAVLRGVTELSAKIFGHMLNPTGQRTGHKILRKKLKGDKVASYYPPYDIKRELPTLLADEEFDDIAEWGRISKLEML 81 (102)
T ss_pred cchHHHHHHHHHHHHHHHhcccCCCCCcchhHHHHHHhccchHhhhcchHHhhhhhhhhhcccccccHHHHHHHHHHHHH
Confidence 44 899999999999999999999999999999999999999999999854 46555 28889999999999999
Q ss_pred HhcCCCCCCCCCchhHhhhcC
Q 044565 79 KRRGKGPPKKGQGRRAAKRSK 99 (99)
Q Consensus 79 k~RGKg~PKKg~gkra~kkk~ 99 (99)
++||||+|||+++++|.+.++
T Consensus 82 kRrgKGapKk~kk~~aa~~~~ 102 (102)
T KOG4844|consen 82 KRRGKGAPKKGKKKRAAKRNK 102 (102)
T ss_pred HHccCCCCcccchhhhhhccC
Confidence 999999999999999998764
No 3
>KOG4104 consensus Ganglioside-induced differentiation associated protein 3 [Signal transduction mechanisms]
Probab=99.95 E-value=7.6e-29 Score=170.24 Aligned_cols=92 Identities=25% Similarity=0.413 Sum_probs=83.9
Q ss_pred cchHHHHHHHHHHHHhhhCcCCCCCCCCchhhH--hhccc--cchhhhccCCCCCc--------ccCCCCcChHHHHHHH
Q 044565 6 FFATIVTTGLTEARAKIFGHVLNLTGQRSPHKI--LRKKL--IDDKVAGWYPYDIK--------KDDPLVMARQEQERLS 73 (99)
Q Consensus 6 ~~s~~r~~~l~~ls~rIFg~~~nPt~~Rsg~kv--lr~~l--kg~~~~~YYP~~~~--------r~~g~~~De~e~~R~~ 73 (99)
.||. +..+|++||++|||+|.+|||.+|+++| ||+.| +-+++.+|||++.. |++|+|+|||++|+.+
T Consensus 10 ~~t~-ya~RM~rLSnRvfGEV~rpTn~KSmKVVr~fSeeP~~kk~~~~~wYPnh~~~h~Lmk~LRf~GLfrDeHqdF~de 88 (113)
T KOG4104|consen 10 QPTP-YAKRMDRLSNRVFGEVVRPTNTKSMKVVRVFSEEPYEKKEQLSKWYPNHPMFHYLMKMLRFHGLFRDEHQDFRDE 88 (113)
T ss_pred CccH-HHHHHHHHHHHHHhhccccCCCcceehhhhccccchhhHHHHHHhccCchHHHHHHHHHHHhhhhhhhHHHHHHH
Confidence 3444 7889999999999999999999999976 99999 56889999999642 9999999999999999
Q ss_pred HHHHHHhcCCCCCCCCCchhHhhhc
Q 044565 74 KLEILKRRGKGPPKKGQGRRAAKRS 98 (99)
Q Consensus 74 ~~~~~k~RGKg~PKKg~gkra~kkk 98 (99)
+.+++++|||.+||||+||||++++
T Consensus 89 qkrLkklRGK~~PkkGeGKRA~kr~ 113 (113)
T KOG4104|consen 89 QKRLKKLRGKVVPKKGEGKRAQKRG 113 (113)
T ss_pred HHHHHHhcCCCCCCCCcchhhhhcC
Confidence 9999999999999999999999864
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=61.71 E-value=8.2 Score=23.54 Aligned_cols=16 Identities=44% Similarity=0.601 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHhhhCc
Q 044565 10 IVTTGLTEARAKIFGH 25 (99)
Q Consensus 10 ~r~~~l~~ls~rIFg~ 25 (99)
+|-..-+++++||||.
T Consensus 42 ERE~eY~~AR~RIFg~ 57 (59)
T PF12752_consen 42 EREAEYAEARARIFGS 57 (59)
T ss_pred HHHHHHHHHHHHHhCC
Confidence 5667778999999996
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=36.43 E-value=43 Score=20.88 Aligned_cols=19 Identities=26% Similarity=0.321 Sum_probs=16.2
Q ss_pred cChHHHHHHHHHHHHHhcC
Q 044565 64 MARQEQERLSKLEILKRRG 82 (99)
Q Consensus 64 ~De~e~~R~~~~~~~k~RG 82 (99)
.||.+|||..|+++-..+|
T Consensus 2 ~DP~~DFr~SM~EMI~~~~ 20 (59)
T PF04844_consen 2 SDPYEDFRESMVEMIEENG 20 (59)
T ss_pred CCHHHHHHHHHHHHHHHcC
Confidence 4899999999999877665
No 6
>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=29.54 E-value=17 Score=23.28 Aligned_cols=13 Identities=31% Similarity=0.629 Sum_probs=11.0
Q ss_pred HHHHhhhCcCCCC
Q 044565 17 EARAKIFGHVLNL 29 (99)
Q Consensus 17 ~ls~rIFg~~~nP 29 (99)
.|-|+||||.+-+
T Consensus 2 KL~CKLFGHKw~~ 14 (64)
T PF07874_consen 2 KLMCKLFGHKWTF 14 (64)
T ss_pred cchhhhcCCCCCC
Confidence 5889999998874
No 7
>PF14907 NTP_transf_5: Uncharacterised nucleotidyltransferase
Probab=28.98 E-value=34 Score=24.94 Aligned_cols=27 Identities=15% Similarity=0.102 Sum_probs=19.3
Q ss_pred ccchhhhccCCCCCcccCCC---CcChHHH
Q 044565 43 LIDDKVAGWYPYDIKKDDPL---VMARQEQ 69 (99)
Q Consensus 43 lkg~~~~~YYP~~~~r~~g~---~~De~e~ 69 (99)
+||..++.+||..-.|..++ ++.+++.
T Consensus 77 lKG~~l~~~Y~~~~~R~~~DiDlLV~~~d~ 106 (249)
T PF14907_consen 77 LKGAALAQLYPDPGLRPMGDIDLLVPPEDL 106 (249)
T ss_pred EchHHHHHhCCCCCCCCCCCeEEEEeCCcH
Confidence 48999999999865577764 5554443
No 8
>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=27.43 E-value=59 Score=24.24 Aligned_cols=26 Identities=15% Similarity=0.160 Sum_probs=21.5
Q ss_pred hHHHHHHHHHHHHhhhCcCCCCCCCC
Q 044565 8 ATIVTTGLTEARAKIFGHVLNLTGQR 33 (99)
Q Consensus 8 s~~r~~~l~~ls~rIFg~~~nPt~~R 33 (99)
..+-|..|....|..|++|..|..-.
T Consensus 132 ~~~fl~~v~~~AC~~F~tVLgP~~na 157 (178)
T PF06904_consen 132 EAAFLRAVRAGACGRFGTVLGPDYNA 157 (178)
T ss_pred HHHHHHHHHHHHHhcCCcccCCCCch
Confidence 45668888999999999999987644
No 9
>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=24.28 E-value=89 Score=19.93 Aligned_cols=20 Identities=25% Similarity=0.145 Sum_probs=17.1
Q ss_pred CcChHHHHHHHHHHHHHhcC
Q 044565 63 VMARQEQERLSKLEILKRRG 82 (99)
Q Consensus 63 ~~De~e~~R~~~~~~~k~RG 82 (99)
-.||.+|||..|+++-..+|
T Consensus 7 S~DPy~DFr~SM~EMI~~~~ 26 (66)
T TIGR01568 7 SDDPYEDFRRSMEEMIEERE 26 (66)
T ss_pred CCChHHHHHHHHHHHHHHcC
Confidence 35999999999999988775
No 10
>TIGR02682 cas_csx11 CRISPR-associated protein, Csx11 family. Members of this uncommon, sporadically distributed protein family are large (900 amino acids) and strictly associated, so far, with CRISPR-associated (Cas) gene clusters. Nearby Cas genes always include members of the RAMP superfamily and the six-gene CRISPR-associated RAMP module. Species in which it is found, so far, include three archaea (Methanosarcina mazei, M. barkeri and Methanobacterium thermoautotrophicum) and two bacteria (Thermodesulfovibrio yellowstonii DSM 11347 and Sulfurihydrogenibium azorense).
Probab=17.29 E-value=75 Score=29.54 Aligned_cols=26 Identities=15% Similarity=0.153 Sum_probs=22.6
Q ss_pred ccccchHHHHHHHHHHHHhhhCcCCC
Q 044565 3 LRTFFATIVTTGLTEARAKIFGHVLN 28 (99)
Q Consensus 3 ~~~~~s~~r~~~l~~ls~rIFg~~~n 28 (99)
+++-||+|||.++-+.-..-|.++.+
T Consensus 481 ~rKnPSpARLrRIWeTT~eFf~~v~~ 506 (918)
T TIGR02682 481 FRKNPSPARLRRIWETTENFFEEILI 506 (918)
T ss_pred hcCCCChHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999998887654
Done!