Query 029878
Match_columns 186
No_of_seqs 79 out of 81
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 05:05:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029878.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029878hhsearch_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 1.1E-49 2.4E-54 307.2 9.6 83 100-183 4-86 (104)
2 CHL00163 ycf65 putative riboso 100.0 1.4E-49 2.9E-54 304.5 9.7 80 102-182 1-80 (99)
3 PF04839 PSRP-3_Ycf65: Plastid 100.0 3.1E-33 6.8E-38 192.0 4.5 48 132-179 1-48 (49)
4 KOG2348 Urea transporter [Amin 30.6 32 0.0007 34.4 1.9 48 129-176 507-560 (667)
5 PF11594 Med28: Mediator compl 29.4 81 0.0018 25.1 3.6 26 145-178 45-70 (106)
6 cd00068 GGL G protein gamma su 26.1 79 0.0017 21.7 2.7 28 145-179 9-36 (57)
7 COG4878 Uncharacterized protei 25.6 60 0.0013 30.1 2.6 40 139-178 203-251 (309)
8 PF02413 Caudo_TAP: Caudoviral 23.2 83 0.0018 24.3 2.7 51 125-179 34-88 (130)
9 smart00224 GGL G protein gamma 23.1 77 0.0017 22.2 2.3 29 145-180 9-37 (63)
10 cd00083 HLH Helix-loop-helix d 20.3 1.9E+02 0.004 18.5 3.5 38 142-179 21-58 (60)
No 1
>PRK02724 hypothetical protein; Provisional
Probab=100.00 E-value=1.1e-49 Score=307.20 Aligned_cols=83 Identities=48% Similarity=1.106 Sum_probs=79.6
Q ss_pred CCCceEEEEEEeecCcEEEEeeeeecCCCcccCcccccccCCchHHHHHhhhcCCCCCChhhHHHHhhhhHHHHHHHHhc
Q 029878 100 NEKRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTS 179 (186)
Q Consensus 100 ~~~~rfvLK~LWlek~IgiAvDQ~v~g~~t~PLT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIINyWQe~ 179 (186)
.+++||+||||||+|||||||||+| |+|++|||+||||||+||||+||.+||+|+||+++|||+|||++||||||||++
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 4678999999999999999999999 999999999999999999999999999999999999999999999999999998
Q ss_pred CCCC
Q 029878 180 GGNL 183 (186)
Q Consensus 180 ~~~l 183 (186)
|++-
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=1.4e-49 Score=304.52 Aligned_cols=80 Identities=54% Similarity=1.166 Sum_probs=77.6
Q ss_pred CceEEEEEEeecCcEEEEeeeeecCCCcccCcccccccCCchHHHHHhhhcCCCCCChhhHHHHhhhhHHHHHHHHhcCC
Q 029878 102 KRRLVLKFIWMQNDIGIALDQVIPGHGTIPLSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTSGG 181 (186)
Q Consensus 102 ~~rfvLK~LWlek~IgiAvDQ~v~g~~t~PLT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIINyWQe~~~ 181 (186)
++||+|||||||++|||||||+| |+|++|||+||||||+||||+||.+||+|+||+++|||+||||+||||||||++++
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 57999999999999999999999 88999999999999999999999999999999999999999999999999999876
Q ss_pred C
Q 029878 182 N 182 (186)
Q Consensus 182 ~ 182 (186)
+
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=3.1e-33 Score=191.98 Aligned_cols=48 Identities=67% Similarity=1.325 Sum_probs=41.8
Q ss_pred CcccccccCCchHHHHHhhhcCCCCCChhhHHHHhhhhHHHHHHHHhc
Q 029878 132 LSPYYFWPRKDAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTS 179 (186)
Q Consensus 132 LT~YfFWPr~DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIINyWQe~ 179 (186)
||+||||||+||||+||.+||+|+||+++|||.|||++||||||||++
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=30.59 E-value=32 Score=34.35 Aligned_cols=48 Identities=25% Similarity=0.360 Sum_probs=32.0
Q ss_pred cccCcccccccCCchHHHHHhhhcCCCC-----CChhhHH-HHhhhhHHHHHHH
Q 029878 129 TIPLSPYYFWPRKDAWEELKVLLDSKPW-----ISQTERI-HLLNQATDVINFW 176 (186)
Q Consensus 129 t~PLT~YfFWPr~DAWEeLK~eLEsK~W-----Is~~e~i-~lLNq~TeIINyW 176 (186)
-+||-+|||=|+++.|+.|++..--..= +.+.|.- .=||++-.|+-+|
T Consensus 507 yi~ilsy~f~pqn~D~n~l~e~~~v~~~a~~~E~~d~e~ek~kl~Ra~~i~~~~ 560 (667)
T KOG2348|consen 507 YIVILSYFFPPQNYDWNNLNEIFVVGDDAEAEEIVDAEQEKKKLNRALRIGIFV 560 (667)
T ss_pred heeeeeEecCCccCchhhhhheEEeccccccchhcchhHHHHHHhhhhhHHHHH
Confidence 4788899999999999999874311111 1122222 2688988888776
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=29.42 E-value=81 Score=25.13 Aligned_cols=26 Identities=31% Similarity=0.621 Sum_probs=21.6
Q ss_pred HHHHhhhcCCCCCChhhHHHHhhhhHHHHHHHHh
Q 029878 145 EELKVLLDSKPWISQTERIHLLNQATDVINFWQT 178 (186)
Q Consensus 145 EeLK~eLEsK~WIs~~e~i~lLNq~TeIINyWQe 178 (186)
++||.|| ..+=.|+++.-+-|.|||.
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
>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=26.06 E-value=79 Score=21.72 Aligned_cols=28 Identities=21% Similarity=0.496 Sum_probs=23.9
Q ss_pred HHHHhhhcCCCCCChhhHHHHhhhhHHHHHHHHhc
Q 029878 145 EELKVLLDSKPWISQTERIHLLNQATDVINFWQTS 179 (186)
Q Consensus 145 EeLK~eLEsK~WIs~~e~i~lLNq~TeIINyWQe~ 179 (186)
|+||.+|+- +||.+-..+.++|+|=.+.
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 6999999999999998876
No 7
>COG4878 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.59 E-value=60 Score=30.14 Aligned_cols=40 Identities=30% Similarity=0.435 Sum_probs=31.8
Q ss_pred cCCchHHHHHhhh--------cCCCCCChhhHHHHhhhhHHHH-HHHHh
Q 029878 139 PRKDAWEELKVLL--------DSKPWISQTERIHLLNQATDVI-NFWQT 178 (186)
Q Consensus 139 Pr~DAWEeLK~eL--------EsK~WIs~~e~i~lLNq~TeII-NyWQe 178 (186)
|+.-+|+||+.+| +++|||.....-++-|..++.. |.||-
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 3567999999666 5799999999999999988764 44544
No 8
>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=23.15 E-value=83 Score=24.26 Aligned_cols=51 Identities=25% Similarity=0.479 Sum_probs=32.5
Q ss_pred cCCCcccCcccccccCCchHH---HH-HhhhcCCCCCChhhHHHHhhhhHHHHHHHHhc
Q 029878 125 PGHGTIPLSPYYFWPRKDAWE---EL-KVLLDSKPWISQTERIHLLNQATDVINFWQTS 179 (186)
Q Consensus 125 ~g~~t~PLT~YfFWPr~DAWE---eL-K~eLEsK~WIs~~e~i~lLNq~TeIINyWQe~ 179 (186)
.|-..-|-+.|.||=. ++|. +. +.++-.. .+.+|-.+|++|++.|+-||+.
T Consensus 34 ~~~~~~~~g~~~~~~g-~~~p~~~~~~~~~~~~~---A~~~k~~ll~~A~~~I~~lqda 88 (130)
T PF02413_consen 34 EGTDGPPPGKWDFWDG-KGWPRWVDAPKEELIAQ---AEAEKQRLLAEASEAIAPLQDA 88 (130)
T ss_pred hcccCCCCCCEEEECC-ccccccchhhHHHHHHH---HHHHHHHHHHHHHHHHHHhHHH
Confidence 3434557777888743 3442 21 2222222 2667899999999999999973
No 9
>smart00224 GGL G protein gamma subunit-like motifs.
Probab=23.08 E-value=77 Score=22.19 Aligned_cols=29 Identities=24% Similarity=0.465 Sum_probs=23.9
Q ss_pred HHHHhhhcCCCCCChhhHHHHhhhhHHHHHHHHhcC
Q 029878 145 EELKVLLDSKPWISQTERIHLLNQATDVINFWQTSG 180 (186)
Q Consensus 145 EeLK~eLEsK~WIs~~e~i~lLNq~TeIINyWQe~~ 180 (186)
|+||.+|+- +||.+-..+.++|+|=.+..
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
>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=20.32 E-value=1.9e+02 Score=18.45 Aligned_cols=38 Identities=32% Similarity=0.434 Sum_probs=28.4
Q ss_pred chHHHHHhhhcCCCCCChhhHHHHhhhhHHHHHHHHhc
Q 029878 142 DAWEELKVLLDSKPWISQTERIHLLNQATDVINFWQTS 179 (186)
Q Consensus 142 DAWEeLK~eLEsK~WIs~~e~i~lLNq~TeIINyWQe~ 179 (186)
++-++|+..|-...=....++..||+.+.+-|.+=|+.
T Consensus 21 ~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~ 58 (60)
T cd00083 21 DAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQEL 58 (60)
T ss_pred HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 45677888776554345678999999999999876653
Done!