Query 030716
Match_columns 173
No_of_seqs 75 out of 77
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 03:31:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030716.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030716hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK02724 hypothetical protein; 100.0 4.6E-50 9.9E-55 306.6 9.7 83 88-171 4-86 (104)
2 CHL00163 ycf65 putative riboso 100.0 5.8E-50 1.3E-54 303.8 9.8 80 90-170 1-80 (99)
3 PF04839 PSRP-3_Ycf65: Plastid 100.0 1.7E-33 3.8E-38 191.5 4.8 48 120-167 1-48 (49)
4 KOG2348 Urea transporter [Amin 31.2 33 0.00071 34.0 2.0 49 116-164 506-560 (667)
5 PF11594 Med28: Mediator compl 30.4 83 0.0018 24.8 3.8 26 133-166 45-70 (106)
6 COG4878 Uncharacterized protei 27.0 57 0.0012 30.0 2.7 40 127-166 203-251 (309)
7 PF02413 Caudo_TAP: Caudoviral 26.0 73 0.0016 24.3 2.8 50 114-167 35-88 (130)
8 cd00068 GGL G protein gamma su 25.7 86 0.0019 21.3 2.8 28 133-167 9-36 (57)
9 smart00224 GGL G protein gamma 22.3 83 0.0018 21.8 2.3 29 133-168 9-37 (63)
10 PF03945 Endotoxin_N: delta en 21.4 1.2E+02 0.0026 24.2 3.3 19 124-142 33-53 (226)
11 cd00083 HLH Helix-loop-helix d 20.7 1.9E+02 0.0042 18.1 3.6 38 130-167 21-58 (60)
12 COG0816 Predicted endonuclease 20.1 96 0.0021 25.0 2.5 44 97-141 7-51 (141)
No 1
>PRK02724 hypothetical protein; Provisional
Probab=100.00 E-value=4.6e-50 Score=306.57 Aligned_cols=83 Identities=51% Similarity=1.037 Sum_probs=79.9
Q ss_pred CCCCcEEEEEEeecCceeEEeeeeecCCCCccCcccccccCCchHHHHHHhhccCCCCChhHHHHHHHHHHHHHHHHHhc
Q 030716 88 LEKPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQS 167 (173)
Q Consensus 88 ~~~~rfvLK~LWlek~IgiAlDQ~v~g~~t~PLT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIIN~WQe~ 167 (173)
.+++||+||||||||||||||||+| |+|++|||+||||||+||||+||.+||+|+||+++|||+|||++||||||||++
T Consensus 4 ~~~~rfvlKvlWle~~iaiAvDQ~v-g~~t~PLT~yfFWPr~DAWe~LK~~LesK~WIs~~~~i~lLN~~TeiIN~WQe~ 82 (104)
T PRK02724 4 ADEGRFILKVLWLDDNVALAVDQIV-GKGTSPLTAYFFWPRNDAWEQLKTELESKHWITENERVEVLNKATEVINYWQEE 82 (104)
T ss_pred cccceEEEEEEEeccceeEEeeeec-CCCCCcCcceeecCCccHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHc
Confidence 4679999999999999999999999 999999999999999999999999999999999999999999999999999998
Q ss_pred CCCC
Q 030716 168 GGNL 171 (173)
Q Consensus 168 ~~~~ 171 (173)
|++-
T Consensus 83 ~~~~ 86 (104)
T PRK02724 83 GKGK 86 (104)
T ss_pred cCCC
Confidence 7653
No 2
>CHL00163 ycf65 putative ribosomal protein 3; Validated
Probab=100.00 E-value=5.8e-50 Score=303.79 Aligned_cols=80 Identities=55% Similarity=1.063 Sum_probs=77.6
Q ss_pred CCcEEEEEEeecCceeEEeeeeecCCCCccCcccccccCCchHHHHHHhhccCCCCChhHHHHHHHHHHHHHHHHHhcCC
Q 030716 90 KPRLVLKFIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQSGG 169 (173)
Q Consensus 90 ~~rfvLK~LWlek~IgiAlDQ~v~g~~t~PLT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIIN~WQe~~~ 169 (173)
++||+|||||||++|||||||+| |+|++|||+||||||+||||+||.+||+||||+++|||+||||+|||||||||+++
T Consensus 1 m~kf~lKvlWl~~~iaiAvDq~v-~~~t~PlT~yfFWPr~DAWe~LK~~LesK~WIs~~~~i~lLN~~TeiIN~Wqe~~~ 79 (99)
T CHL00163 1 MQKFTLKVLWLENNIGIAVDQIV-GNGTSPLTSYFFWPRTDAWELLKLELESKPWISEDERIEILNKTTEIINYWQENKK 79 (99)
T ss_pred CCeEEEEEEEecCceEEEEeeee-CCCCccCcceeecCCccHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHccC
Confidence 58999999999999999999999 88999999999999999999999999999999999999999999999999999876
Q ss_pred C
Q 030716 170 N 170 (173)
Q Consensus 170 ~ 170 (173)
+
T Consensus 80 ~ 80 (99)
T CHL00163 80 K 80 (99)
T ss_pred C
Confidence 5
No 3
>PF04839 PSRP-3_Ycf65: Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65); InterPro: IPR006924 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 small acidic protein is found in 30S ribosomal subunit of cyanobacteria and plant plastids. In plants it has been named plastid-specific ribosomal protein 3 (PSRP-3), and in cyanobacteria it is named Ycf65. Plastid-specific ribosomal proteins may mediate the effects of nuclear factors on plastid translation. The acidic PSRPs are thought to contribute to protein-protein interactions in the 30S subunit, and are not thought to bind RNA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome, 0009536 plastid; PDB: 2KT9_A.
Probab=99.98 E-value=1.7e-33 Score=191.53 Aligned_cols=48 Identities=71% Similarity=1.297 Sum_probs=41.8
Q ss_pred CcccccccCCchHHHHHHhhccCCCCChhHHHHHHHHHHHHHHHHHhc
Q 030716 120 LSQYFFWPRKDAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQS 167 (173)
Q Consensus 120 LT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIIN~WQe~ 167 (173)
||+||||||+||||+||.+||+|+||+++|||.|||++||||||||++
T Consensus 1 lT~yfFWPr~DAWe~lk~eLe~K~WIs~~e~i~lLN~~TeiIN~Wqe~ 48 (49)
T PF04839_consen 1 LTEYFFWPREDAWEQLKNELESKPWISEKERIELLNQATEIINYWQEE 48 (49)
T ss_dssp -S--EEETTS-HHHHHHHHHHHSTTS-HHHHHHHHHHHHHHHHHHHH-
T ss_pred CCCcccCCCCcHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 799999999999999999999999999999999999999999999996
No 4
>KOG2348 consensus Urea transporter [Amino acid transport and metabolism]
Probab=31.19 E-value=33 Score=34.00 Aligned_cols=49 Identities=24% Similarity=0.222 Sum_probs=32.5
Q ss_pred CCccCcccccccCCchHHHHHHhhccCCC-----CChhHHHH-HHHHHHHHHHHH
Q 030716 116 GTIPLSQYFFWPRKDAWEELKTTLESKPW-----ISQKMMII-LLNQATDIINLW 164 (173)
Q Consensus 116 ~t~PLT~YfFWPr~DAWEeLK~eLEsK~W-----Is~~e~i~-lLNq~TeIIN~W 164 (173)
--+||-+|||=|+++.|+.|++..-=..= +.+.|.-+ =||++-.|+-+|
T Consensus 506 iyi~ilsy~f~pqn~D~n~l~e~~~v~~~a~~~E~~d~e~ek~kl~Ra~~i~~~~ 560 (667)
T KOG2348|consen 506 IYIVILSYFFPPQNYDWNNLNEIFVVGDDAEAEEIVDAEQEKKKLNRALRIGIFV 560 (667)
T ss_pred hheeeeeEecCCccCchhhhhheEEeccccccchhcchhHHHHHHhhhhhHHHHH
Confidence 35788999999999999999864311110 11222222 688988888776
No 5
>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].
Probab=30.40 E-value=83 Score=24.80 Aligned_cols=26 Identities=31% Similarity=0.526 Sum_probs=21.6
Q ss_pred HHHHHhhccCCCCChhHHHHHHHHHHHHHHHHHh
Q 030716 133 EELKTTLESKPWISQKMMIILLNQATDIINLWQQ 166 (173)
Q Consensus 133 EeLK~eLEsK~WIs~~e~i~lLNq~TeIIN~WQe 166 (173)
++||.|| ..+=.|+++.-+-|.|||.
T Consensus 45 ~eLK~El--------qRKe~Ll~Kh~~kI~~w~~ 70 (106)
T PF11594_consen 45 NELKEEL--------QRKEQLLQKHYEKIDYWEK 70 (106)
T ss_pred HHHHHHH--------HHHHHHHHHHHHHHHHHHH
Confidence 6788888 4556788999999999986
No 6
>COG4878 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.03 E-value=57 Score=29.99 Aligned_cols=40 Identities=28% Similarity=0.395 Sum_probs=31.8
Q ss_pred cCCchHHHHHHhh--------ccCCCCChhHHHHHHHHHHHHH-HHHHh
Q 030716 127 PRKDAWEELKTTL--------ESKPWISQKMMIILLNQATDII-NLWQQ 166 (173)
Q Consensus 127 Pr~DAWEeLK~eL--------EsK~WIs~~e~i~lLNq~TeII-N~WQe 166 (173)
|+.-+|+||+.+| +++|||...+.-++-|..++.. |.||-
T Consensus 203 ~k~k~Wnel~k~~~sl~~e~k~n~pwL~~~~Asel~n~~k~y~dnkp~s 251 (309)
T COG4878 203 CKVKAWNELSKQLTSLLWEKKYNKPWLLYTNASELANKIKRYLDNKPVS 251 (309)
T ss_pred cccccHHHHHHHHHHHHHHHhcCCCeeeeccHHHHHHHHhhhhhcCcee
Confidence 4567999999666 5799999999999999988764 44543
No 7
>PF02413 Caudo_TAP: Caudovirales tail fibre assembly protein; InterPro: IPR003458 This family contains Bacteriophage T4 gp38 and related bacterial prophage and phage proteins. Gene 38 of phage T4 codes for a protein containing 183 amino acid residues with molecular weight of 22.3 kDa. Together with genes 36 and 37, whose products are structural proteins of the fibre distal part, gene 38 forms one transcription unit. Gp38, is a chaperone, which is required for assembly of the distal part of the long fibres and which is absent from the mature phage particle. In the absence of gp38 gp37, which is a component of the distal part of the long tail fibre, fails to oligomerise. The carboxy-terminal region of gp37 forms the tip of the distal fibre that interacts with the cell receptors. Functionally the role of gp38 can be replaced by pTfa of Bacteriophage lambda [, , ]. The function of many of the other members of this family remain to be elucidated.
Probab=26.04 E-value=73 Score=24.30 Aligned_cols=50 Identities=24% Similarity=0.440 Sum_probs=32.1
Q ss_pred CCCCccCcccccccCCchHH---HH-HHhhccCCCCChhHHHHHHHHHHHHHHHHHhc
Q 030716 114 GYGTIPLSQYFFWPRKDAWE---EL-KTTLESKPWISQKMMIILLNQATDIINLWQQS 167 (173)
Q Consensus 114 g~~t~PLT~YfFWPr~DAWE---eL-K~eLEsK~WIs~~e~i~lLNq~TeIIN~WQe~ 167 (173)
|-..-|-+.|.||=. ++|. +. +.++-.. .+.+|-.+|++|++.|+-||+.
T Consensus 35 ~~~~~~~g~~~~~~g-~~~p~~~~~~~~~~~~~---A~~~k~~ll~~A~~~I~~lqda 88 (130)
T PF02413_consen 35 GTDGPPPGKWDFWDG-KGWPRWVDAPKEELIAQ---AEAEKQRLLAEASEAIAPLQDA 88 (130)
T ss_pred cccCCCCCCEEEECC-ccccccchhhHHHHHHH---HHHHHHHHHHHHHHHHHHhHHH
Confidence 434557777887743 3442 21 2222222 2667899999999999999973
No 8
>cd00068 GGL G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors
Probab=25.67 E-value=86 Score=21.31 Aligned_cols=28 Identities=18% Similarity=0.355 Sum_probs=23.7
Q ss_pred HHHHHhhccCCCCChhHHHHHHHHHHHHHHHHHhc
Q 030716 133 EELKTTLESKPWISQKMMIILLNQATDIINLWQQS 167 (173)
Q Consensus 133 EeLK~eLEsK~WIs~~e~i~lLNq~TeIIN~WQe~ 167 (173)
|+||.+|+- +||.+-..+.++|+|=.+.
T Consensus 9 eqLr~el~~-------~RikvS~a~~~l~~y~e~~ 36 (57)
T cd00068 9 EQLRKELSR-------ERLKVSKAAAELLKYCEQN 36 (57)
T ss_pred HHHHHHHCC-------chhhHHHHHHHHHHHHHhc
Confidence 678888854 6999999999999998775
No 9
>smart00224 GGL G protein gamma subunit-like motifs.
Probab=22.35 E-value=83 Score=21.80 Aligned_cols=29 Identities=21% Similarity=0.329 Sum_probs=23.6
Q ss_pred HHHHHhhccCCCCChhHHHHHHHHHHHHHHHHHhcC
Q 030716 133 EELKTTLESKPWISQKMMIILLNQATDIINLWQQSG 168 (173)
Q Consensus 133 EeLK~eLEsK~WIs~~e~i~lLNq~TeIIN~WQe~~ 168 (173)
|+||.+|+- +||.+-..+.++|+|=.+..
T Consensus 9 e~Lr~el~~-------~RikvS~a~~~li~y~e~~~ 37 (63)
T smart00224 9 EQLRKELSR-------ERIKVSKAAEELLAYCEQHA 37 (63)
T ss_pred HHHHHHHCC-------ceehHHHHHHHHHHHHHcCC
Confidence 678888864 68999999999999987643
No 10
>PF03945 Endotoxin_N: delta endotoxin, N-terminal domain; InterPro: IPR005639 This family contains insecticidal toxins produced by Bacillus species of bacteria. During spore formation the bacteria produce crystals of this protein. When an insect ingests these proteins, they are activated by proteolytic cleavage. The N terminus is cleaved in all of the proteins and a C-terminal extension is cleaved in some members. Once activated, the endotoxin binds to the gut epithelium and causes cell lysis by the formation of cation-selective channels, which leads to death. The activated region of the delta toxin is composed of three distinct structural domains: an N-terminal helical bundle domain involved in membrane insertion and pore formation; a beta-sheet central domain (IPR001178 from INTERPRO) involved in receptor binding; and a C-terminal beta-sandwich domain (IPR005638 from INTERPRO) that interacts with the N-terminal domain to form a channel [, ]. This entry represents the conserved N-terminal domain.; GO: 0009405 pathogenesis; PDB: 3EB7_A 1I5P_A 2C9K_A 1CIY_A 1JI6_A 1DLC_A 1W99_A.
Probab=21.38 E-value=1.2e+02 Score=24.17 Aligned_cols=19 Identities=32% Similarity=0.910 Sum_probs=16.2
Q ss_pred ccccCCch--HHHHHHhhccC
Q 030716 124 FFWPRKDA--WEELKTTLESK 142 (173)
Q Consensus 124 fFWPr~DA--WEeLK~eLEsK 142 (173)
++||..+. |+++....|+-
T Consensus 33 ~lwp~~~~~~~~~~~~~ve~l 53 (226)
T PF03945_consen 33 ILWPSSSPDIWEEIIKQVENL 53 (226)
T ss_dssp HCSSTGSHHHHHHHHHHHHHH
T ss_pred HHCCCCCchHHHHHHHHHHHH
Confidence 68999986 99999988765
No 11
>cd00083 HLH Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and
Probab=20.71 E-value=1.9e+02 Score=18.15 Aligned_cols=38 Identities=29% Similarity=0.353 Sum_probs=28.4
Q ss_pred chHHHHHHhhccCCCCChhHHHHHHHHHHHHHHHHHhc
Q 030716 130 DAWEELKTTLESKPWISQKMMIILLNQATDIINLWQQS 167 (173)
Q Consensus 130 DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIIN~WQe~ 167 (173)
++-++|+..|-...=....++..||+.+.+-|.+=|+.
T Consensus 21 ~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~ 58 (60)
T cd00083 21 DAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQEL 58 (60)
T ss_pred HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 45677777776554345678999999999999876654
No 12
>COG0816 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]
Probab=20.12 E-value=96 Score=24.98 Aligned_cols=44 Identities=20% Similarity=0.191 Sum_probs=32.0
Q ss_pred EEeecCceeEEeeeeecCCCCccCcccccccCC-chHHHHHHhhcc
Q 030716 97 FIWMEKNIGLALDQSIPGYGTIPLSQYFFWPRK-DAWEELKTTLES 141 (173)
Q Consensus 97 ~LWlek~IgiAlDQ~v~g~~t~PLT~YfFWPr~-DAWEeLK~eLEs 141 (173)
|=--.|.||||+=+.. |.--+|+..+-.==+. -+|++|+..++.
T Consensus 7 lD~G~KrIGvA~sd~~-~~~A~pl~~i~~~~~~~~~~~~l~~li~~ 51 (141)
T COG0816 7 LDVGTKRIGVAVSDIL-GSLASPLETIKRKNGKPQDFNALLKLVKE 51 (141)
T ss_pred EecCCceEEEEEecCC-CccccchhhheeccccHhhHHHHHHHHHH
Confidence 3345789999999998 6668899887654444 378888777654
Done!