Query 026298
Match_columns 240
No_of_seqs 79 out of 81
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 06:10:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026298.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026298hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09812 MRP-L28: Mitochondria 99.9 2.2E-26 4.8E-31 193.1 9.4 97 128-224 39-145 (157)
2 KOG4778 Mitochondrial ribosoma 99.7 1.8E-17 3.9E-22 143.7 10.6 95 129-223 66-171 (186)
3 PF12824 MRP-L20: Mitochondria 60.3 54 0.0012 28.4 7.7 84 76-187 41-149 (164)
4 PF02095 Extensin_1: Extensin- 49.6 9.4 0.0002 19.8 0.9 10 212-221 1-10 (10)
5 PF08248 Tryp_FSAP: Tryptophyl 29.0 32 0.00069 18.7 0.9 8 212-219 2-9 (12)
6 PF05924 SAMP: SAMP Motif; In 28.4 21 0.00046 21.7 0.2 16 16-31 4-19 (20)
7 KOG0493 Transcription factor E 26.0 1.1E+02 0.0023 29.6 4.4 44 142-185 246-291 (342)
8 PF05764 YL1: YL1 nuclear prot 22.6 1.2E+02 0.0027 27.2 4.0 53 73-125 177-234 (240)
9 KOG3410 Conserved alpha-helica 22.5 2.9E+02 0.0062 23.5 5.8 76 99-183 30-107 (120)
10 PF13904 DUF4207: Domain of un 22.4 6E+02 0.013 23.2 8.4 71 144-214 172-248 (264)
11 PRK08881 rpsN 30S ribosomal pr 21.9 50 0.0011 26.4 1.2 23 10-32 53-75 (101)
No 1
>PF09812 MRP-L28: Mitochondrial ribosomal protein L28; InterPro: IPR019192 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 [, ]. Members of this family are components of the mitochondrial large ribosomal subunit. Mature mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S subunit contains at least 33 different proteins and 1 molecule of RNA (15S). The 54S subunit contains at least 45 different proteins and 1 molecule of RNA (21S) [, ].
Probab=99.93 E-value=2.2e-26 Score=193.06 Aligned_cols=97 Identities=28% Similarity=0.363 Sum_probs=92.4
Q ss_pred CCCCccc-cccCCcc---cCCCCCCCCHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc---CHHHHHH
Q 026298 128 TPGMDLI-SLGLVDA---DKIPKYELTAEDGKR---LAKECSRVLMRRHRARQAAESTLLRLKKEAIEAL---PEDLKKA 197 (240)
Q Consensus 128 ~p~lDfi-plkllDe---R~Rp~~eLs~EE~er---L~KEWSRyKmrEH~a~~~aI~~~l~aQqeAL~eL---sEeLy~A 197 (240)
.|.-||+ |..++++ |+++.++||+||.++ |.|+|++|++++|+++.++|++++++|++||++| |++||++
T Consensus 39 ~Pi~e~~v~~~~~~~~~~R~r~~~~ls~Ee~erh~~i~kaW~~yk~~~~~~~~~~l~~~~~sq~~AleeLr~~S~eLY~a 118 (157)
T PF09812_consen 39 KPIEEFEVPQKSVDSASRRQRPLLKLSREELERHATIQKAWSLYKQQQREAREQQLRRQYESQQKALEELRLESPELYQA 118 (157)
T ss_pred CCchhhhhhHHHHhhhcccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence 5777888 9999888 899999999999995 9999999999999999999999999999999999 9999999
Q ss_pred hhCCCCCCCCcccCCCccCCCCCChHH
Q 026298 198 ALVPDLTPFPVNRFMATLTPPIEGYME 224 (240)
Q Consensus 198 Ai~pD~~lfP~~R~gPt~TPPIegY~e 224 (240)
|+++|.++|||+..|||+||||+||+.
T Consensus 119 A~~~d~~~fP~e~~~Pt~TPPi~~Y~~ 145 (157)
T PF09812_consen 119 AIQPDPGLFPLEMRGPTDTPPIKNYEA 145 (157)
T ss_pred HhccCCCCCCeeecCCCCCCCCCCCCC
Confidence 999999999999999999999999973
No 2
>KOG4778 consensus Mitochondrial ribosomal protein L28 [Translation, ribosomal structure and biogenesis]
Probab=99.73 E-value=1.8e-17 Score=143.67 Aligned_cols=95 Identities=25% Similarity=0.283 Sum_probs=89.4
Q ss_pred CCCccc-cccCCcc---cCCCCCCCCHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc---CHHHHHHh
Q 026298 129 PGMDLI-SLGLVDA---DKIPKYELTAEDGKR---LAKECSRVLMRRHRARQAAESTLLRLKKEAIEAL---PEDLKKAA 198 (240)
Q Consensus 129 p~lDfi-plkllDe---R~Rp~~eLs~EE~er---L~KEWSRyKmrEH~a~~~aI~~~l~aQqeAL~eL---sEeLy~AA 198 (240)
|=-|++ |+++.|+ |++|..+|+.|+.+. +.|.|+.|++++..++...|+.++++|+.|+++| |++||+||
T Consensus 66 pvd~l~~p~~~~~~~~~rqrp~~klt~e~~e~rav~~k~W~~y~~~~rq~~d~~Ir~~~kaq~~al~eLk~es~~Ly~aA 145 (186)
T KOG4778|consen 66 PVDDLMVPLESEKKDYKRQRPLLKLTDEQLEKRAVILKTWSIYKQQQRQLEDVGIRPQSKAQFKALNELKSESEELYEAA 145 (186)
T ss_pred chHHhhhHHHhcCccccccCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence 445777 9999988 999999999999993 9999999999999999999999999999999999 99999999
Q ss_pred hCCCC-CCCCcccCCCccCCCCCChH
Q 026298 199 LVPDL-TPFPVNRFMATLTPPIEGYM 223 (240)
Q Consensus 199 i~pD~-~lfP~~R~gPt~TPPIegY~ 223 (240)
+.+|. ..||+..+||++||||.+|.
T Consensus 146 ~~~s~gk~lPve~~gP~~tPPi~~y~ 171 (186)
T KOG4778|consen 146 IEFSPGKRLPVEVKGPTDTPPIKNYK 171 (186)
T ss_pred hccccccccceeecCCCCCCCccccc
Confidence 99999 89999999999999999985
No 3
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 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 the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=60.34 E-value=54 Score=28.37 Aligned_cols=84 Identities=26% Similarity=0.341 Sum_probs=51.4
Q ss_pred CCcccCChhhHHHHHHHHHhccchhhhHHHHHHHHhhcccccCCCCCCcccCCCCCccccccCCcccCCCCCCCCHHHHH
Q 026298 76 TPVRFLTPKDKKREIEREKLGLISKDRQREIDILKKGGKQAMGISDEPMIMGTPGMDLISLGLVDADKIPKYELTAEDGK 155 (240)
Q Consensus 76 ~p~r~l~pk~r~rea~reklgl~sk~rqreld~~k~~~~~~~~~~~~~~~~~~p~lDfiplkllDeR~Rp~~eLs~EE~e 155 (240)
||.-||.+.|--|+......-..+.. +.+.|.+.+... +.-+.|-||.||.+
T Consensus 41 tP~~FLP~~DpRr~~~~~~~~~~~~~-----------------~~~lPp~l~~~~-----------~~~k~y~Lt~e~i~ 92 (164)
T PF12824_consen 41 TPFKFLPKSDPRRELNAASQSTSSPS-----------------SEDLPPILRYKS-----------PHEKKYHLTPEDIQ 92 (164)
T ss_pred CCcccCCCcchHHHHHhhhcccCCcc-----------------hhhCCccccccc-----------cccccccCCHHHHH
Confidence 89999977776555544333322222 567777766554 11256999999987
Q ss_pred ---HHHHH----HHHHHHH------------------HHHHHHHHHHHHHHHHHHHH
Q 026298 156 ---RLAKE----CSRVLMR------------------RHRARQAAESTLLRLKKEAI 187 (240)
Q Consensus 156 ---rL~KE----WSRyKmr------------------EH~a~~~aI~~~l~aQqeAL 187 (240)
+|-.+ ||+.+-. +|.++++..-..++++|-.-
T Consensus 93 Eir~LR~~DP~~wTr~~LAkkF~~S~~fV~~v~~~~~e~~~~~~~~le~~k~rWg~~ 149 (164)
T PF12824_consen 93 EIRRLRAEDPEKWTRKKLAKKFNCSPLFVSMVAPAPKEKKKEMEARLEAIKSRWGPR 149 (164)
T ss_pred HHHHHHHcCchHhhHHHHHHHhCCCHHHHHHhcCCCHHHHHHHHHHHHHHHHhccHH
Confidence 36554 8877643 56666666665555555433
No 4
>PF02095 Extensin_1: Extensin-like protein repeat; InterPro: IPR003883 Extensins are plant cell-wall proteins; they can account for up to 20% of the dry weight of the cell wall. They are highly-glycosylated, possibly reflecting their interactions with cell-wall carbohydrates. Amongst their functions is cell wall strengthening in response to mechanical stress (e.g., during attack by pests, plant-bending in the wind, etc.). This repeat occurs within extensin-like proteins.; GO: 0005199 structural constituent of cell wall
Probab=49.61 E-value=9.4 Score=19.81 Aligned_cols=10 Identities=30% Similarity=0.627 Sum_probs=7.9
Q ss_pred CCccCCCCCC
Q 026298 212 MATLTPPIEG 221 (240)
Q Consensus 212 gPt~TPPIeg 221 (240)
.|+|.|||+.
T Consensus 1 PP~ykPpvek 10 (10)
T PF02095_consen 1 PPVYKPPVEK 10 (10)
T ss_pred CCccCCCccC
Confidence 3889999974
No 5
>PF08248 Tryp_FSAP: Tryptophyllin-3 skin active peptide; InterPro: IPR013266 PdT-3 or Tryptophyllin-3 peptide is a subfamily of the family Tryptophyllin and of the superfamily FSAP (Frog Skin Active Peptide). Originally identified in skin extracts of Neotropical leaf frogs, Phyllomedusa sp. This subfamily has an average length of 13 amino acids. The pharmacological activity of the tryptophyllins remains to be established [] but it seems that these peptides possess an action on liver protein synthesis and body weight []. It is thought to possesses insulin-releasing activity [].
Probab=29.00 E-value=32 Score=18.67 Aligned_cols=8 Identities=38% Similarity=0.638 Sum_probs=6.8
Q ss_pred CCccCCCC
Q 026298 212 MATLTPPI 219 (240)
Q Consensus 212 gPt~TPPI 219 (240)
-|.|.|||
T Consensus 2 kpfw~ppi 9 (12)
T PF08248_consen 2 KPFWPPPI 9 (12)
T ss_pred CccCCCCc
Confidence 48899998
No 6
>PF05924 SAMP: SAMP Motif; InterPro: IPR009224 This short region is found repeated in the mid region of the adenomatous polyposis proteins (APCs). This motif binds axin [].; GO: 0008013 beta-catenin binding, 0016055 Wnt receptor signaling pathway; PDB: 1EMU_B 2RQU_B.
Probab=28.44 E-value=21 Score=21.74 Aligned_cols=16 Identities=38% Similarity=0.725 Sum_probs=10.1
Q ss_pred hhhhhcccCCCccccc
Q 026298 16 QFLQKCSASGTPKGKA 31 (240)
Q Consensus 16 ~~~q~~~~sgt~kgk~ 31 (240)
.+||.|+.|.-||...
T Consensus 4 eiL~~CI~sAmPk~~~ 19 (20)
T PF05924_consen 4 EILQECIGSAMPKRRR 19 (20)
T ss_dssp HHHHHHHHCTS-----
T ss_pred HHHHHHHHHhcccccC
Confidence 6899999999998754
No 7
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=25.96 E-value=1.1e+02 Score=29.61 Aligned_cols=44 Identities=32% Similarity=0.360 Sum_probs=34.7
Q ss_pred cCCCCCCCCHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHH
Q 026298 142 DKIPKYELTAEDGKRLAKEC--SRVLMRRHRARQAAESTLLRLKKE 185 (240)
Q Consensus 142 R~Rp~~eLs~EE~erL~KEW--SRyKmrEH~a~~~aI~~~l~aQqe 185 (240)
++||..-||-|...||..|| +||+-.+.+.+....-.+-++|-+
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIK 291 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIK 291 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhh
Confidence 77888999999999988887 689988888877766655555543
No 8
>PF05764 YL1: YL1 nuclear protein; InterPro: IPR008895 The proteins in this family are designated YL1 []. They have been shown to be DNA-binding and may be transcription factors [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=22.61 E-value=1.2e+02 Score=27.17 Aligned_cols=53 Identities=25% Similarity=0.209 Sum_probs=40.4
Q ss_pred cCCCCcccCChhhHHHHHHH-HHhccchhhhHHHHHHHHhh---cccccCCC-CCCcc
Q 026298 73 NAPTPVRFLTPKDKKREIER-EKLGLISKDRQREIDILKKG---GKQAMGIS-DEPMI 125 (240)
Q Consensus 73 nap~p~r~l~pk~r~rea~r-eklgl~sk~rqreld~~k~~---~~~~~~~~-~~~~~ 125 (240)
-....++.||..|+..||.. |+..+.|=.+-.+++..|+. ........ ..|+|
T Consensus 177 k~~~~~~~lTQeElL~EAk~TE~~N~~SL~~~~~~EeekKk~~~~~~~~K~~~~GP~i 234 (240)
T PF05764_consen 177 KKKQEERPLTQEELLEEAKETEEENLKSLNKYEELEEEKKKAQRQAQKKKKIYTGPVI 234 (240)
T ss_pred cccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCeE
Confidence 34578899999999999976 78889999999888888777 33344433 56655
No 9
>KOG3410 consensus Conserved alpha-helical protein [Function unknown]
Probab=22.52 E-value=2.9e+02 Score=23.49 Aligned_cols=76 Identities=22% Similarity=0.186 Sum_probs=45.6
Q ss_pred hhhhHHHHHHHHhhcccccCCCCCCcccCCCCCccccccCCcccCCCCCCCCHHHHH--HHHHHHHHHHHHHHHHHHHHH
Q 026298 99 SKDRQREIDILKKGGKQAMGISDEPMIMGTPGMDLISLGLVDADKIPKYELTAEDGK--RLAKECSRVLMRRHRARQAAE 176 (240)
Q Consensus 99 sk~rqreld~~k~~~~~~~~~~~~~~~~~~p~lDfiplkllDeR~Rp~~eLs~EE~e--rL~KEWSRyKmrEH~a~~~aI 176 (240)
+|.+++|-|+.........-..+.|.++++-|+|= .-...++-||... +..+.--.--..-|++.+...
T Consensus 30 ~K~k~~~e~~~r~~~~~~~~~~~t~~~~~~~G~d~---------k~T~Ae~~~e~~qe~~~~kril~~a~ktHk~rve~~ 100 (120)
T KOG3410|consen 30 HKHKDEEEDLSRDHVDAEIEERDTPKKEYSFGLDG---------KFTKAELRFEKVQEKRPCKRILKEAGKTHKERVEKF 100 (120)
T ss_pred ccchHHHHHHHhhcchhhhhcccccccccCCCCcc---------cccHHHHHHHHHHHhhHHHHHHHHHHhHHHHHHHHH
Confidence 46677777776655555666678899999999742 1134555555544 233333333344577777777
Q ss_pred HHHHHHH
Q 026298 177 STLLRLK 183 (240)
Q Consensus 177 ~~~l~aQ 183 (240)
+..|..+
T Consensus 101 n~~Ld~~ 107 (120)
T KOG3410|consen 101 NRHLDEM 107 (120)
T ss_pred HHHHhhc
Confidence 6665443
No 10
>PF13904 DUF4207: Domain of unknown function (DUF4207)
Probab=22.44 E-value=6e+02 Score=23.17 Aligned_cols=71 Identities=18% Similarity=0.235 Sum_probs=49.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh---cCHHHHHHhh---CCCCCCCCcccCCCc
Q 026298 144 IPKYELTAEDGKRLAKECSRVLMRRHRARQAAESTLLRLKKEAIEA---LPEDLKKAAL---VPDLTPFPVNRFMAT 214 (240)
Q Consensus 144 Rp~~eLs~EE~erL~KEWSRyKmrEH~a~~~aI~~~l~aQqeAL~e---LsEeLy~AAi---~pD~~lfP~~R~gPt 214 (240)
++....+.|+......+|-+.|+.+-.............+++.+++ ++++-|+.=| ..=+.|+|++..+..
T Consensus 172 ~~~~~~~~e~a~~~~q~W~~kK~~e~~~~r~~~~~~~~~~~~e~~eRk~~ae~A~~~Wl~~~~~kpkpvp~~~G~~s 248 (264)
T PF13904_consen 172 KPEREVSQEEAKQRYQEWERKKKEEQQQKREEEREKEQQKQQEEQERKEQAEEAFQKWLKNVKNKPKPVPLNQGYDS 248 (264)
T ss_pred ccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCCCCcCCCCCc
Confidence 5677888899989999999999998888877766655554444443 3666444332 333457788887774
No 11
>PRK08881 rpsN 30S ribosomal protein S14; Reviewed
Probab=21.85 E-value=50 Score=26.43 Aligned_cols=23 Identities=17% Similarity=0.482 Sum_probs=19.0
Q ss_pred ccchhhhhhhhcccCCCcccccc
Q 026298 10 LEYLSHQFLQKCSASGTPKGKAK 32 (240)
Q Consensus 10 ~~~~~~~~~q~~~~sgt~kgk~k 32 (240)
-+|+..++-.||.++|-|+|--.
T Consensus 53 r~ss~tRi~NRC~~TGR~Rgv~r 75 (101)
T PRK08881 53 RNSSPTRLRNRCELTGRPRGYYR 75 (101)
T ss_pred cccchHHHhccccCCCCCCcccc
Confidence 36778888889999999998653
Done!