Query psy16814
Match_columns 124
No_of_seqs 133 out of 563
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 22:46:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16814.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16814hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4122|consensus 99.9 1.4E-24 3E-29 134.8 1.7 38 66-103 1-38 (38)
2 PF00444 Ribosomal_L36: Riboso 99.9 6.8E-24 1.5E-28 131.6 3.6 38 66-103 1-38 (38)
3 COG0257 RpmJ Ribosomal protein 99.9 2.9E-23 6.2E-28 129.3 3.6 38 66-103 1-38 (38)
4 PRK00465 rpmJ 50S ribosomal pr 99.9 3E-23 6.5E-28 128.4 3.4 37 66-103 1-37 (37)
5 TIGR01022 rpmJ_bact ribosomal 99.9 1.2E-22 2.6E-27 125.7 3.3 37 66-103 1-37 (37)
6 PRK00831 rpmJ 50S ribosomal pr 99.8 3.6E-22 7.7E-27 126.0 3.1 38 66-103 1-41 (41)
7 CHL00029 rpl36 ribosomal prote 99.3 9.2E-13 2E-17 76.2 2.3 26 66-91 1-26 (26)
8 PF13018 ESPR: Extended Signal 67.5 2.1 4.4E-05 24.3 0.3 16 1-21 1-16 (24)
9 cd00472 Ribosomal_L24e_L24 Rib 44.7 13 0.00028 24.4 1.2 34 80-113 20-53 (54)
10 PRK00807 50S ribosomal protein 41.4 16 0.00035 23.5 1.2 33 80-112 18-50 (52)
11 PRK14891 50S ribosomal protein 35.8 13 0.00027 28.9 0.1 36 79-114 20-55 (131)
12 KOG2463|consensus 32.5 11 0.00024 33.5 -0.8 34 49-83 217-252 (376)
13 PF12762 DDE_Tnp_IS1595: ISXO2 31.2 52 0.0011 23.4 2.7 27 93-119 18-44 (151)
14 PF04945 YHS: YHS domain; Int 29.0 89 0.0019 18.8 3.1 27 61-93 3-29 (47)
15 KOG1774|consensus 28.8 23 0.0005 25.9 0.5 14 1-14 14-30 (88)
16 PF14836 Ubiquitin_3: Ubiquiti 27.4 29 0.00063 24.9 0.8 26 1-27 33-60 (88)
17 COG3012 Uncharacterized protei 23.5 71 0.0015 25.4 2.3 43 54-96 88-130 (151)
18 cd01278 aprataxin_related apra 20.6 1.9E+02 0.0041 19.3 3.8 30 78-115 15-44 (104)
No 1
>KOG4122|consensus
Probab=99.89 E-value=1.4e-24 Score=134.83 Aligned_cols=38 Identities=45% Similarity=0.827 Sum_probs=37.4
Q ss_pred ceEecceeccCCCceEEEeCCEEEEEcCCCCCcccccC
Q psy16814 66 WKYKAKVKKRCKGCYFLYKEGVLHNLCHLKPKHKQILF 103 (124)
Q Consensus 66 MKVrsSlKkrC~~C~vVRR~gRlyViCk~nPRHKQRQg 103 (124)
|||++|||++|+|||+|+|+||+||||++|||||||||
T Consensus 1 fKvk~svkk~C~~Cy~VrRrgR~yViC~~~prHKqrqg 38 (38)
T KOG4122|consen 1 FKVKASVKKRCKDCYLVRRRGRVYVICKTHPRHKQRQG 38 (38)
T ss_pred CchhHHHHHhhhhceEEEEcccEEEEcCCCcchhhhcC
Confidence 89999999999999999999999999999999999997
No 2
>PF00444 Ribosomal_L36: Ribosomal protein L36; InterPro: IPR000473 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 [, ]. Ribosomal protein L36 is the smallest protein from the large subunit of the prokaryotic ribosome. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [] can be grouped into: bacterial L36; algal and plant chloroplast L36; Cyanelle L36. L36 is a small basic and cysteine-rich protein of 37 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBO_6 2HGU_8 2HGJ_8 1DGZ_A 1DFE_A 2HGQ_8 1VSP_b 1VSA_b 3PIP_4 1VOU_6 ....
Probab=99.89 E-value=6.8e-24 Score=131.55 Aligned_cols=38 Identities=39% Similarity=0.761 Sum_probs=33.9
Q ss_pred ceEecceeccCCCceEEEeCCEEEEEcCCCCCcccccC
Q psy16814 66 WKYKAKVKKRCKGCYFLYKEGVLHNLCHLKPKHKQILF 103 (124)
Q Consensus 66 MKVrsSlKkrC~~C~vVRR~gRlyViCk~nPRHKQRQg 103 (124)
|||++||+++|++|++|+|+||+||||++|||||||||
T Consensus 1 MKVr~slk~~c~~C~~vrR~gr~~Vick~nprhKqrQg 38 (38)
T PF00444_consen 1 MKVRSSLKKRCKDCYVVRRKGRLYVICKKNPRHKQRQG 38 (38)
T ss_dssp -BESSS-S-SSSTSEEEEETTEEEEEESSSGGGCEEE-
T ss_pred CcchhhhhhcCCCCceEEECCEEEEECCCCCchhccCC
Confidence 99999999999999999999999999999999999997
No 3
>COG0257 RpmJ Ribosomal protein L36 [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=2.9e-23 Score=129.25 Aligned_cols=38 Identities=39% Similarity=0.689 Sum_probs=37.5
Q ss_pred ceEecceeccCCCceEEEeCCEEEEEcCCCCCcccccC
Q psy16814 66 WKYKAKVKKRCKGCYFLYKEGVLHNLCHLKPKHKQILF 103 (124)
Q Consensus 66 MKVrsSlKkrC~~C~vVRR~gRlyViCk~nPRHKQRQg 103 (124)
|||++|+|++|++|++|||+|++||||++|||||||||
T Consensus 1 MKV~~SvK~~c~~CkivrRkGrv~VIck~~prhKqrQg 38 (38)
T COG0257 1 MKVRASVKKRCRDCKIVRRKGRVYVICKKNPKHKQRQG 38 (38)
T ss_pred CccccccccccCCceEEEecCEEEEEeCCCcchhhhcC
Confidence 99999999999999999999999999999999999997
No 4
>PRK00465 rpmJ 50S ribosomal protein L36; Reviewed
Probab=99.87 E-value=3e-23 Score=128.37 Aligned_cols=37 Identities=41% Similarity=0.679 Sum_probs=36.3
Q ss_pred ceEecceeccCCCceEEEeCCEEEEEcCCCCCcccccC
Q psy16814 66 WKYKAKVKKRCKGCYFLYKEGVLHNLCHLKPKHKQILF 103 (124)
Q Consensus 66 MKVrsSlKkrC~~C~vVRR~gRlyViCk~nPRHKQRQg 103 (124)
|||++|||++|++|++|||+|++|||| +|||||||||
T Consensus 1 MKVr~SvKk~c~~C~vvrR~gr~~Vic-~nprhKqRQg 37 (37)
T PRK00465 1 MKVRASVKKICEKCKVIKRKGVVRVIC-ENPKHKQRQG 37 (37)
T ss_pred CcchhhhhhcCCCCEEEEECCEEEEEc-CCCCcccccC
Confidence 999999999999999999999999999 7999999997
No 5
>TIGR01022 rpmJ_bact ribosomal protein L36, bacterial type. Proteins found by this model occur exclusively in bacteria and organelles.
Probab=99.86 E-value=1.2e-22 Score=125.72 Aligned_cols=37 Identities=41% Similarity=0.718 Sum_probs=36.1
Q ss_pred ceEecceeccCCCceEEEeCCEEEEEcCCCCCcccccC
Q psy16814 66 WKYKAKVKKRCKGCYFLYKEGVLHNLCHLKPKHKQILF 103 (124)
Q Consensus 66 MKVrsSlKkrC~~C~vVRR~gRlyViCk~nPRHKQRQg 103 (124)
|||++|||++|++|++|||+|++||||+ |||||||||
T Consensus 1 MKVr~SvKk~c~~C~vvrR~grv~Vick-~prhKqRQG 37 (37)
T TIGR01022 1 MKVRASVKKICEKCKIIKRKGVVRVICK-NPKHKQRQG 37 (37)
T ss_pred CcchhhhhhhCcCCeEEEECCEEEEEeC-CCCccccCC
Confidence 9999999999999999999999999998 799999997
No 6
>PRK00831 rpmJ 50S ribosomal protein L36; Validated
Probab=99.85 E-value=3.6e-22 Score=125.98 Aligned_cols=38 Identities=18% Similarity=0.308 Sum_probs=36.5
Q ss_pred ceEecceec---cCCCceEEEeCCEEEEEcCCCCCcccccC
Q psy16814 66 WKYKAKVKK---RCKGCYFLYKEGVLHNLCHLKPKHKQILF 103 (124)
Q Consensus 66 MKVrsSlKk---rC~~C~vVRR~gRlyViCk~nPRHKQRQg 103 (124)
|||++|||+ +|++|++|||+|++||||++|||||||||
T Consensus 1 MKVr~SvKk~~~~~~~c~vvrR~grv~Vick~nprhKqRQG 41 (41)
T PRK00831 1 MKVRNSLKSLKNRHRDCQVVRRKGRVYVINKKNPRFKARQG 41 (41)
T ss_pred CchhhhhhhhhccCCCCEEEEeCCEEEEEcCCCCcccccCC
Confidence 999999999 56999999999999999999999999997
No 7
>CHL00029 rpl36 ribosomal protein L36
Probab=99.31 E-value=9.2e-13 Score=76.19 Aligned_cols=26 Identities=27% Similarity=0.627 Sum_probs=25.5
Q ss_pred ceEecceeccCCCceEEEeCCEEEEE
Q psy16814 66 WKYKAKVKKRCKGCYFLYKEGVLHNL 91 (124)
Q Consensus 66 MKVrsSlKkrC~~C~vVRR~gRlyVi 91 (124)
|||++|||++|++|++|||+|++|||
T Consensus 1 MKVr~Svkk~c~~c~ivrR~g~v~Vi 26 (26)
T CHL00029 1 MKIRASVRKICEKCRLIRRRGRIFVI 26 (26)
T ss_pred CcccccccccCCCCEEEeecCEEEEC
Confidence 99999999999999999999999996
No 8
>PF13018 ESPR: Extended Signal Peptide of Type V secretion system
Probab=67.52 E-value=2.1 Score=24.28 Aligned_cols=16 Identities=38% Similarity=0.802 Sum_probs=11.9
Q ss_pred Chhhhhhhhhcceeeecccee
Q psy16814 1 MNKIFKIFQSTLVINNVQRTF 21 (124)
Q Consensus 1 ~~~~~~~~q~~~~~n~~~r~F 21 (124)
|||||++ +||.+...+
T Consensus 1 MNkiyr~-----iwn~~~~~~ 16 (24)
T PF13018_consen 1 MNKIYRL-----IWNKARGTW 16 (24)
T ss_pred CCccEEE-----EEECCCCeE
Confidence 8999885 688766655
No 9
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=44.71 E-value=13 Score=24.42 Aligned_cols=34 Identities=15% Similarity=0.378 Sum_probs=23.3
Q ss_pred eEEEeCCEEEEEcCCCCCcccccCCCCCCceeEE
Q psy16814 80 YFLYKEGVLHNLCHLKPKHKQILFHPKDKNTWIL 113 (124)
Q Consensus 80 ~vVRR~gRlyViCk~nPRHKQRQg~k~~~~twil 113 (124)
.+||+||+++..|...-+.--.++++.-+-.|+.
T Consensus 20 ~~Vr~Dgkv~~F~s~Kc~~~~~~krnPRkv~WT~ 53 (54)
T cd00472 20 MYVRNDGKVFRFCSSKCEKNFLRKRNPRKLKWTV 53 (54)
T ss_pred EEEecCCCEEEEECHHHHHHHHCcCCCCcceeec
Confidence 6899999999999744433333456666667754
No 10
>PRK00807 50S ribosomal protein L24e; Validated
Probab=41.43 E-value=16 Score=23.52 Aligned_cols=33 Identities=21% Similarity=0.378 Sum_probs=22.3
Q ss_pred eEEEeCCEEEEEcCCCCCcccccCCCCCCceeE
Q psy16814 80 YFLYKEGVLHNLCHLKPKHKQILFHPKDKNTWI 112 (124)
Q Consensus 80 ~vVRR~gRlyViCk~nPRHKQRQg~k~~~~twi 112 (124)
.+|+.+|++|..|...=+.-=.++++.-+-.|+
T Consensus 18 ~~vr~Dgkv~~Fcs~KC~~~f~~~~nprk~~WT 50 (52)
T PRK00807 18 MYVKKDGTILYFCSSKCEKNYKLGRVPRKLKWT 50 (52)
T ss_pred EEEEeCCcEEEEeCHHHHHHHHccCCCCccccc
Confidence 478999999999974443333455555566675
No 11
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=35.78 E-value=13 Score=28.87 Aligned_cols=36 Identities=17% Similarity=0.232 Sum_probs=24.8
Q ss_pred ceEEEeCCEEEEEcCCCCCcccccCCCCCCceeEEe
Q psy16814 79 CYFLYKEGVLHNLCHLKPKHKQILFHPKDKNTWILS 114 (124)
Q Consensus 79 C~vVRR~gRlyViCk~nPRHKQRQg~k~~~~twilt 114 (124)
=.+||++|++|..|...=+.--.++++.-+-.|+..
T Consensus 20 ~~fVR~DGkvf~FcssKC~k~f~~kRnPRKlkWT~~ 55 (131)
T PRK14891 20 TMFVRKDGTVLHFVDSKCEKNYDLGREARDLEWTEA 55 (131)
T ss_pred cEEEecCCCEEEEecHHHHHHHHccCCCccchhHHH
Confidence 368999999999996444333345666666777643
No 12
>KOG2463|consensus
Probab=32.48 E-value=11 Score=33.53 Aligned_cols=34 Identities=29% Similarity=0.436 Sum_probs=22.0
Q ss_pred cccccCCccccccccccceEec--ceeccCCCceEEE
Q psy16814 49 QINLLQPILPSVMLVNTWKYKA--KVKKRCKGCYFLY 83 (124)
Q Consensus 49 q~~Ll~p~~p~~~~~~gMKVrs--SlKkrC~~C~vVR 83 (124)
|+.||+=.+-++ ...|||+|. +-..||-.|+-|-
T Consensus 217 QNVlLqm~L~l~-~~~G~~Ir~~r~~iLRCh~Cfsit 252 (376)
T KOG2463|consen 217 QNVLLQMNLNLL-AMSGMKIRSVRSYILRCHGCFSIT 252 (376)
T ss_pred HHHHHHhccccc-CccchhhhhhhhheeEeeeeeEec
Confidence 355554434333 488999997 4567788888663
No 13
>PF12762 DDE_Tnp_IS1595: ISXO2-like transposase domain; InterPro: IPR024445 This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2.
Probab=31.20 E-value=52 Score=23.44 Aligned_cols=27 Identities=19% Similarity=0.191 Sum_probs=21.9
Q ss_pred CCCCCcccccCCCCCCceeEEeeeecC
Q psy16814 93 HLKPKHKQILFHPKDKNTWILSGVSTN 119 (124)
Q Consensus 93 k~nPRHKQRQg~k~~~~twilt~atq~ 119 (124)
+..|+++.++|+....++|+++.+.-.
T Consensus 18 ~~~~~~~~~~gr~~~~k~~V~~~ver~ 44 (151)
T PF12762_consen 18 NKKPRRKGKRGRGSKNKVPVFGAVERN 44 (151)
T ss_pred cccccCCCCCCCcCCCCcEEEEEEeec
Confidence 556788888888778999999998764
No 14
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=29.02 E-value=89 Score=18.82 Aligned_cols=27 Identities=19% Similarity=0.174 Sum_probs=16.6
Q ss_pred cccccceEecceeccCCCceEEEeCCEEEEEcC
Q psy16814 61 MLVNTWKYKAKVKKRCKGCYFLYKEGVLHNLCH 93 (124)
Q Consensus 61 ~~~~gMKVrsSlKkrC~~C~vVRR~gRlyViCk 93 (124)
.+++||+|.++ .=+.+.-+|+.|-.|.
T Consensus 3 DPvcg~~v~~~------~~~~~~y~G~~Y~FCS 29 (47)
T PF04945_consen 3 DPVCGMKVPGN------AAYSVEYNGRTYYFCS 29 (47)
T ss_dssp B-GGG-BE-----------EEEEETTEEEEESS
T ss_pred CCCCCCEEccC------ccEEEEECCEEEEEcC
Confidence 47899999332 2245678999999996
No 15
>KOG1774|consensus
Probab=28.78 E-value=23 Score=25.86 Aligned_cols=14 Identities=29% Similarity=0.572 Sum_probs=11.1
Q ss_pred Chhhhhhhhhc---cee
Q psy16814 1 MNKIFKIFQST---LVI 14 (124)
Q Consensus 1 ~~~~~~~~q~~---~~~ 14 (124)
.|.||++||+. .+|
T Consensus 14 in~Ifr~Lq~~t~VqIW 30 (88)
T KOG1774|consen 14 INLIFRFLQNRTRVQIW 30 (88)
T ss_pred HHHHHHHHhcCCceEEE
Confidence 37899999987 456
No 16
>PF14836 Ubiquitin_3: Ubiquitin-like domain; PDB: 3JYU_A 4A3O_B 3PPA_A 3T9L_A 4A3P_A 3PV1_A.
Probab=27.44 E-value=29 Score=24.91 Aligned_cols=26 Identities=31% Similarity=0.575 Sum_probs=17.4
Q ss_pred Chhhhhhhhhc-ceeee-ccceeeeeeec
Q psy16814 1 MNKIFKIFQST-LVINN-VQRTFTTLYKP 27 (124)
Q Consensus 1 ~~~~~~~~q~~-~~~n~-~~r~F~~l~rp 27 (124)
|.|+|.| |.- ||||- ..-+|-.|..|
T Consensus 33 ~rklf~i-~~E~RLW~~~~~~~~e~L~~~ 60 (88)
T PF14836_consen 33 MRKLFNI-QEETRLWNKYSENSYELLNNP 60 (88)
T ss_dssp HHHHCT--TS-EEEEEECTTTCEEEE--T
T ss_pred HHHHhCC-CccceehhccCCcchhhhCCC
Confidence 4578999 555 99996 77788888777
No 17
>COG3012 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.48 E-value=71 Score=25.36 Aligned_cols=43 Identities=19% Similarity=0.118 Sum_probs=35.2
Q ss_pred CCccccccccccceEecceeccCCCceEEEeCCEEEEEcCCCC
Q psy16814 54 QPILPSVMLVNTWKYKAKVKKRCKGCYFLYKEGVLHNLCHLKP 96 (124)
Q Consensus 54 ~p~~p~~~~~~gMKVrsSlKkrC~~C~vVRR~gRlyViCk~nP 96 (124)
.|.-..+..++-||.-...-..-+...||+.+|+||-|=-+-|
T Consensus 88 ~~~~~~VeF~A~f~~~~~~~a~~ErSrFvk~ngrWyyiDgtv~ 130 (151)
T COG3012 88 APNHGFVEFVARFKGGGKTGAHHERSRFVKINGRWYYIDGTVP 130 (151)
T ss_pred CCcceeEEEEEEEccCCccchhhhhhhheEECCEEEEECCCCC
Confidence 3555667788888888877777899999999999999977666
No 18
>cd01278 aprataxin_related aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are predominantly eukaryotic in origin.
Probab=20.56 E-value=1.9e+02 Score=19.30 Aligned_cols=30 Identities=10% Similarity=0.153 Sum_probs=23.0
Q ss_pred CceEEEeCCEEEEEcCCCCCcccccCCCCCCceeEEee
Q psy16814 78 GCYFLYKEGVLHNLCHLKPKHKQILFHPKDKNTWILSG 115 (124)
Q Consensus 78 ~C~vVRR~gRlyViCk~nPRHKQRQg~k~~~~twilt~ 115 (124)
..++|.+++..++++...|+. +.+.||+.-
T Consensus 15 ~~~iv~~~~~~~a~~~~~p~~--------~~h~lIiPk 44 (104)
T cd01278 15 PEDQVYEDDRVVVFKDIYPKA--------RHHYLVIPK 44 (104)
T ss_pred CccEEEeCCCEEEEECCCCCC--------CceEEEEec
Confidence 567888999999999877765 467777653
Done!