Query 037293
Match_columns 82
No_of_seqs 108 out of 230
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 10:46:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037293.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037293hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3424 40S ribosomal protein 100.0 3.3E-33 7E-38 194.6 4.5 75 2-76 54-131 (132)
2 PTZ00071 40S ribosomal protein 100.0 5.3E-31 1.1E-35 184.2 5.3 72 2-73 56-130 (132)
3 PRK01178 rps24e 30S ribosomal 99.8 7.9E-19 1.7E-23 117.5 4.2 44 2-45 50-96 (99)
4 PF01282 Ribosomal_S24e: Ribos 99.7 2.3E-18 5.1E-23 111.6 4.4 49 2-50 32-84 (84)
5 COG2004 RPS24A Ribosomal prote 99.6 1.3E-16 2.7E-21 108.7 4.5 52 2-58 51-105 (107)
6 smart00360 RRM RNA recognition 72.4 6.5 0.00014 20.9 3.1 25 9-33 29-54 (71)
7 PF00076 RRM_1: RNA recognitio 51.1 32 0.0007 18.8 3.4 21 13-33 34-55 (70)
8 PF09016 Pas_Saposin: Pas fact 46.8 1.6 3.4E-05 28.4 -2.8 24 21-44 3-30 (76)
9 smart00361 RRM_1 RNA recogniti 44.5 24 0.00051 20.8 2.3 18 15-32 34-52 (70)
10 PF14259 RRM_6: RNA recognitio 34.4 48 0.001 18.6 2.4 18 15-32 36-54 (70)
11 PRK03839 putative kinase; Prov 29.7 20 0.00044 24.2 0.3 15 1-18 1-15 (180)
12 TIGR02581 cas_cyan_RAMP CRISPR 29.3 29 0.00064 25.3 1.1 14 11-24 197-210 (217)
13 COG0070 GltB Glutamate synthas 28.9 42 0.00091 26.6 2.0 34 3-36 190-226 (301)
14 TIGR01661 ELAV_HUD_SF ELAV/HuD 27.3 48 0.001 24.5 2.0 18 14-31 307-325 (352)
15 PRK00625 shikimate kinase; Pro 25.6 28 0.00061 24.4 0.4 15 1-18 1-15 (173)
16 smart00362 RRM_2 RNA recogniti 25.0 93 0.002 16.2 2.4 18 15-32 36-54 (72)
17 KOG3883 Ras family small GTPas 22.9 45 0.00097 25.1 1.1 13 17-29 85-97 (198)
No 1
>KOG3424 consensus 40S ribosomal protein S24 [Translation, ribosomal structure and biogenesis]
Probab=99.98 E-value=3.3e-33 Score=194.64 Aligned_cols=75 Identities=40% Similarity=0.440 Sum_probs=72.2
Q ss_pred CeeeecccccCCCCeeeeEEEeecCHHHHhhcccc---cccCCcccccchhHHHHHHhhhhhhccchhhhhcchHHhh
Q 037293 2 PLPVNDHRNLVNAGRVTFAGWVFESVESKSRFSFS---FKNGLDTKAEKSRKQLKERKNMAKKIGGVKKTKASDAAKK 76 (82)
Q Consensus 2 ~I~VfgfrT~FGggkstGfa~IYDs~d~akk~Epk---~Rngl~ek~k~~Rkq~Ke~knr~KKvrGt~k~k~~~~~kk 76 (82)
+||||||+||||||+|||||+||||+|+|++|||+ +|+||.|+.+++|+||||++||++|++||.|++++.++++
T Consensus 54 ~V~vfgfrt~~GggkstgfalIYdsve~akkfEpkyrl~r~gl~e~~kt~RkqrKerknr~kKi~Gt~K~~~~~~~k~ 131 (132)
T KOG3424|consen 54 AVFVFGFRTHFGGGKSTGFALIYDSVEYAKKFEPKYRLVRLGLAEKIKTSRKQRKERKNRMKKIFGTGKRKAKKAKKK 131 (132)
T ss_pred eEEEEEeeeccCCcccceeeeeeehHHHHHhcCcceeeeecccccccccHHHHHHHHhhccchheeHHHHHhhhhhcc
Confidence 69999999999999999999999999999999999 9999999998899999999999999999999999877765
No 2
>PTZ00071 40S ribosomal protein S24; Provisional
Probab=99.97 E-value=5.3e-31 Score=184.20 Aligned_cols=72 Identities=28% Similarity=0.385 Sum_probs=68.7
Q ss_pred CeeeecccccCCCCeeeeEEEeecCHHHHhhcccc---cccCCcccccchhHHHHHHhhhhhhccchhhhhcchH
Q 037293 2 PLPVNDHRNLVNAGRVTFAGWVFESVESKSRFSFS---FKNGLDTKAEKSRKQLKERKNMAKKIGGVKKTKASDA 73 (82)
Q Consensus 2 ~I~VfgfrT~FGggkstGfa~IYDs~d~akk~Epk---~Rngl~ek~k~~Rkq~Ke~knr~KKvrGt~k~k~~~~ 73 (82)
+||||||+|+||+|+|+|||+||||+|+|++|||+ +||+|.+..+.+|+|+||+|||+||+||++++++..+
T Consensus 56 ~Vvv~~~~T~fG~g~StG~a~IYds~e~~kk~Epk~~l~Rngl~~~~~~~rk~rke~knr~kk~rg~~k~k~~~~ 130 (132)
T PTZ00071 56 TIVLFGFKTKFGGGKTTGFGLIYDNLAALKKFEPKYRLIRLGLIKKKKAGRKARKELKNRRKKVRGKEKTKVSGK 130 (132)
T ss_pred EEEEEccEecCCCceEEEEEEEECCHHHHHhhCchheeeecCccccCccchHHHHHHHhhhhhhccchhhhhhhc
Confidence 69999999999999999999999999999999999 9999999888899999999999999999999988544
No 3
>PRK01178 rps24e 30S ribosomal protein S24e; Reviewed
Probab=99.75 E-value=7.9e-19 Score=117.54 Aligned_cols=44 Identities=11% Similarity=0.137 Sum_probs=41.9
Q ss_pred CeeeecccccCCCCeeeeEEEeecCHHHHhhcccc---cccCCcccc
Q 037293 2 PLPVNDHRNLVNAGRVTFAGWVFESVESKSRFSFS---FKNGLDTKA 45 (82)
Q Consensus 2 ~I~VfgfrT~FGggkstGfa~IYDs~d~akk~Epk---~Rngl~ek~ 45 (82)
+||||||+|+||+|+|+|||+||||+|+|++|||+ .||++.+++
T Consensus 50 ~vvv~~~~t~fG~g~s~G~a~IYds~e~~kk~Epk~~l~Rn~~~~~~ 96 (99)
T PRK01178 50 LVVVRKIKTEYGMGKSKGYAKVYDDKERARKIEPKYILERNKIEEEE 96 (99)
T ss_pred EEEEEccCccCCCceEEEEEEEECCHHHHHhhCchheeeecCccccc
Confidence 59999999999999999999999999999999999 999998764
No 4
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 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 family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V94_B 1YWX_A 2G1D_A 3IZ6_U 1XN9_A 2XZM_P 2XZN_P 3U5G_Y 3J16_D 3IZB_U ....
Probab=99.73 E-value=2.3e-18 Score=111.60 Aligned_cols=49 Identities=27% Similarity=0.362 Sum_probs=43.9
Q ss_pred CeeeecccccCCCCeeeeEEEeecCHHHHhhcccc---cccCCccccc-chhH
Q 037293 2 PLPVNDHRNLVNAGRVTFAGWVFESVESKSRFSFS---FKNGLDTKAE-KSRK 50 (82)
Q Consensus 2 ~I~VfgfrT~FGggkstGfa~IYDs~d~akk~Epk---~Rngl~ek~k-~~Rk 50 (82)
+|||++|+|+||+|.|+|||+||||+|+|++|||+ .||++.++.. .+|+
T Consensus 32 ~ivv~~~~t~fG~~~s~g~a~IYd~~e~~kk~Ep~~~l~R~~~~e~~~~~~r~ 84 (84)
T PF01282_consen 32 LIVVFGIKTEFGGGKSTGFAKIYDSAEALKKFEPKYRLKRNGLEEKKEKEGRK 84 (84)
T ss_dssp CEEEEEEEESSSSSEEEEEEEEESSHHHHHHHSTHHHHHHTTSSSS-S-S-HH
T ss_pred eEEEeccEecCCCceEEEEEEEeCCHHHHHHhCcHHHhHhcCccccccccccC
Confidence 69999999999999999999999999999999999 9999999864 4553
No 5
>COG2004 RPS24A Ribosomal protein S24E [Translation, ribosomal structure and biogenesis]
Probab=99.65 E-value=1.3e-16 Score=108.70 Aligned_cols=52 Identities=21% Similarity=0.242 Sum_probs=48.7
Q ss_pred CeeeecccccCCCCeeeeEEEeecCHHHHhhcccc---cccCCcccccchhHHHHHHhhh
Q 037293 2 PLPVNDHRNLVNAGRVTFAGWVFESVESKSRFSFS---FKNGLDTKAEKSRKQLKERKNM 58 (82)
Q Consensus 2 ~I~VfgfrT~FGggkstGfa~IYDs~d~akk~Epk---~Rngl~ek~k~~Rkq~Ke~knr 58 (82)
+|+|++++|+||+|+|+|||+||||.+.|++|||+ +||+. ..+.+++|.+||
T Consensus 51 ~VvV~~ikt~fG~~~s~g~akIY~s~e~~~~iEp~yiL~Rn~~-----~~~~~~eE~e~r 105 (107)
T COG2004 51 LVVVDYIKTEFGKGRSKGYAKIYDSVERAKKIEPEYILERNGG-----AERQEAEEAENR 105 (107)
T ss_pred eEEEEehhhhcCCcceeEEEEEECCHHHHHhcCcceEEEeccc-----hhhhhhHhhhcc
Confidence 68999999999999999999999999999999999 99998 467888888888
No 6
>smart00360 RRM RNA recognition motif.
Probab=72.44 E-value=6.5 Score=20.85 Aligned_cols=25 Identities=24% Similarity=0.255 Sum_probs=17.8
Q ss_pred cccCCCCeeeeEEEe-ecCHHHHhhc
Q 037293 9 RNLVNAGRVTFAGWV-FESVESKSRF 33 (82)
Q Consensus 9 rT~FGggkstGfa~I-YDs~d~akk~ 33 (82)
......+.+.|||+| |++.+.|...
T Consensus 29 ~~~~~~~~~~~~a~v~f~~~~~a~~a 54 (71)
T smart00360 29 VRDKDTGKSKGFAFVEFESEEDAEKA 54 (71)
T ss_pred EeCCCCCCCCceEEEEeCCHHHHHHH
Confidence 344446788899988 7888877653
No 7
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=51.07 E-value=32 Score=18.84 Aligned_cols=21 Identities=29% Similarity=0.409 Sum_probs=16.1
Q ss_pred CCCeeeeEEEe-ecCHHHHhhc
Q 037293 13 NAGRVTFAGWV-FESVESKSRF 33 (82)
Q Consensus 13 GggkstGfa~I-YDs~d~akk~ 33 (82)
..+.+.|||.| |+|.++|...
T Consensus 34 ~~~~~~~~a~V~F~~~~~a~~a 55 (70)
T PF00076_consen 34 SSGKSKGYAFVEFESEEDAEKA 55 (70)
T ss_dssp TTSSEEEEEEEEESSHHHHHHH
T ss_pred ccccccceEEEEEcCHHHHHHH
Confidence 77888889887 7888777653
No 8
>PF09016 Pas_Saposin: Pas factor saposin fold; InterPro: IPR015106 Members of this entry adopt a compact structure comprising five alpha helices. Charged and polar residues are exposed mostly on the surface, while most of the hydrophobic residues are buried inside the hydrophobic core of the helical bundle. The precise function of this domain is unknown, but it is has been shown to induce secretion of periplasmic proteins, especially collagenase []. ; PDB: 2B8I_A.
Probab=46.83 E-value=1.6 Score=28.43 Aligned_cols=24 Identities=4% Similarity=0.159 Sum_probs=19.7
Q ss_pred EEeecCHHHHhhcccc----cccCCccc
Q 037293 21 GWVFESVESKSRFSFS----FKNGLDTK 44 (82)
Q Consensus 21 a~IYDs~d~akk~Epk----~Rngl~ek 44 (82)
.+|||++..+..-||. +|..|+|.
T Consensus 3 tlIYdTL~~LA~~ePeqhA~IRQ~LYeq 30 (76)
T PF09016_consen 3 TLIYDTLINLANQEPEQHAQIRQNLYEQ 30 (76)
T ss_dssp HHHHHHHHHHHHS-GGGHHHHHHHHHHH
T ss_pred hHHHHHHHHHHccChHHHHHHHHHHHHH
Confidence 3799999999999999 88887764
No 9
>smart00361 RRM_1 RNA recognition motif.
Probab=44.54 E-value=24 Score=20.75 Aligned_cols=18 Identities=22% Similarity=0.305 Sum_probs=12.5
Q ss_pred CeeeeEEEe-ecCHHHHhh
Q 037293 15 GRVTFAGWV-FESVESKSR 32 (82)
Q Consensus 15 gkstGfa~I-YDs~d~akk 32 (82)
|.+.||+.| |+|.+.|.+
T Consensus 34 ~~~rG~~fV~f~~~~dA~~ 52 (70)
T smart00361 34 NHKRGNVYITFERSEDAAR 52 (70)
T ss_pred CCCcEEEEEEECCHHHHHH
Confidence 556788888 677776654
No 10
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=34.40 E-value=48 Score=18.65 Aligned_cols=18 Identities=33% Similarity=0.425 Sum_probs=13.0
Q ss_pred CeeeeEEEe-ecCHHHHhh
Q 037293 15 GRVTFAGWV-FESVESKSR 32 (82)
Q Consensus 15 gkstGfa~I-YDs~d~akk 32 (82)
|.++|+|+| |.|.+.|..
T Consensus 36 ~~~~~~a~v~f~~~~~a~~ 54 (70)
T PF14259_consen 36 GQSRGFAFVEFSSEEDAKR 54 (70)
T ss_dssp SSEEEEEEEEESSHHHHHH
T ss_pred cccCCEEEEEeCCHHHHHH
Confidence 577888888 567776654
No 11
>PRK03839 putative kinase; Provisional
Probab=29.72 E-value=20 Score=24.24 Aligned_cols=15 Identities=20% Similarity=0.437 Sum_probs=11.8
Q ss_pred CCeeeecccccCCCCeee
Q 037293 1 MPLPVNDHRNLVNAGRVT 18 (82)
Q Consensus 1 ~~I~VfgfrT~FGggkst 18 (82)
|.|+|.|+- |.||||
T Consensus 1 m~I~l~G~p---GsGKsT 15 (180)
T PRK03839 1 MIIAITGTP---GVGKTT 15 (180)
T ss_pred CEEEEECCC---CCCHHH
Confidence 678888875 888885
No 12
>TIGR02581 cas_cyan_RAMP CRISPR-associated RAMP protein, SSO1426 family. Members of this CRISPR-associated (cas) gene family are found in the RAMP-2 subtype of CRISPR/cas locus and designated TM1809 family.
Probab=29.26 E-value=29 Score=25.34 Aligned_cols=14 Identities=14% Similarity=0.119 Sum_probs=12.6
Q ss_pred cCCCCeeeeEEEee
Q 037293 11 LVNAGRVTFAGWVF 24 (82)
Q Consensus 11 ~FGggkstGfa~IY 24 (82)
.+|+++|.||+.|-
T Consensus 197 ~lGg~~srG~G~v~ 210 (217)
T TIGR02581 197 FIGGKKSRGFGLVK 210 (217)
T ss_pred eeCCCCCeeceEEE
Confidence 69999999999884
No 13
>COG0070 GltB Glutamate synthase domain 3 [Amino acid transport and metabolism]
Probab=28.88 E-value=42 Score=26.55 Aligned_cols=34 Identities=18% Similarity=0.039 Sum_probs=24.5
Q ss_pred eeeeccccc-CCCCeeeeEEEeecCHHH--Hhhcccc
Q 037293 3 LPVNDHRNL-VNAGRVTFAGWVFESVES--KSRFSFS 36 (82)
Q Consensus 3 I~VfgfrT~-FGggkstGfa~IYDs~d~--akk~Epk 36 (82)
|+|.|---. ||.|.|-|++.|||+.++ ..+..+.
T Consensus 190 VvVLG~~G~nfgaGMsGG~aYV~~~~~~~f~~~~n~~ 226 (301)
T COG0070 190 VVVLGDTGRNFGAGMSGGVAYVRGEVGSDFPLGVNAE 226 (301)
T ss_pred EEEeCCcchhhcCcccceEEEEecCccchhhcCccce
Confidence 555554444 999999999999999973 3444444
No 14
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=27.33 E-value=48 Score=24.53 Aligned_cols=18 Identities=11% Similarity=0.255 Sum_probs=13.9
Q ss_pred CCeeeeEEEe-ecCHHHHh
Q 037293 14 AGRVTFAGWV-FESVESKS 31 (82)
Q Consensus 14 ggkstGfa~I-YDs~d~ak 31 (82)
.|.+.|||.| |+|.++|.
T Consensus 307 t~~skG~aFV~F~~~~~A~ 325 (352)
T TIGR01661 307 TNQCKGYGFVSMTNYDEAA 325 (352)
T ss_pred CCCccceEEEEECCHHHHH
Confidence 5778899987 78877664
No 15
>PRK00625 shikimate kinase; Provisional
Probab=25.63 E-value=28 Score=24.45 Aligned_cols=15 Identities=13% Similarity=0.244 Sum_probs=12.5
Q ss_pred CCeeeecccccCCCCeee
Q 037293 1 MPLPVNDHRNLVNAGRVT 18 (82)
Q Consensus 1 ~~I~VfgfrT~FGggkst 18 (82)
|||++.|| .|.||||
T Consensus 1 ~~I~LiG~---pGsGKTT 15 (173)
T PRK00625 1 MQIFLCGL---PTVGKTS 15 (173)
T ss_pred CEEEEECC---CCCCHHH
Confidence 78999998 4888887
No 16
>smart00362 RRM_2 RNA recognition motif.
Probab=25.02 E-value=93 Score=16.23 Aligned_cols=18 Identities=33% Similarity=0.481 Sum_probs=11.5
Q ss_pred CeeeeEEEe-ecCHHHHhh
Q 037293 15 GRVTFAGWV-FESVESKSR 32 (82)
Q Consensus 15 gkstGfa~I-YDs~d~akk 32 (82)
+.+.|+|+| |++.+.+..
T Consensus 36 ~~~~~~~~v~f~~~~~a~~ 54 (72)
T smart00362 36 GKSKGFAFVEFESEEDAEK 54 (72)
T ss_pred CCCCceEEEEeCCHHHHHH
Confidence 556677766 667666654
No 17
>KOG3883 consensus Ras family small GTPase [Signal transduction mechanisms]
Probab=22.92 E-value=45 Score=25.08 Aligned_cols=13 Identities=8% Similarity=0.138 Sum_probs=10.3
Q ss_pred eeeEEEeecCHHH
Q 037293 17 VTFAGWVFESVES 29 (82)
Q Consensus 17 stGfa~IYDs~d~ 29 (82)
+.||.+||++.|.
T Consensus 85 aDafVLVYs~~d~ 97 (198)
T KOG3883|consen 85 ADAFVLVYSPMDP 97 (198)
T ss_pred CceEEEEecCCCH
Confidence 5789999987653
Done!