Query psy14468
Match_columns 108
No_of_seqs 93 out of 111
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 20:37:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14468.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14468hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03196 MOC1-like protein; Pr 99.4 3.1E-13 6.8E-18 114.3 5.2 82 9-99 363-445 (487)
2 PF02536 mTERF: mTERF; InterP 99.3 5.2E-13 1.1E-17 105.1 2.6 76 9-91 266-345 (345)
3 KOG1267|consensus 97.4 4.1E-05 8.9E-10 63.1 0.8 90 11-104 291-389 (413)
4 smart00733 Mterf Mitochondrial 96.8 0.00097 2.1E-08 34.5 2.0 28 38-65 3-30 (31)
5 PLN03196 MOC1-like protein; Pr 96.0 0.011 2.4E-07 50.6 5.0 54 11-65 330-388 (487)
6 PF02536 mTERF: mTERF; InterP 95.4 0.027 5.8E-07 44.4 4.5 55 10-65 232-291 (345)
7 smart00733 Mterf Mitochondrial 94.2 0.038 8.2E-07 28.3 1.8 25 10-35 7-31 (31)
8 KOG1267|consensus 93.6 0.072 1.6E-06 44.0 3.4 55 11-65 354-410 (413)
9 KOG3890|consensus 59.7 2.8 6E-05 35.4 -0.2 30 53-82 192-221 (391)
10 smart00153 VHP Villin headpiec 47.0 25 0.00054 20.2 2.5 19 84-103 2-20 (36)
11 PF11802 CENP-K: Centromere-as 46.8 13 0.00028 30.3 1.7 24 58-81 243-266 (268)
12 KOG1079|consensus 41.6 26 0.00056 32.2 2.9 64 39-104 465-539 (739)
13 PF10245 MRP-S22: Mitochondria 40.0 4.9 0.00011 32.3 -1.6 27 54-80 155-181 (243)
14 PF09012 FeoC: FeoC like trans 39.6 44 0.00096 20.7 3.1 44 21-67 2-45 (69)
15 PF02209 VHP: Villin headpiece 38.9 36 0.00079 19.6 2.3 19 84-103 2-20 (36)
16 PF08410 DUF1737: Domain of un 36.3 25 0.00054 22.1 1.5 15 81-95 9-23 (54)
17 KOG0721|consensus 33.3 1.4E+02 0.003 24.0 5.6 68 28-106 86-163 (230)
18 COG3598 RepA RecA-family ATPas 29.1 52 0.0011 28.3 2.7 50 17-67 138-194 (402)
19 COG1839 Uncharacterized conser 27.4 51 0.0011 25.0 2.1 16 49-64 144-159 (162)
20 PF03875 Statherin: Statherin; 25.6 56 0.0012 19.5 1.6 11 57-67 5-15 (42)
21 COG5515 Uncharacterized conser 25.3 39 0.00084 22.2 1.0 19 78-96 5-24 (70)
22 PF00536 SAM_1: SAM domain (St 25.3 17 0.00038 21.8 -0.6 39 58-97 10-49 (64)
23 PF12435 DUF3678: Protein of u 24.6 36 0.00077 20.0 0.7 16 47-62 20-35 (38)
24 PF11809 DUF3330: Domain of un 23.7 1.1E+02 0.0024 20.3 2.9 30 75-106 20-49 (70)
25 KOG3265|consensus 22.2 19 0.00041 29.1 -1.1 25 56-85 69-93 (250)
26 PF04682 Herpes_BTRF1: Herpesv 20.9 44 0.00095 27.2 0.7 36 31-66 90-125 (256)
27 CHL00027 rps15 ribosomal prote 20.7 1.4E+02 0.003 20.5 3.1 48 5-66 20-70 (90)
28 PRK05626 rpsO 30S ribosomal pr 20.3 1.1E+02 0.0024 20.7 2.6 49 5-67 23-74 (89)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=99.39 E-value=3.1e-13 Score=114.33 Aligned_cols=82 Identities=21% Similarity=0.297 Sum_probs=75.1
Q ss_pred HhHhhhhcChhhHHHHHHHHHHhhCCChhhHhhhhhhhhccHH-HHHHHHHHHHHhCCcCCCCCCCCcccccccccCChH
Q psy14468 9 LQAIFLSLDATELVKTFNYVHSDMKVPHERILEFPNILTSRRF-RIENRHSYLKSLGRDQYDPCKENYVSMKSLVSGTDA 87 (108)
Q Consensus 9 ~~~~ll~~~~~~L~~kf~Y~~~~M~i~~~~I~k~P~~l~~s~~-~Ir~RH~FL~~LGr~qyDP~~p~y~~L~~lv~~~D~ 87 (108)
..|.+|..+.++|..|++|++|+||.++++|+++|.+|.+|++ ||++||.+|+.-|. ..+|..++..+|+
T Consensus 363 k~P~lL~~S~~~l~~k~dFlvneMg~~~~~Iv~fP~~LsySLEkRI~PR~~~L~~kGl---------~~sL~~~L~~sd~ 433 (487)
T PLN03196 363 RCPQILALNLEIMKPSLEFFKKEMKRPLKELVEFPAYFTYGLESRIKPRYERVAKKGI---------KCSLAWFLNCSDD 433 (487)
T ss_pred hCCceeeccHHHHHHHHHHHHHHhCCCHHHHHhChHHhccChhhhhHHHHHHHHHcCC---------CCCHHHHhccCHH
Confidence 4688999999999999999999999999999999999999965 99999999998887 3699999999999
Q ss_pred HHHHHHhcCCHH
Q psy14468 88 EFCANVAKTTPE 99 (108)
Q Consensus 88 ~F~~~vA~~s~e 99 (108)
.|+++++.-..|
T Consensus 434 ~F~~r~v~~y~e 445 (487)
T PLN03196 434 KFEQRMSGDFIE 445 (487)
T ss_pred HHHHHHhhhccc
Confidence 999998876544
No 2
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=99.33 E-value=5.2e-13 Score=105.07 Aligned_cols=76 Identities=33% Similarity=0.424 Sum_probs=60.4
Q ss_pred HhHhhhhcChhhHHHHHHHHHHhhCCChhhHhhhhhhhhccH-HHHHHH---HHHHHHhCCcCCCCCCCCcccccccccC
Q psy14468 9 LQAIFLSLDATELVKTFNYVHSDMKVPHERILEFPNILTSRR-FRIENR---HSYLKSLGRDQYDPCKENYVSMKSLVSG 84 (108)
Q Consensus 9 ~~~~ll~~~~~~L~~kf~Y~~~~M~i~~~~I~k~P~~l~~s~-~~Ir~R---H~FL~~LGr~qyDP~~p~y~~L~~lv~~ 84 (108)
.+|+||..+.+.|.++++|++++||+++++|+++|.+|.+|+ .||++| |.+|...|+ ..++||.+++..
T Consensus 266 ~~P~iL~~s~e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~~~l~~~g~-------~~~~sl~~~l~~ 338 (345)
T PF02536_consen 266 RFPQILSYSIEKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVLKVLKSKGL-------IINPSLSSMLSC 338 (345)
T ss_dssp HSGGGGGS-HHHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHHHTT--TTT-------GGGGGS-HHHHH
T ss_pred hCcchhhcchhhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHHHHHHHCcC-------CCCCCHHHHhhc
Confidence 479999999999999999999999999999999999999996 589999 555555552 337999999999
Q ss_pred ChHHHHH
Q psy14468 85 TDAEFCA 91 (108)
Q Consensus 85 ~D~~F~~ 91 (108)
||++|+.
T Consensus 339 s~~~F~~ 345 (345)
T PF02536_consen 339 SDEEFLK 345 (345)
T ss_dssp HHHHHT-
T ss_pred cHHHhcC
Confidence 9999973
No 3
>KOG1267|consensus
Probab=97.44 E-value=4.1e-05 Score=63.14 Aligned_cols=90 Identities=21% Similarity=0.383 Sum_probs=70.9
Q ss_pred HhhhhcChhhHHHHHHHHHHhhCCChhhHhhhhhhhhccHHHHHHHHHHHHHhCCcC----CCCCC-CCccc--cccccc
Q psy14468 11 AIFLSLDATELVKTFNYVHSDMKVPHERILEFPNILTSRRFRIENRHSYLKSLGRDQ----YDPCK-ENYVS--MKSLVS 83 (108)
Q Consensus 11 ~~ll~~~~~~L~~kf~Y~~~~M~i~~~~I~k~P~~l~~s~~~Ir~RH~FL~~LGr~q----yDP~~-p~y~~--L~~lv~ 83 (108)
|.+|+.+.+.+..++.|+.+. .++ +.++|++++++...|.+||+||..+|.-- ..++. |.++. +..++.
T Consensus 291 P~~l~~s~~~~~~~~~~~~~~---~~~-~~k~p~~l~~s~~~l~~~ie~l~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~ 366 (413)
T KOG1267|consen 291 PQILGYSVKKNLKTTEYLLKN---PKH-ILKFPQLLRSSEDKLKPRIEFLLSLGFSDVQILEMVKRFPQYLSFSLEKILK 366 (413)
T ss_pred chheEeehhhhhHHHHHHHhc---chh-hhhhhhhhhccchhhhhhHHHHHHcCCcHHHHHHHHhhccHHhhhhHHhhhh
Confidence 788999999999999999999 333 99999999999999999999999999642 33444 65554 666888
Q ss_pred CChHHHHHHHhc--CCHHHHHHH
Q psy14468 84 GTDAEFCANVAK--TTPETYNLF 104 (108)
Q Consensus 84 ~~D~~F~~~vA~--~s~eey~~F 104 (108)
..++-+++.++. ..+-.|..|
T Consensus 367 ~~~~~~~~~~~~p~~~~~~~p~~ 389 (413)
T KOG1267|consen 367 RKYEYLLKGLLRPLSALVSFPAF 389 (413)
T ss_pred hhHHHHHHHcCchHHHHhccchh
Confidence 888888888873 344444444
No 4
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=96.81 E-value=0.00097 Score=34.53 Aligned_cols=28 Identities=29% Similarity=0.516 Sum_probs=25.9
Q ss_pred hHhhhhhhhhccHHHHHHHHHHHHHhCC
Q psy14468 38 RILEFPNILTSRRFRIENRHSYLKSLGR 65 (108)
Q Consensus 38 ~I~k~P~~l~~s~~~Ir~RH~FL~~LGr 65 (108)
.|.++|.+|.++...|++|..||+.+|.
T Consensus 3 ~~~~~P~il~~~~~~l~~~~~~l~~~g~ 30 (31)
T smart00733 3 ILKKFPQILGYSEKKLKPKVEFLKELGF 30 (31)
T ss_pred hhhhCcCcccccHHHhhHHHHHHHHcCC
Confidence 4788999999999999999999999985
No 5
>PLN03196 MOC1-like protein; Provisional
Probab=96.04 E-value=0.011 Score=50.57 Aligned_cols=54 Identities=15% Similarity=0.292 Sum_probs=39.6
Q ss_pred HhhhhcChhhHHHHHHHHHHhhCCChhhH----hhhhhhhhccHHHHHHHHHHHHH-hCC
Q psy14468 11 AIFLSLDATELVKTFNYVHSDMKVPHERI----LEFPNILTSRRFRIENRHSYLKS-LGR 65 (108)
Q Consensus 11 ~~ll~~~~~~L~~kf~Y~~~~M~i~~~~I----~k~P~~l~~s~~~Ir~RH~FL~~-LGr 65 (108)
|.++..+.+.+.++++|+.+ +|++.++| .++|++|.+|...|+..-.||+. +|+
T Consensus 330 P~il~lSe~kl~~kvefL~~-~Gls~edI~~mv~k~P~lL~~S~~~l~~k~dFlvneMg~ 388 (487)
T PLN03196 330 PQIVSLNRNVALKHVEFLRG-RGFSAQDVAKMVVRCPQILALNLEIMKPSLEFFKKEMKR 388 (487)
T ss_pred chhhcccHHHHHHHHHHHHH-cCCCHHHHHHHHHhCCceeeccHHHHHHHHHHHHHHhCC
Confidence 55666666777777887765 78887777 57788888888888888887753 665
No 6
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=95.39 E-value=0.027 Score=44.43 Aligned_cols=55 Identities=24% Similarity=0.432 Sum_probs=41.5
Q ss_pred hHhhhhcChhhHHHHHHHHHHhhCCChhhH----hhhhhhhhccHHHHHHHHHHHHH-hCC
Q psy14468 10 QAIFLSLDATELVKTFNYVHSDMKVPHERI----LEFPNILTSRRFRIENRHSYLKS-LGR 65 (108)
Q Consensus 10 ~~~ll~~~~~~L~~kf~Y~~~~M~i~~~~I----~k~P~~l~~s~~~Ir~RH~FL~~-LGr 65 (108)
-|.++..+.+.+.++.+|+.. +|++.++| .++|++|.++.++|+++-.||.. +|.
T Consensus 232 ~p~il~~~~~~l~~~i~~L~~-lG~s~~ei~~mv~~~P~iL~~s~e~l~~k~~fl~~~m~~ 291 (345)
T PF02536_consen 232 FPQILSLSEEKLKPKIEFLQS-LGFSEEEIAKMVRRFPQILSYSIEKLKPKFEFLVKEMGL 291 (345)
T ss_dssp -----THHHHHHHHHHHHHHT-TT--HHHHHHHHHHSGGGGGS-HHHHHHHHHHHHHCCT-
T ss_pred cccccccchHhHHHHHHHHHH-hcCcHHHHHHHHHhCcchhhcchhhhhHHHHHHHHHhCc
Confidence 467788888899999999998 99999998 57999999999999999999964 665
No 7
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=94.17 E-value=0.038 Score=28.27 Aligned_cols=25 Identities=8% Similarity=0.244 Sum_probs=22.6
Q ss_pred hHhhhhcChhhHHHHHHHHHHhhCCC
Q psy14468 10 QAIFLSLDATELVKTFNYVHSDMKVP 35 (108)
Q Consensus 10 ~~~ll~~~~~~L~~kf~Y~~~~M~i~ 35 (108)
-|.+|..+.+.|.++++|+. .||++
T Consensus 7 ~P~il~~~~~~l~~~~~~l~-~~g~~ 31 (31)
T smart00733 7 FPQILGYSEKKLKPKVEFLK-ELGFS 31 (31)
T ss_pred CcCcccccHHHhhHHHHHHH-HcCCC
Confidence 48899999999999999999 99975
No 8
>KOG1267|consensus
Probab=93.62 E-value=0.072 Score=44.03 Aligned_cols=55 Identities=24% Similarity=0.452 Sum_probs=49.4
Q ss_pred HhhhhcChh-hHHHHHHHHHHhhCCChhhHhhhhhhhhcc-HHHHHHHHHHHHHhCC
Q psy14468 11 AIFLSLDAT-ELVKTFNYVHSDMKVPHERILEFPNILTSR-RFRIENRHSYLKSLGR 65 (108)
Q Consensus 11 ~~ll~~~~~-~L~~kf~Y~~~~M~i~~~~I~k~P~~l~~s-~~~Ir~RH~FL~~LGr 65 (108)
|+++..+.+ .+..++.|....|+.+.+.++.+|++|.++ ..+|++||....++|.
T Consensus 354 Pq~l~~s~~~~~~~~~~~~~~~~~~p~~~~~~~p~~~~y~le~ri~pr~~~~~~~~~ 410 (413)
T KOG1267|consen 354 PQYLSFSLEKILKRKYEYLLKGLLRPLSALVSFPAFFGYSLEKRIRPRFNVIKKLGV 410 (413)
T ss_pred cHHhhhhHHhhhhhhHHHHHHHcCchHHHHhccchhhccchhhcchhHHHHHHHHhc
Confidence 666666666 888999999999999999999999999999 8999999999988875
No 9
>KOG3890|consensus
Probab=59.74 E-value=2.8 Score=35.36 Aligned_cols=30 Identities=23% Similarity=0.415 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhCCcCCCCCCCCcccccccc
Q psy14468 53 IENRHSYLKSLGRDQYDPCKENYVSMKSLV 82 (108)
Q Consensus 53 Ir~RH~FL~~LGr~qyDP~~p~y~~L~~lv 82 (108)
-+.||.|..-+-.+||.|+.|.|+.+++.|
T Consensus 192 ~~~~hefVLd~~~~qyEPd~pey~~is~~v 221 (391)
T KOG3890|consen 192 AEHKHEFVLDRLLVQYEPDEPEYHNISARV 221 (391)
T ss_pred hhcchHHHHHHHHHhcCCCChHHhhhHHHH
Confidence 467999999999999999999999888765
No 10
>smart00153 VHP Villin headpiece domain.
Probab=47.05 E-value=25 Score=20.17 Aligned_cols=19 Identities=26% Similarity=0.274 Sum_probs=15.7
Q ss_pred CChHHHHHHHhcCCHHHHHH
Q psy14468 84 GTDAEFCANVAKTTPETYNL 103 (108)
Q Consensus 84 ~~D~~F~~~vA~~s~eey~~ 103 (108)
.+|++|. .|-+.|-++|+.
T Consensus 2 LsdeeF~-~vfgmsr~eF~~ 20 (36)
T smart00153 2 LSDEDFE-EVFGMTREEFYK 20 (36)
T ss_pred CCHHHHH-HHHCCCHHHHHh
Confidence 4799999 788889999875
No 11
>PF11802 CENP-K: Centromere-associated protein K; InterPro: IPR020993 Cenp-K is one of seven new Cenp-A-nucleosome distal (CAD) centromere components (the others being Cenp-L, Cenp-O, Cenp-P, Cenp-Q, Cenp-R and Cenp-S) that are identified as assembling on the Cenp-A nucleosome associated complex, NAC []. The Cenp-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival despite continued centromere-derived mitotic checkpoint signalling. Cenp-K is centromere-associated through its interaction with one or more components of the Cenp-A NAC.; GO: 0005634 nucleus
Probab=46.77 E-value=13 Score=30.32 Aligned_cols=24 Identities=13% Similarity=0.189 Sum_probs=21.3
Q ss_pred HHHHHhCCcCCCCCCCCccccccc
Q psy14468 58 SYLKSLGRDQYDPCKENYVSMKSL 81 (108)
Q Consensus 58 ~FL~~LGr~qyDP~~p~y~~L~~l 81 (108)
.||.|.|.|.++|.+|+-|.|.++
T Consensus 243 e~LlR~GIa~rHP~D~~kIRL~~F 266 (268)
T PF11802_consen 243 ELLLRSGIALRHPEDPSKIRLEDF 266 (268)
T ss_pred HHHHHcCCeeeCCCCcccccchhc
Confidence 799999999999999998887653
No 12
>KOG1079|consensus
Probab=41.60 E-value=26 Score=32.23 Aligned_cols=64 Identities=23% Similarity=0.366 Sum_probs=49.1
Q ss_pred HhhhhhhhhccHHHHHHHHHHHHHhCCcC-------CC----CCCCCcccccccccCChHHHHHHHhcCCHHHHHHH
Q psy14468 39 ILEFPNILTSRRFRIENRHSYLKSLGRDQ-------YD----PCKENYVSMKSLVSGTDAEFCANVAKTTPETYNLF 104 (108)
Q Consensus 39 I~k~P~~l~~s~~~Ir~RH~FL~~LGr~q-------yD----P~~p~y~~L~~lv~~~D~~F~~~vA~~s~eey~~F 104 (108)
++..|.-.+.+..++.-||.++.++.+.- |. |+.+| ....=.....+.||+++|.++.++=|.|
T Consensus 465 ~~~~~~~~r~~~~r~~g~~r~k~q~kk~~~~~~v~~~qpC~hp~~c~--c~~~C~C~~n~~~CEk~C~C~~dC~nrF 539 (739)
T KOG1079|consen 465 RVELPGPKRARKLRLWGRHRRKIQNKKDSRHTVVWNYQPCDHPGPCN--CGVGCPCIDNETFCEKFCYCSPDCRNRF 539 (739)
T ss_pred ccccCcchhhHHHHhhhhHHHhhhcccccCCceeeecCcccCCCCCC--CCCCCcccccCcchhhcccCCHHHHhcC
Confidence 34455556677899999999999888752 22 34343 6777778889999999999999998877
No 13
>PF10245 MRP-S22: Mitochondrial 28S ribosomal protein S22; InterPro: IPR019374 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 is the conserved N terminus and central portion of the mitochondrial small subunit 28S ribosomal protein S22. Mammalian mitochondria carry out the synthesis of 13 polypeptides that are essential for oxidative phosphorylation and, hence, for the synthesis of the majority of the ATP used by eukaryotic organisms. The number of proteins produced by prokaryotes is smaller, reflected in the lower number of ribosomal proteins present in them [].
Probab=40.00 E-value=4.9 Score=32.30 Aligned_cols=27 Identities=19% Similarity=0.529 Sum_probs=22.3
Q ss_pred HHHHHHHHHhCCcCCCCCCCCcccccc
Q psy14468 54 ENRHSYLKSLGRDQYDPCKENYVSMKS 80 (108)
Q Consensus 54 r~RH~FL~~LGr~qyDP~~p~y~~L~~ 80 (108)
+.||+|+.-+--+||+|++|+|+.+.+
T Consensus 155 ~~~~e~iLD~ac~QfEPdd~~y~rv~~ 181 (243)
T PF10245_consen 155 RDRHEFILDRACVQFEPDDPDYIRVHH 181 (243)
T ss_pred cccHHHHHHHHHHhcCCCCHHHHHHHH
Confidence 568889888888899999998876544
No 14
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=39.63 E-value=44 Score=20.72 Aligned_cols=44 Identities=14% Similarity=0.068 Sum_probs=36.6
Q ss_pred HHHHHHHHHHhhCCChhhHhhhhhhhhccHHHHHHHHHHHHHhCCcC
Q psy14468 21 LVKTFNYVHSDMKVPHERILEFPNILTSRRFRIENRHSYLKSLGRDQ 67 (108)
Q Consensus 21 L~~kf~Y~~~~M~i~~~~I~k~P~~l~~s~~~Ir~RH~FL~~LGr~q 67 (108)
|.+.-+|+...=.++..+|++. |..+...|+.--.+|++.|+..
T Consensus 2 L~~i~~~l~~~~~~S~~eLa~~---~~~s~~~ve~mL~~l~~kG~I~ 45 (69)
T PF09012_consen 2 LQEIRDYLRERGRVSLAELARE---FGISPEAVEAMLEQLIRKGYIR 45 (69)
T ss_dssp CHHHHHHHHHS-SEEHHHHHHH---TT--HHHHHHHHHHHHCCTSCE
T ss_pred HHHHHHHHHHcCCcCHHHHHHH---HCcCHHHHHHHHHHHHHCCcEE
Confidence 5567789999999999999977 9999999999999999999975
No 15
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=38.89 E-value=36 Score=19.57 Aligned_cols=19 Identities=21% Similarity=0.254 Sum_probs=14.2
Q ss_pred CChHHHHHHHhcCCHHHHHH
Q psy14468 84 GTDAEFCANVAKTTPETYNL 103 (108)
Q Consensus 84 ~~D~~F~~~vA~~s~eey~~ 103 (108)
.+|++|. +|-+.|-+||+.
T Consensus 2 Lsd~dF~-~vFgm~~~eF~~ 20 (36)
T PF02209_consen 2 LSDEDFE-KVFGMSREEFYK 20 (36)
T ss_dssp S-HHHHH-HHHSS-HHHHHH
T ss_pred cCHHHHH-HHHCCCHHHHHH
Confidence 4799998 677899999975
No 16
>PF08410 DUF1737: Domain of unknown function (DUF1737); InterPro: IPR013619 This domain of unknown function is found at the N terminus of bacterial and viral hypothetical proteins.
Probab=36.26 E-value=25 Score=22.06 Aligned_cols=15 Identities=33% Similarity=0.707 Sum_probs=11.5
Q ss_pred cccCChHHHHHHHhc
Q psy14468 81 LVSGTDAEFCANVAK 95 (108)
Q Consensus 81 lv~~~D~~F~~~vA~ 95 (108)
|..++|+.||.+|..
T Consensus 9 lt~~d~~~fc~rVt~ 23 (54)
T PF08410_consen 9 LTGPDDSAFCHRVTE 23 (54)
T ss_pred EECCChHHHHHHHHH
Confidence 445678899999864
No 17
>KOG0721|consensus
Probab=33.27 E-value=1.4e+02 Score=23.96 Aligned_cols=68 Identities=25% Similarity=0.231 Sum_probs=45.3
Q ss_pred HHHhhCCChhhHhhhhh-hhh----ccHHHHHHHHHHHHHhCCcCCCCCCCCcccccccccCChHHHHHHHhcC-----C
Q psy14468 28 VHSDMKVPHERILEFPN-ILT----SRRFRIENRHSYLKSLGRDQYDPCKENYVSMKSLVSGTDAEFCANVAKT-----T 97 (108)
Q Consensus 28 ~~~~M~i~~~~I~k~P~-~l~----~s~~~Ir~RH~FL~~LGr~qyDP~~p~y~~L~~lv~~~D~~F~~~vA~~-----s 97 (108)
+++.|+..++.....|- +|. .+..+||-|..=|- .+|.|++--.+ +.|++|.+.|||+ .
T Consensus 86 ~y~i~~~~~~~~~fDPyEILGl~pgas~~eIKkaYR~LS----ik~HPDK~~~~-------~~~e~~~~~I~KAY~aLTD 154 (230)
T KOG0721|consen 86 IYKIMNSRRERQKFDPYEILGLDPGASEKEIKKAYRRLS----IKYHPDKQPPE-------EGDEEFFEAIAKAYQALTD 154 (230)
T ss_pred HHHHhhhhHHhhcCCcHHhhCCCCCCCHHHHHHHHHHhh----hhhCCCcCCCc-------chhHHHHHHHHHHHHHhcc
Confidence 35677777777777775 443 34888998876654 47778773111 7889999999874 3
Q ss_pred HHHHHHHHh
Q psy14468 98 PETYNLFLK 106 (108)
Q Consensus 98 ~eey~~FlK 106 (108)
.+..++|.|
T Consensus 155 ~~sreN~ek 163 (230)
T KOG0721|consen 155 KKSRENWEK 163 (230)
T ss_pred hhhHHHHHH
Confidence 445555544
No 18
>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]
Probab=29.05 E-value=52 Score=28.25 Aligned_cols=50 Identities=8% Similarity=0.153 Sum_probs=33.8
Q ss_pred ChhhHHHHHHHHHHhhCCChhhHhhhhhhhhcc-----HHHH--HHHHHHHHHhCCcC
Q psy14468 17 DATELVKTFNYVHSDMKVPHERILEFPNILTSR-----RFRI--ENRHSYLKSLGRDQ 67 (108)
Q Consensus 17 ~~~~L~~kf~Y~~~~M~i~~~~I~k~P~~l~~s-----~~~I--r~RH~FL~~LGr~q 67 (108)
+++.+..+++|+...||+++.+|-+- ++-..+ .+.| +-=|.|++-+--..
T Consensus 138 ~re~~L~Rl~~v~a~mgLsPadvrn~-dltd~~Gaa~~~d~l~pkl~rRfek~~~Q~r 194 (402)
T COG3598 138 YREDILERLEPVRARMGLSPADVRNM-DLTDVSGAADESDVLSPKLYRRFEKILEQKR 194 (402)
T ss_pred ChHHHHHHHHHHHHHcCCChHhhhhe-eccccccCCCccccccHHHHHHHHHHHHHhC
Confidence 67889999999999999999999776 331111 1222 33667776654443
No 19
>COG1839 Uncharacterized conserved protein [Function unknown]
Probab=27.38 E-value=51 Score=24.98 Aligned_cols=16 Identities=25% Similarity=0.457 Sum_probs=14.2
Q ss_pred cHHHHHHHHHHHHHhC
Q psy14468 49 RRFRIENRHSYLKSLG 64 (108)
Q Consensus 49 s~~~Ir~RH~FL~~LG 64 (108)
+...|++|++||..+|
T Consensus 144 ~d~d~~~Rr~~lr~Ig 159 (162)
T COG1839 144 TDEDIAERRELLRKIG 159 (162)
T ss_pred cHHHHHHHHHHHHHhc
Confidence 3678999999999999
No 20
>PF03875 Statherin: Statherin; InterPro: IPR005575 Statherin functions biologically to inhibit the nucleation and growth of calcium phosphate minerals. The N terminus of statherin is highly charged, the glutamic acids of which have been shown to be important in the recognition hydroxyapatite [].
Probab=25.65 E-value=56 Score=19.51 Aligned_cols=11 Identities=36% Similarity=0.616 Sum_probs=8.7
Q ss_pred HHHHHHhCCcC
Q psy14468 57 HSYLKSLGRDQ 67 (108)
Q Consensus 57 H~FL~~LGr~q 67 (108)
..||.+||++-
T Consensus 5 ekflrrl~r~~ 15 (42)
T PF03875_consen 5 EKFLRRLGRFF 15 (42)
T ss_pred HHHHHHHHhhc
Confidence 47899998875
No 21
>COG5515 Uncharacterized conserved small protein [Function unknown]
Probab=25.33 E-value=39 Score=22.25 Aligned_cols=19 Identities=21% Similarity=0.572 Sum_probs=12.6
Q ss_pred ccccc-cCChHHHHHHHhcC
Q psy14468 78 MKSLV-SGTDAEFCANVAKT 96 (108)
Q Consensus 78 L~~lv-~~~D~~F~~~vA~~ 96 (108)
|..++ .++|..||.+|..+
T Consensus 5 LYRfiTGpDDssFChrvta~ 24 (70)
T COG5515 5 LYRFITGPDDSSFCHRVTAA 24 (70)
T ss_pred eeEeecCCchHHHHHHHHHH
Confidence 44444 45677999998653
No 22
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=25.26 E-value=17 Score=21.77 Aligned_cols=39 Identities=33% Similarity=0.537 Sum_probs=28.2
Q ss_pred HHHHHhCCcCCCC-CCCCcccccccccCChHHHHHHHhcCC
Q psy14468 58 SYLKSLGRDQYDP-CKENYVSMKSLVSGTDAEFCANVAKTT 97 (108)
Q Consensus 58 ~FL~~LGr~qyDP-~~p~y~~L~~lv~~~D~~F~~~vA~~s 97 (108)
.||..+|..+|-+ -..++++...|+..+++++.. +.-..
T Consensus 10 ~WL~~~~l~~y~~~F~~~~i~g~~L~~lt~~dL~~-lgi~~ 49 (64)
T PF00536_consen 10 EWLKSLGLEQYAENFEKNYIDGEDLLSLTEEDLEE-LGITK 49 (64)
T ss_dssp HHHHHTTGGGGHHHHHHTTSSHHHHTTSCHHHHHH-TT-SS
T ss_pred HHHHHCCCHHHHHHHHcCCchHHHHHhcCHHHHHH-cCCCC
Confidence 5788889888732 234689999999999999775 44333
No 23
>PF12435 DUF3678: Protein of unknown function (DUF3678) ; InterPro: IPR022146 This domain family is found in eukaryotes, and is approximately 40 amino acids in length.
Probab=24.57 E-value=36 Score=19.99 Aligned_cols=16 Identities=25% Similarity=0.387 Sum_probs=12.9
Q ss_pred hccHHHHHHHHHHHHH
Q psy14468 47 TSRRFRIENRHSYLKS 62 (108)
Q Consensus 47 ~~s~~~Ir~RH~FL~~ 62 (108)
+++..+.++||.||..
T Consensus 20 S~~~~H~~~~~~fl~~ 35 (38)
T PF12435_consen 20 SSSMLHRQCRHIFLDY 35 (38)
T ss_pred ccchhhhhhcchhhhc
Confidence 4558899999999863
No 24
>PF11809 DUF3330: Domain of unknown function (DUF3330); InterPro: IPR021767 This family of proteins are functionally uncharacterised. This family is only found in bacteria.
Probab=23.71 E-value=1.1e+02 Score=20.31 Aligned_cols=30 Identities=13% Similarity=0.269 Sum_probs=25.4
Q ss_pred cccccccccCChHHHHHHHhcCCHHHHHHHHh
Q psy14468 75 YVSMKSLVSGTDAEFCANVAKTTPETYNLFLK 106 (108)
Q Consensus 75 y~~L~~lv~~~D~~F~~~vA~~s~eey~~FlK 106 (108)
.|||+....+.-.+++...++ +|.|+.|++
T Consensus 20 EIPl~~a~t~E~~eYV~hFCG--LeCY~~w~a 49 (70)
T PF11809_consen 20 EIPLDAAFTPEAAEYVEHFCG--LECYQRWQA 49 (70)
T ss_pred hCChhhccCcchHHHHHHHhh--HHHHHHHHH
Confidence 589999888888888888876 899999975
No 25
>KOG3265|consensus
Probab=22.18 E-value=19 Score=29.10 Aligned_cols=25 Identities=24% Similarity=0.254 Sum_probs=19.7
Q ss_pred HHHHHHHhCCcCCCCCCCCcccccccccCC
Q psy14468 56 RHSYLKSLGRDQYDPCKENYVSMKSLVSGT 85 (108)
Q Consensus 56 RH~FL~~LGr~qyDP~~p~y~~L~~lv~~~ 85 (108)
||.| -+|.||-+|+.||+..+|..|
T Consensus 69 ~~~F-----Vf~AD~Pd~~kIP~~d~vGVT 93 (250)
T KOG3265|consen 69 RHKF-----VFQADAPDPSKIPEDDIVGVT 93 (250)
T ss_pred ceEE-----EEecCCCCcccCcccceeeeE
Confidence 5555 368899999999999998654
No 26
>PF04682 Herpes_BTRF1: Herpesvirus BTRF1 protein conserved region; InterPro: IPR006772 This is a family of Herpesvirus proteins of unknown function.
Probab=20.87 E-value=44 Score=27.16 Aligned_cols=36 Identities=19% Similarity=0.224 Sum_probs=28.7
Q ss_pred hhCCChhhHhhhhhhhhccHHHHHHHHHHHHHhCCc
Q psy14468 31 DMKVPHERILEFPNILTSRRFRIENRHSYLKSLGRD 66 (108)
Q Consensus 31 ~M~i~~~~I~k~P~~l~~s~~~Ir~RH~FL~~LGr~ 66 (108)
.|.-+|+.+--.|..--...+++==-|..|.|+|.-
T Consensus 90 IM~rShNsL~~~P~~~inp~Q~LfLKHvlL~r~GLE 125 (256)
T PF04682_consen 90 IMNRSHNSLRLVPDSDINPLQHLFLKHVLLKRMGLE 125 (256)
T ss_pred eeecccCceeecCCCCcCHHHHHHHHHHHHHHhChH
Confidence 477788888888866666788888889999999984
No 27
>CHL00027 rps15 ribosomal protein S15
Probab=20.71 E-value=1.4e+02 Score=20.49 Aligned_cols=48 Identities=17% Similarity=0.200 Sum_probs=32.0
Q ss_pred hhHHHhHhhhhcChhhHHHHHHHHHHhhCCChhhHhhhhhhhhcc---HHHHHHHHHHHHHhCCc
Q psy14468 5 TSTALQAIFLSLDATELVKTFNYVHSDMKVPHERILEFPNILTSR---RFRIENRHSYLKSLGRD 66 (108)
Q Consensus 5 ~~~~~~~~ll~~~~~~L~~kf~Y~~~~M~i~~~~I~k~P~~l~~s---~~~Ir~RH~FL~~LGr~ 66 (108)
.|.+.|..+|+.....|.+ .|. ++|.-+.++ ...|-.|...|.+|.+-
T Consensus 20 GS~evQiA~LT~rI~~Lt~-------Hlk-------~hkKD~~s~RgL~~lv~kRkrLL~YL~r~ 70 (90)
T CHL00027 20 GSVEFQVFSFTNKIRRLTS-------HLE-------LHKKDYSSQRGLRKILGKRQRLLAYLSKK 70 (90)
T ss_pred CChHHHHHHHHHHHHHHHH-------HHH-------HCCCcchhHHHHHHHHHHHHHHHHHHHhC
Confidence 4778899988776666654 443 333434443 44567899999999874
No 28
>PRK05626 rpsO 30S ribosomal protein S15; Reviewed
Probab=20.34 E-value=1.1e+02 Score=20.74 Aligned_cols=49 Identities=22% Similarity=0.250 Sum_probs=31.9
Q ss_pred hhHHHhHhhhhcChhhHHHHHHHHHHhhCCChhhHhhhhhhhhcc---HHHHHHHHHHHHHhCCcC
Q psy14468 5 TSTALQAIFLSLDATELVKTFNYVHSDMKVPHERILEFPNILTSR---RFRIENRHSYLKSLGRDQ 67 (108)
Q Consensus 5 ~~~~~~~~ll~~~~~~L~~kf~Y~~~~M~i~~~~I~k~P~~l~~s---~~~Ir~RH~FL~~LGr~q 67 (108)
.|.+.|.++|+.....|++ .|. .+|.-+.++ ...+-.|...|.+|.+-.
T Consensus 23 GS~eVQiA~LT~rI~~L~~-------Hlk-------~~~KD~~srrgL~~lv~kRkrlL~YL~~~d 74 (89)
T PRK05626 23 GSPEVQVALLTERINHLTE-------HLK-------EHKKDHHSRRGLLKMVGQRRKLLDYLKKKD 74 (89)
T ss_pred CCHHHHHHHHHHHHHHHHH-------HHH-------HcccchhhHHHHHHHHHhHHHHHHHHHhcC
Confidence 4778888888776666654 333 333434443 445678999999997743
Done!