Query 033353
Match_columns 121
No_of_seqs 141 out of 266
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 12:51:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033353.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033353hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1762 60s acidic ribosomal p 99.9 2E-23 4.4E-28 153.0 3.6 91 30-121 22-114 (114)
2 cd05833 Ribosomal_P2 Ribosomal 99.8 2.3E-19 4.9E-24 130.2 2.8 88 31-121 18-109 (109)
3 PTZ00373 60S Acidic ribosomal 99.7 1.1E-18 2.3E-23 127.6 2.2 84 33-121 22-112 (112)
4 PLN00138 large subunit ribosom 99.7 4.5E-18 9.8E-23 124.2 4.0 89 31-121 18-113 (113)
5 cd04411 Ribosomal_P1_P2_L12p R 99.7 8.6E-18 1.9E-22 121.1 2.6 87 31-120 17-105 (105)
6 cd05831 Ribosomal_P1 Ribosomal 99.6 1.2E-16 2.7E-21 114.6 3.2 85 32-120 19-103 (103)
7 KOG3449 60S acidic ribosomal p 99.5 1.2E-14 2.5E-19 106.6 2.0 85 36-121 23-112 (112)
8 PF00428 Ribosomal_60s: 60s Ac 99.4 1.6E-16 3.5E-21 109.8 -10.2 79 37-120 8-88 (88)
9 COG2058 RPP1A Ribosomal protei 99.4 1.5E-13 3.3E-18 100.4 1.6 86 35-121 21-109 (109)
10 PRK06402 rpl12p 50S ribosomal 99.0 5.4E-11 1.2E-15 86.5 0.6 42 32-74 18-59 (106)
11 TIGR03685 L21P_arch 50S riboso 98.5 5.7E-08 1.2E-12 70.2 1.4 43 31-74 17-59 (105)
12 PTZ00135 60S acidic ribosomal 98.4 3.2E-08 7E-13 82.4 -0.3 21 42-62 227-247 (310)
13 cd05832 Ribosomal_L12p Ribosom 98.4 7.7E-08 1.7E-12 70.0 1.2 43 31-74 17-59 (106)
14 PTZ00240 60S ribosomal protein 97.3 0.00015 3.3E-09 61.3 2.3 15 104-118 306-320 (323)
15 KOG3449 60S acidic ribosomal p 92.9 0.09 2E-06 39.0 2.6 80 30-118 33-112 (112)
16 cd05833 Ribosomal_P2 Ribosomal 89.5 0.2 4.2E-06 36.5 1.4 19 95-113 86-104 (109)
17 cd04411 Ribosomal_P1_P2_L12p R 88.2 0.29 6.3E-06 35.4 1.6 28 31-58 33-60 (105)
18 cd05831 Ribosomal_P1 Ribosomal 83.6 0.82 1.8E-05 32.8 1.9 18 34-51 37-54 (103)
19 PLN00138 large subunit ribosom 82.2 0.92 2E-05 33.3 1.8 15 97-112 93-107 (113)
20 PTZ00373 60S Acidic ribosomal 79.5 1.4 3.1E-05 32.4 2.0 18 35-52 40-57 (112)
21 PTZ00240 60S ribosomal protein 70.8 2.8 6.1E-05 35.7 1.9 11 102-112 307-317 (323)
22 PRK06402 rpl12p 50S ribosomal 67.8 4 8.7E-05 29.8 1.9 38 14-52 16-54 (106)
23 cd05832 Ribosomal_L12p Ribosom 65.5 3.8 8.1E-05 29.9 1.4 13 38-50 40-52 (106)
24 PRK04019 rplP0 acidic ribosoma 60.3 4.6 0.0001 33.9 1.2 8 63-70 282-289 (330)
25 COG2058 RPP1A Ribosomal protei 56.9 6.8 0.00015 29.0 1.5 8 113-120 98-105 (109)
26 smart00834 CxxC_CXXC_SSSS Puta 50.5 13 0.00028 21.2 1.7 21 1-21 1-21 (41)
27 PTZ00135 60S acidic ribosomal 37.5 21 0.00045 30.1 1.6 18 104-121 293-310 (310)
28 PF08465 Herpes_TK_C: Thymidin 35.5 17 0.00036 21.7 0.6 26 46-71 4-29 (33)
29 cd06888 PX_FISH The phosphoino 34.8 37 0.0008 24.8 2.4 29 7-43 25-53 (119)
30 TIGR02605 CxxC_CxxC_SSSS putat 29.5 47 0.001 20.0 1.9 20 1-20 1-20 (52)
31 cd06882 PX_p40phox The phospho 28.0 74 0.0016 23.0 3.0 34 3-44 22-56 (123)
32 PF09723 Zn-ribbon_8: Zinc rib 26.6 58 0.0013 19.4 1.9 21 1-21 1-21 (42)
33 cd06887 PX_p47phox The phospho 25.2 86 0.0019 22.9 2.9 29 8-44 26-54 (118)
34 PF02751 TFIIA_gamma_C: Transc 24.7 49 0.0011 21.4 1.4 9 2-10 20-28 (52)
35 PF08228 RNase_P_pop3: RNase P 22.7 51 0.0011 25.5 1.4 9 3-11 75-83 (158)
36 cd06889 PX_NoxO1 The phosphoin 22.7 1.1E+02 0.0023 22.7 3.1 18 27-44 38-55 (121)
37 KOG2240 RNA polymerase II gene 22.6 78 0.0017 24.9 2.4 48 8-56 17-64 (162)
No 1
>KOG1762 consensus 60s acidic ribosomal protein P1 [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=2e-23 Score=153.01 Aligned_cols=91 Identities=35% Similarity=0.464 Sum_probs=66.6
Q ss_pred cchHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCCCCCcc-CCCCCCCCCCCCCCCC-CCCchhhhhccc
Q 033353 30 ASTYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAVGSGFI-GGGAAASAPSGGGGAA-AEAPAAEEKKEE 107 (121)
Q Consensus 30 ~~~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~g~~~~-gggaAa~aaagg~~aa-a~~~k~EekkEE 107 (121)
..|-+.-.+|++++. ++|++|||.||++.|+++||.++|+|+|.|++++ ++.++++.|+++++++ ++++|+|.||||
T Consensus 22 ~it~dki~tl~kaa~-v~ve~~Wp~lfakale~vni~~li~n~gag~~a~a~~~~~~~~aa~~~~aA~~~Ekk~eak~Ee 100 (114)
T KOG1762|consen 22 EVTADKINTLTKAAG-VNVEPYWPGLFAKALEGVNIKELICNVGAGGGALAAGAAAAGGAAAAGGAAAAEEKKEEAKKEE 100 (114)
T ss_pred eeehhhhhhHHHhcc-CcccccchhHHHHHhccCChHHHHHhcccCCccCCCccccccccccccccccchHHHHHhhhhh
Confidence 345566677777665 9999999999999999999999999999754443 2222222333333233 456666667778
Q ss_pred ccccccccCcCCCC
Q 033353 108 KEESDEDMGFSLFD 121 (121)
Q Consensus 108 ~EEsddDmGF~LFD 121 (121)
.|||||||||+|||
T Consensus 101 seesddDmgfGLfd 114 (114)
T KOG1762|consen 101 SEESDDDMGFGLFD 114 (114)
T ss_pred hcccccccccCCCC
Confidence 89999999999998
No 2
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=99.76 E-value=2.3e-19 Score=130.16 Aligned_cols=88 Identities=33% Similarity=0.389 Sum_probs=55.8
Q ss_pred chHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCC--CCCcc-CCCCCCCCCCCCCCCCCCCchhhhhc-c
Q 033353 31 STYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAV--GSGFI-GGGAAASAPSGGGGAAAEAPAAEEKK-E 106 (121)
Q Consensus 31 ~~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~--g~~~~-gggaAa~aaagg~~aaa~~~k~Eekk-E 106 (121)
.|-+=-+++++++- ++|+++|+.+|++.|.+|||.+||.++.. +..++ +++++++ ++++++++.++++++|| |
T Consensus 18 pTa~dI~~IL~AaG-veVe~~~~~lf~~~L~GKdi~eLIa~g~~kl~s~~~~~~~aa~a--~~~~a~aa~~~~~e~kkee 94 (109)
T cd05833 18 PSAADVKKILGSVG-VEVDDEKLNKVISELEGKDVEELIAAGKEKLASVPAGAGGAAPA--AAAAAAAAAAAKKEEKKEE 94 (109)
T ss_pred CCHHHHHHHHHHcC-CCccHHHHHHHHHHHcCCCHHHHHHHhHhhhcCCCccccccccc--cccccccccchhhhhhccC
Confidence 34444566777766 99999999999999999999999997665 22111 1112121 11111222223334444 4
Q ss_pred cccccccccCcCCCC
Q 033353 107 EKEESDEDMGFSLFD 121 (121)
Q Consensus 107 E~EEsddDmGF~LFD 121 (121)
++||+||||||+|||
T Consensus 95 ~eee~ddDmGf~LFd 109 (109)
T cd05833 95 SEEESDDDMGFGLFD 109 (109)
T ss_pred CccccccccCCCCCC
Confidence 445679999999998
No 3
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=99.73 E-value=1.1e-18 Score=127.63 Aligned_cols=84 Identities=27% Similarity=0.346 Sum_probs=53.9
Q ss_pred HHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeee-------ccCCCCCccCCCCCCCCCCCCCCCCCCCchhhhhc
Q 033353 33 YELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVII-------GGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKK 105 (121)
Q Consensus 33 ~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~-------g~g~g~~~~gggaAa~aaagg~~aaa~~~k~Eekk 105 (121)
-+=-+++++++- ++|+++|+.+|.+.|.+|||.+||. .+|++++++. ++++ +++++ ++++++++++|+
T Consensus 22 addI~kIL~AaG-veVd~~~~~l~~~~L~GKdI~ELIa~G~~kl~svgg~~~aa~-a~a~-~~~~~--~~~~~~~~e~k~ 96 (112)
T PTZ00373 22 KKEVKNVLSAVN-ADVEDDVLDNFFKSLEGKTPHELIAAGMKKLQNIGGGVAAAA-APAA-GAATA--GAKAEAKKEEKK 96 (112)
T ss_pred HHHHHHHHHHcC-CCccHHHHHHHHHHHcCCCHHHHHHHhHHHHhcccCcccccc-cccc-ccccc--ccchhhhhhhcc
Confidence 344456677666 9999999999999999999999996 2322111111 1111 11011 222334445556
Q ss_pred ccccccccccCcCCCC
Q 033353 106 EEKEESDEDMGFSLFD 121 (121)
Q Consensus 106 EE~EEsddDmGF~LFD 121 (121)
||+|||||||||+|||
T Consensus 97 ee~ee~ddDmgf~LFd 112 (112)
T PTZ00373 97 EEEEEEEDDLGFSLFG 112 (112)
T ss_pred cccccccccccccccC
Confidence 6667899999999998
No 4
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=99.71 E-value=4.5e-18 Score=124.22 Aligned_cols=89 Identities=35% Similarity=0.419 Sum_probs=55.3
Q ss_pred chHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeee-------ccCCCCCccCCCCCCCCCCCCCCCCCCCchhhh
Q 033353 31 STYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVII-------GGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEE 103 (121)
Q Consensus 31 ~~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~-------g~g~g~~~~gggaAa~aaagg~~aaa~~~k~Ee 103 (121)
.|-+=-++|+.++- ++|+++|+.+|++.|++|+|.+||. ++++|++++..++++++++++ +++++++++++
T Consensus 18 pta~dI~~IL~AaG-vevd~~~~~~f~~~L~gK~i~eLIa~G~~kl~sv~~gg~aa~a~a~a~~~~~~-~~~~~~~~~e~ 95 (113)
T PLN00138 18 PSAEDLKDILGSVG-ADADDDRIELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAAAPAAGGA-AAPAAEAKKEE 95 (113)
T ss_pred CCHHHHHHHHHHcC-CcccHHHHHHHHHHHcCCCHHHHHHhchhccccCCCCCccccccccccccccc-cccccchhhhh
Confidence 34455567777776 9999999999999999999999994 344333211111111111111 11122333344
Q ss_pred hcccccccccccCcCCCC
Q 033353 104 KKEEKEESDEDMGFSLFD 121 (121)
Q Consensus 104 kkEE~EEsddDmGF~LFD 121 (121)
|+|++||+||||||+|||
T Consensus 96 k~e~eeE~ddDmGfgLFd 113 (113)
T PLN00138 96 KVEEKEESDDDMGFSLFD 113 (113)
T ss_pred hccccccccccccccccC
Confidence 455557889999999998
No 5
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=99.69 E-value=8.6e-18 Score=121.13 Aligned_cols=87 Identities=29% Similarity=0.319 Sum_probs=57.2
Q ss_pred chHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCC--CCCccCCCCCCCCCCCCCCCCCCCchhhhhcccc
Q 033353 31 STYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAV--GSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEK 108 (121)
Q Consensus 31 ~~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~--g~~~~gggaAa~aaagg~~aaa~~~k~EekkEE~ 108 (121)
-|-+=-++++..+. ++|+++|+.+|.+.|.+++|.+||.++.. ++.+.++++ +++++++ +++++++++|+|+||+
T Consensus 17 ~ta~~I~~IL~aaG-veVe~~~~~~~~~aLaGk~V~eli~~g~~kl~~~~~~~~a-~~~a~~~-~~~~~~~~~e~k~ee~ 93 (105)
T cd04411 17 LTEDKIKELLSAAG-AEIEPERVKLFLSALNGKNIDEVISKGKELMSSQAAAAAA-PAATAAA-TAEPAEKAEEAKEEEE 93 (105)
T ss_pred CCHHHHHHHHHHcC-CCcCHHHHHHHHHHHcCCCHHHHHHHHHhhccCCCCcccc-ccccccc-cccchhhhhhhhcccc
Confidence 34445567777776 99999999999999999999999987654 222222222 2111111 1222233444445566
Q ss_pred cccccccCcCCC
Q 033353 109 EESDEDMGFSLF 120 (121)
Q Consensus 109 EEsddDmGF~LF 120 (121)
||+||||||+||
T Consensus 94 eE~dddmgf~LF 105 (105)
T cd04411 94 EEEDEDFGFGLF 105 (105)
T ss_pred cccccccCcccC
Confidence 788999999999
No 6
>cd05831 Ribosomal_P1 Ribosomal protein P1. This subfamily represents the eukaryotic large ribosomal protein P1. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P1 is located in the L12 stalk, with proteins P2, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers) and bacteria may have four or six copies (two or three homodimers), depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and
Probab=99.63 E-value=1.2e-16 Score=114.61 Aligned_cols=85 Identities=33% Similarity=0.374 Sum_probs=53.7
Q ss_pred hHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCCCCCccCCCCCCCCCCCCCCCCCCCchhhhhccccccc
Q 033353 32 TYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKEES 111 (121)
Q Consensus 32 ~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~g~~~~gggaAa~aaagg~~aaa~~~k~EekkEE~EEs 111 (121)
|-+--+++++++. ++|+++|+.+|.+.|.+++|.+||.+++++++.+++ +++++++++ +..+++++++|+|++||+
T Consensus 19 Tae~I~~ilkAaG-veve~~~~~~f~~~L~gk~i~elIa~~~~~~~~aap-~a~~a~~~~--~~~~~~~~~kk~e~eee~ 94 (103)
T cd05831 19 TADNINALLKAAG-VNVEPYWPGLFAKALEGKDIKDLLSNVGGGGGGAAP-AAAAAAAAA--AAAEAKKEEKKEEEEEES 94 (103)
T ss_pred CHHHHHHHHHHcC-CcccHHHHHHHHHHHcCCCHHHHhhccccccccccc-ccccccccc--ccccchhhhccccccccc
Confidence 3334466666665 999999999999999999999999877643322111 111111111 112222334344555678
Q ss_pred ccccCcCCC
Q 033353 112 DEDMGFSLF 120 (121)
Q Consensus 112 ddDmGF~LF 120 (121)
||||||+||
T Consensus 95 d~dmgfglF 103 (103)
T cd05831 95 DDDMGFGLF 103 (103)
T ss_pred ccccccccC
Confidence 999999999
No 7
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=99.48 E-value=1.2e-14 Score=106.60 Aligned_cols=85 Identities=38% Similarity=0.481 Sum_probs=54.4
Q ss_pred HHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCC--CCCccCCC--CCCCCCCCCCC-CCCCCchhhhhcccccc
Q 033353 36 QRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAV--GSGFIGGG--AAASAPSGGGG-AAAEAPAAEEKKEEKEE 110 (121)
Q Consensus 36 q~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~--g~~~~ggg--aAa~aaagg~~-aaa~~~k~EekkEE~EE 110 (121)
.++++..+- ++++.-+..+|-.-|.+|+|.+||..+=. ...+.||+ +++++++++++ +++...++|+|+||+||
T Consensus 23 ikkIl~sVG-~E~d~e~i~~visel~GK~i~ElIA~G~eklAsvpsGGa~~aaa~~aaggaa~aa~~a~~~e~keEe~ee 101 (112)
T KOG3449|consen 23 IKKILESVG-AEIDDERINLVLSELKGKDIEELIAAGREKLASVPSGGAVAAAAAPAAGGAAGAAPAAAKEEEKEEEKEE 101 (112)
T ss_pred HHHHHHHhC-cccCHHHHHHHHHHhcCCCHHHHHHHhHHHHhcCCCCCccccccCcCCCCCccCCccchhhhhhhhhccc
Confidence 356666665 89999999999999999999999873221 22222222 11111122222 22233344556666689
Q ss_pred cccccCcCCCC
Q 033353 111 SDEDMGFSLFD 121 (121)
Q Consensus 111 sddDmGF~LFD 121 (121)
|||||||+|||
T Consensus 102 sddDmgf~lFd 112 (112)
T KOG3449|consen 102 SDDDMGFGLFD 112 (112)
T ss_pred ccccccccccC
Confidence 99999999998
No 8
>PF00428 Ribosomal_60s: 60s Acidic ribosomal protein; InterPro: IPR001813 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 [, ]. The 60S acidic ribosomal protein plays an important role in the elongation step of protein synthesis. This family includes archaebacterial L12, eukaryotic P0, P1 and P2 []. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Alt a 6, Alt a 12, Cla h 3, Cla h 4 and Cla h 12.; GO: 0003735 structural constituent of ribosome, 0006414 translational elongation, 0005622 intracellular, 0005840 ribosome; PDB: 3A1Y_C 3N2D_B 2LBF_A 3IZS_t 3IZR_t 1S4J_A 2JDL_C 2W1O_B 1S4H_A 2ZKR_g.
Probab=99.43 E-value=1.6e-16 Score=109.83 Aligned_cols=79 Identities=37% Similarity=0.495 Sum_probs=47.5
Q ss_pred HHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCCCCCccCCCCCCCCCCCCCCCCCCCchhhhhc-ccc-cccccc
Q 033353 37 RKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKK-EEK-EESDED 114 (121)
Q Consensus 37 ~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~g~~~~gggaAa~aaagg~~aaa~~~k~Eekk-EE~-EEsddD 114 (121)
++|++++. ++|+++|+.+|++.|.+++|.+||.+++.+.+++++++++++++ .+++.++++++| +++ ||+|||
T Consensus 8 ~~vl~aag-~~v~~~~~~~~~~~l~~~~i~~li~~~~~~~~~~aaa~aaa~aa----~~~a~a~~e~kkEeeeeEEed~d 82 (88)
T PF00428_consen 8 KKVLKAAG-VEVEAIWLELFAKALEGKDIKELIANGSAGMAAAAAAAAAAAAA----AAAAAAAEEEKKEEEEEEEEDDD 82 (88)
T ss_dssp HHHHHHHT-HHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHTTSSHHH----HHHHHHHSTTHHHHT--SS-SSS
T ss_pred HHHHHHhC-CchhHHHHHHHHHHHcCCcHHHHHhccccccccccccccccccc----ccccccchhcccccccccccccc
Confidence 56677776 79999999999999999999999997664321111111110000 111112222222 222 588999
Q ss_pred cCcCCC
Q 033353 115 MGFSLF 120 (121)
Q Consensus 115 mGF~LF 120 (121)
|||+||
T Consensus 83 mGf~LF 88 (88)
T PF00428_consen 83 MGFGLF 88 (88)
T ss_dssp SSTTTT
T ss_pred cCcCCC
Confidence 999999
No 9
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=99.37 E-value=1.5e-13 Score=100.39 Aligned_cols=86 Identities=28% Similarity=0.352 Sum_probs=54.8
Q ss_pred HHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCCCCCcc-CCCCCCCCCCCCCCCCCC-Cchhhhhc-cccccc
Q 033353 35 LQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAVGSGFI-GGGAAASAPSGGGGAAAE-APAAEEKK-EEKEES 111 (121)
Q Consensus 35 lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~g~~~~-gggaAa~aaagg~~aaa~-~~k~Eekk-EE~EEs 111 (121)
--+++++++. ++|++.|..+|...|+++||.++|.++....+++ .+++++++++++.++++. ++++|+++ +.+||+
T Consensus 21 ~l~~vl~aaG-veve~~r~k~lvaaLeg~~idE~i~~~~~~~~a~a~a~aaaa~~A~~~~a~~~~ea~eEe~eEe~~EE~ 99 (109)
T COG2058 21 NLKSVLEAAG-VEVEEARAKALVAALEGVDIDEVIKNAAEAPAAAAAAGAAAAAAAGAEAAAEADEAEEEEKEEEAEEES 99 (109)
T ss_pred HHHHHHHHcC-CCccHHHHHHHHHHhcCCCHHHHHHHhcccccccCCcccccccccccccccchhhHHHHHhhhchhhcc
Confidence 3456666554 9999999999999999999999999877642222 222222222333212222 33333333 344688
Q ss_pred ccccCcCCCC
Q 033353 112 DEDMGFSLFD 121 (121)
Q Consensus 112 ddDmGF~LFD 121 (121)
++||+|+|||
T Consensus 100 ~~~~lf~LF~ 109 (109)
T COG2058 100 DDDMLFGLFG 109 (109)
T ss_pred cccchhhccC
Confidence 9999999998
No 10
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=99.02 E-value=5.4e-11 Score=86.46 Aligned_cols=42 Identities=7% Similarity=0.048 Sum_probs=35.2
Q ss_pred hHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCC
Q 033353 32 TYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAV 74 (121)
Q Consensus 32 ~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~ 74 (121)
|-+=-+++++++. ++|+++|+.+|.+.|.++||.++|.+.+.
T Consensus 18 t~e~I~~IL~AAG-veVee~~~k~~v~aL~GkdIeElI~~a~~ 59 (106)
T PRK06402 18 NEDNLKKVLEAAG-VEVDEARVKALVAALEDVNIEEAIKKAAA 59 (106)
T ss_pred CHHHHHHHHHHcC-CCccHHHHHHHHHHHcCCCHHHHHHhccc
Confidence 3444566677666 99999999999999999999999998775
No 11
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=98.46 E-value=5.7e-08 Score=70.22 Aligned_cols=43 Identities=7% Similarity=0.003 Sum_probs=36.0
Q ss_pred chHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCC
Q 033353 31 STYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAV 74 (121)
Q Consensus 31 ~~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~ 74 (121)
.|-+--.+|+++|. ++|+++|+.+|++.|++++|.++|.+...
T Consensus 17 iT~e~I~~IL~AAG-v~ve~~~~~~la~~L~gk~i~eli~~~~~ 59 (105)
T TIGR03685 17 INEENLKAVLEAAG-VEVDEARVKALVAALEGVNIEEAIKKAAA 59 (105)
T ss_pred CCHHHHHHHHHHhC-CcccHHHHHHHHHHHcCCCHHHHHHhhhc
Confidence 34455667788777 99999999999999999999999987653
No 12
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=98.44 E-value=3.2e-08 Score=82.36 Aligned_cols=21 Identities=5% Similarity=-0.088 Sum_probs=16.4
Q ss_pred HhhhccCCcchhhhhhccCCC
Q 033353 42 TSLSADSSGGVQSSFSLVTPT 62 (121)
Q Consensus 42 ~a~~~eVe~~w~slFA~~L~~ 62 (121)
.+.+..++++||.+|++++.+
T Consensus 227 ~aag~pt~~s~p~~ia~a~k~ 247 (310)
T PTZ00135 227 LAAGYPTEASAPHSILNAFKN 247 (310)
T ss_pred HHhCCCcHHHHHHHHHHHHHH
Confidence 334678899999999987754
No 13
>cd05832 Ribosomal_L12p Ribosomal protein L12p. This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera
Probab=98.42 E-value=7.7e-08 Score=70.03 Aligned_cols=43 Identities=12% Similarity=0.053 Sum_probs=36.5
Q ss_pred chHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCC
Q 033353 31 STYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAV 74 (121)
Q Consensus 31 ~~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~ 74 (121)
-|-+--++|+++|. ++|+++|+.+|+..|+++||.++|.+.+.
T Consensus 17 ITae~I~~IL~AAG-veVd~~~~~ala~aL~gkdIeElIa~~~~ 59 (106)
T cd05832 17 INEENLKKVLEAAG-IEVDEARVKALVAALEEVNIDEAIKKAAV 59 (106)
T ss_pred CCHHHHHHHHHHhC-CcccHHHHHHHHHHHcCCCHHHHHHhccc
Confidence 34455677788777 99999999999999999999999988774
No 14
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=97.27 E-value=0.00015 Score=61.25 Aligned_cols=15 Identities=40% Similarity=0.831 Sum_probs=11.0
Q ss_pred hcccccccccccCcC
Q 033353 104 KKEEKEESDEDMGFS 118 (121)
Q Consensus 104 kkEE~EEsddDmGF~ 118 (121)
++||+||+||||||+
T Consensus 306 ~~~~~e~~~~d~~~~ 320 (323)
T PTZ00240 306 KEEEEESDEDDFGMG 320 (323)
T ss_pred ccCCccCcccccCcc
Confidence 345556788999995
No 15
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=92.92 E-value=0.09 Score=38.98 Aligned_cols=80 Identities=25% Similarity=0.182 Sum_probs=37.1
Q ss_pred cchHHHHHHHHHHhhhccCCcchhhhhhccCCCcceeeeeeccCCCCCccCCCCCCCCCCCCCCCCCCCchhhhhccccc
Q 033353 30 ASTYELQRKLVQTSLSADSSGGVQSSFSLVTPTSAVFQVIIGGAVGSGFIGGGAAASAPSGGGGAAAEAPAAEEKKEEKE 109 (121)
Q Consensus 30 ~~~~~lq~~lv~~a~~~eVe~~w~slFA~~L~~k~V~~~i~g~g~g~~~~gggaAa~aaagg~~aaa~~~k~EekkEE~E 109 (121)
+..-+--+.++....+-+++..++.--.+ +-.|-++++. +.+..++++++ ++.+.+++.++++|+++||++
T Consensus 33 E~d~e~i~~visel~GK~i~ElIA~G~ek------lAsvpsGGa~--~aaa~~aagga-a~aa~~a~~~e~keEe~eesd 103 (112)
T KOG3449|consen 33 EIDDERINLVLSELKGKDIEELIAAGREK------LASVPSGGAV--AAAAAPAAGGA-AGAAPAAAKEEEKEEEKEESD 103 (112)
T ss_pred ccCHHHHHHHHHHhcCCCHHHHHHHhHHH------HhcCCCCCcc--ccccCcCCCCC-ccCCccchhhhhhhhhccccc
Confidence 44556667788888877766544432222 1222222221 11111111111 112224444444444458888
Q ss_pred ccccccCcC
Q 033353 110 ESDEDMGFS 118 (121)
Q Consensus 110 EsddDmGF~ 118 (121)
++..-+-|+
T Consensus 104 dDmgf~lFd 112 (112)
T KOG3449|consen 104 DDMGFGLFD 112 (112)
T ss_pred ccccccccC
Confidence 887766553
No 16
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=89.46 E-value=0.2 Score=36.52 Aligned_cols=19 Identities=26% Similarity=0.349 Sum_probs=11.1
Q ss_pred CCCCchhhhhccccccccc
Q 033353 95 AAEAPAAEEKKEEKEESDE 113 (121)
Q Consensus 95 aa~~~k~EekkEE~EEsdd 113 (121)
+..++++|+++||++++..
T Consensus 86 ~~~e~kkee~eee~ddDmG 104 (109)
T cd05833 86 AKKEEKKEESEEESDDDMG 104 (109)
T ss_pred hhhhhhccCCccccccccC
Confidence 3455556666767666543
No 17
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=88.25 E-value=0.29 Score=35.37 Aligned_cols=28 Identities=7% Similarity=-0.039 Sum_probs=15.2
Q ss_pred chHHHHHHHHHHhhhccCCcchhhhhhc
Q 033353 31 STYELQRKLVQTSLSADSSGGVQSSFSL 58 (121)
Q Consensus 31 ~~~~lq~~lv~~a~~~eVe~~w~slFA~ 58 (121)
.+=+.-..+++...+.+++..+...-++
T Consensus 33 Ve~~~~~~~~~aLaGk~V~eli~~g~~k 60 (105)
T cd04411 33 IEPERVKLFLSALNGKNIDEVISKGKEL 60 (105)
T ss_pred cCHHHHHHHHHHHcCCCHHHHHHHHHhh
Confidence 3334445566665677776655444333
No 18
>cd05831 Ribosomal_P1 Ribosomal protein P1. This subfamily represents the eukaryotic large ribosomal protein P1. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P1 is located in the L12 stalk, with proteins P2, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers) and bacteria may have four or six copies (two or three homodimers), depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and
Probab=83.55 E-value=0.82 Score=32.84 Aligned_cols=18 Identities=6% Similarity=-0.158 Sum_probs=9.6
Q ss_pred HHHHHHHHHhhhccCCcc
Q 033353 34 ELQRKLVQTSLSADSSGG 51 (121)
Q Consensus 34 ~lq~~lv~~a~~~eVe~~ 51 (121)
.+-..+++...+.++...
T Consensus 37 ~~~~~f~~~L~gk~i~el 54 (103)
T cd05831 37 YWPGLFAKALEGKDIKDL 54 (103)
T ss_pred HHHHHHHHHHcCCCHHHH
Confidence 344455666666565543
No 19
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=82.20 E-value=0.92 Score=33.29 Aligned_cols=15 Identities=27% Similarity=0.415 Sum_probs=7.1
Q ss_pred CCchhhhhcccccccc
Q 033353 97 EAPAAEEKKEEKEESD 112 (121)
Q Consensus 97 ~~~k~EekkEE~EEsd 112 (121)
.++++ +++||+|++.
T Consensus 93 ~e~k~-e~eeE~ddDm 107 (113)
T PLN00138 93 KEEKV-EEKEESDDDM 107 (113)
T ss_pred hhhhc-cccccccccc
Confidence 34333 4445556554
No 20
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=79.46 E-value=1.4 Score=32.38 Aligned_cols=18 Identities=0% Similarity=-0.016 Sum_probs=9.2
Q ss_pred HHHHHHHHhhhccCCcch
Q 033353 35 LQRKLVQTSLSADSSGGV 52 (121)
Q Consensus 35 lq~~lv~~a~~~eVe~~w 52 (121)
.-+.+++...+.+++..+
T Consensus 40 ~~~l~~~~L~GKdI~ELI 57 (112)
T PTZ00373 40 VLDNFFKSLEGKTPHELI 57 (112)
T ss_pred HHHHHHHHHcCCCHHHHH
Confidence 334455555565655443
No 21
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=70.79 E-value=2.8 Score=35.70 Aligned_cols=11 Identities=36% Similarity=0.492 Sum_probs=5.4
Q ss_pred hhhcccccccc
Q 033353 102 EEKKEEKEESD 112 (121)
Q Consensus 102 EekkEE~EEsd 112 (121)
++++||++|+.
T Consensus 307 ~~~~e~~~~d~ 317 (323)
T PTZ00240 307 EEEEESDEDDF 317 (323)
T ss_pred cCCccCccccc
Confidence 44555555543
No 22
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=67.79 E-value=4 Score=29.79 Aligned_cols=38 Identities=16% Similarity=0.147 Sum_probs=17.6
Q ss_pred cccceeccCCcccccc-cchHHHHHHHHHHhhhccCCcch
Q 033353 14 EWSGKQIEGGDLEASA-ASTYELQRKLVQTSLSADSSGGV 52 (121)
Q Consensus 14 ~w~~k~~~~~~~~~~~-~~~~~lq~~lv~~a~~~eVe~~w 52 (121)
+=|...++ -=|.+++ ...-..-+.+++.-.++++.-.+
T Consensus 16 ~it~e~I~-~IL~AAGveVee~~~k~~v~aL~GkdIeElI 54 (106)
T PRK06402 16 EINEDNLK-KVLEAAGVEVDEARVKALVAALEDVNIEEAI 54 (106)
T ss_pred CCCHHHHH-HHHHHcCCCccHHHHHHHHHHHcCCCHHHHH
Confidence 33443333 2344444 22333344555555677776544
No 23
>cd05832 Ribosomal_L12p Ribosomal protein L12p. This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera
Probab=65.45 E-value=3.8 Score=29.94 Aligned_cols=13 Identities=15% Similarity=0.077 Sum_probs=5.4
Q ss_pred HHHHHhhhccCCc
Q 033353 38 KLVQTSLSADSSG 50 (121)
Q Consensus 38 ~lv~~a~~~eVe~ 50 (121)
.|++...+.+++-
T Consensus 40 ala~aL~gkdIeE 52 (106)
T cd05832 40 ALVAALEEVNIDE 52 (106)
T ss_pred HHHHHHcCCCHHH
Confidence 3444444444433
No 24
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=60.30 E-value=4.6 Score=33.89 Aligned_cols=8 Identities=13% Similarity=0.031 Sum_probs=3.6
Q ss_pred cceeeeee
Q 033353 63 SAVFQVII 70 (121)
Q Consensus 63 k~V~~~i~ 70 (121)
.+|.+.|-
T Consensus 282 ~~~~~~~~ 289 (330)
T PRK04019 282 DALDEELK 289 (330)
T ss_pred ccccHHHH
Confidence 44444443
No 25
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=56.93 E-value=6.8 Score=28.98 Aligned_cols=8 Identities=38% Similarity=0.264 Sum_probs=3.4
Q ss_pred cccCcCCC
Q 033353 113 EDMGFSLF 120 (121)
Q Consensus 113 dDmGF~LF 120 (121)
++..++||
T Consensus 98 E~~~~~lf 105 (109)
T COG2058 98 ESDDDMLF 105 (109)
T ss_pred cccccchh
Confidence 34444444
No 26
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=50.50 E-value=13 Score=21.18 Aligned_cols=21 Identities=24% Similarity=0.455 Sum_probs=17.5
Q ss_pred CceEEEEEecCCCcccceecc
Q 033353 1 MGVFTYVCRKNGGEWSGKQIE 21 (121)
Q Consensus 1 ~~v~~fv~~~~g~~w~~k~~~ 21 (121)
|=+|+|.|++-|..|..-+..
T Consensus 1 Mp~Y~y~C~~Cg~~fe~~~~~ 21 (41)
T smart00834 1 MPIYEYRCEDCGHTFEVLQKI 21 (41)
T ss_pred CCCEEEEcCCCCCEEEEEEec
Confidence 779999999999988766643
No 27
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=37.49 E-value=21 Score=30.08 Aligned_cols=18 Identities=61% Similarity=1.090 Sum_probs=15.0
Q ss_pred hcccccccccccCcCCCC
Q 033353 104 KKEEKEESDEDMGFSLFD 121 (121)
Q Consensus 104 kkEE~EEsddDmGF~LFD 121 (121)
++||+||+||||||+|||
T Consensus 293 ~~~~~ee~~~~~g~~lf~ 310 (310)
T PTZ00135 293 PAEEEEEEEDDMGFGLFD 310 (310)
T ss_pred ccccccCcchhccccCCC
Confidence 355667899999999998
No 28
>PF08465 Herpes_TK_C: Thymidine kinase from Herpesvirus C-terminal; InterPro: IPR013672 This domain is found towards the C terminus in Herpesvirus Thymidine kinases. ; GO: 0004797 thymidine kinase activity, 0005524 ATP binding
Probab=35.54 E-value=17 Score=21.73 Aligned_cols=26 Identities=12% Similarity=0.173 Sum_probs=23.2
Q ss_pred ccCCcchhhhhhccCCCcceeeeeec
Q 033353 46 ADSSGGVQSSFSLVTPTSAVFQVIIG 71 (121)
Q Consensus 46 ~eVe~~w~slFA~~L~~k~V~~~i~g 71 (121)
.||.+-|-.++..++.+.+|+...++
T Consensus 4 dDvpGlW~~IY~qi~kn~aIKt~~~~ 29 (33)
T PF08465_consen 4 DDVPGLWTEIYTQILKNPAIKTRFVD 29 (33)
T ss_pred CccccHHHHHHHHHHhCccccceecc
Confidence 48899999999999999999987764
No 29
>cd06888 PX_FISH The phosphoinositide binding Phox Homology domain of Five SH protein. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Five SH (FISH), also called Tks5, is a scaffolding protein and Src substrate that is localized in podosomes, which are electron-dense structures found in Src-transformed fibroblasts, osteoclasts, macrophages, and some invasive cancer cells. FISH contains an N-terminal PX domain and five Src homology 3 (SH3) domains. FISH binds and regulates some members of the ADAMs family of transmembrane metalloproteases, which function as sheddases and mediators of cell and matrix interactions. It is required for podosome formation, degradation of the extracellular matrix, and cancer cell invasion. This subfamily also includes proteins with a different number of SH3 domains than FISH, such as Tks4, which contains
Probab=34.84 E-value=37 Score=24.76 Aligned_cols=29 Identities=17% Similarity=0.186 Sum_probs=18.9
Q ss_pred EEecCCCcccceeccCCcccccccchHHHHHHHHHHh
Q 033353 7 VCRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTS 43 (121)
Q Consensus 7 v~~~~g~~w~~k~~~~~~~~~~~~~~~~lq~~lv~~a 43 (121)
|++++|..|+-.. .=...|+||++|+..=
T Consensus 25 V~~~dg~~~~v~R--------rYs~F~~Lh~~L~~~F 53 (119)
T cd06888 25 VTWSDGSSNVIYR--------RYSKFFDLQMQLLDKF 53 (119)
T ss_pred EEEcCCCEEEEEE--------eHHHHHHHHHHHHHhC
Confidence 4455555554332 3457899999999874
No 30
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=29.50 E-value=47 Score=20.00 Aligned_cols=20 Identities=25% Similarity=0.506 Sum_probs=15.3
Q ss_pred CceEEEEEecCCCcccceec
Q 033353 1 MGVFTYVCRKNGGEWSGKQI 20 (121)
Q Consensus 1 ~~v~~fv~~~~g~~w~~k~~ 20 (121)
|=+|.|.|++-|..+..-+.
T Consensus 1 MP~Yey~C~~Cg~~fe~~~~ 20 (52)
T TIGR02605 1 MPIYEYRCTACGHRFEVLQK 20 (52)
T ss_pred CCCEEEEeCCCCCEeEEEEe
Confidence 77999999988876654443
No 31
>cd06882 PX_p40phox The phosphoinositide binding Phox Homology domain of the p40phox subunit of NADPH oxidase. The PX domain is a phosphoinositide binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. p40phox contains an N-terminal PX domain, a central SH3 domain that binds p47phox, and a C-terminal PB1 domain that interacts with p67phox. It is a cytosolic subunit of the phagocytic NADPH oxidase complex (also called Nox2 or gp91phox) which plays a crucial role in the cellular response to bacterial infection. NADPH oxidase catalyzes the transfer of electrons from NADPH to oxygen during phagocytosis forming superoxide and reactive oxygen species. p40phox positively regulates NADPH oxidase in both phosphatidylinositol-3-phosphate (PI3P)-dependent and PI3P-independent manner. The PX domain is a phospholipid-binding module involved in the membrane targeting of proteins. The p40phox
Probab=28.00 E-value=74 Score=23.00 Aligned_cols=34 Identities=24% Similarity=0.196 Sum_probs=23.3
Q ss_pred eEEEEE-ecCCCcccceeccCCcccccccchHHHHHHHHHHhh
Q 033353 3 VFTYVC-RKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSL 44 (121)
Q Consensus 3 v~~fv~-~~~g~~w~~k~~~~~~~~~~~~~~~~lq~~lv~~a~ 44 (121)
||+.-| .++|..|+-..+= ...++||++|++.--
T Consensus 22 vY~I~v~~~~~~~~~V~RRY--------seF~~L~~~L~~~fp 56 (123)
T cd06882 22 VFVIEVKTKGGSKYLIYRRY--------RQFFALQSKLEERFG 56 (123)
T ss_pred EEEEEEEEcCCCEEEEEEEH--------HHHHHHHHHHHHhCC
Confidence 444444 3455578877664 467899999998755
No 32
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=26.55 E-value=58 Score=19.36 Aligned_cols=21 Identities=29% Similarity=0.529 Sum_probs=16.7
Q ss_pred CceEEEEEecCCCcccceecc
Q 033353 1 MGVFTYVCRKNGGEWSGKQIE 21 (121)
Q Consensus 1 ~~v~~fv~~~~g~~w~~k~~~ 21 (121)
|=+|.|.|++-|.....-|.-
T Consensus 1 MP~Yey~C~~Cg~~fe~~~~~ 21 (42)
T PF09723_consen 1 MPIYEYRCEECGHEFEVLQSI 21 (42)
T ss_pred CCCEEEEeCCCCCEEEEEEEc
Confidence 778999999988877665543
No 33
>cd06887 PX_p47phox The phosphoinositide binding Phox Homology domain of the p47phox subunit of NADPH oxidase. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. p47phox is a cytosolic subunit of the phagocytic NADPH oxidase complex (also called Nox2 or gp91phox), which plays a key role in the ability of phagocytes to defend against bacterial infections. NADPH oxidase catalyzes the transfer of electrons from NADPH to oxygen during phagocytosis forming superoxide and reactive oxygen species. p47phox is required for activation of NADH oxidase and plays a role in translocation. It contains an N-terminal PX domain, two Src Homology 3 (SH3) domains, and a C-terminal domain that contains PxxP motifs for binding SH3 domains. The PX domain of p47phox is unique in that it contains two distinct basic pockets on the membrane-binding surface: one
Probab=25.17 E-value=86 Score=22.87 Aligned_cols=29 Identities=14% Similarity=0.010 Sum_probs=18.9
Q ss_pred EecCCCcccceeccCCcccccccchHHHHHHHHHHhh
Q 033353 8 CRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSL 44 (121)
Q Consensus 8 ~~~~g~~w~~k~~~~~~~~~~~~~~~~lq~~lv~~a~ 44 (121)
+.++|.+|+-..+ =...|+||++|+..--
T Consensus 26 ~~s~~~~~~v~Rr--------YsdF~~L~~~L~~~fp 54 (118)
T cd06887 26 KWQDLSEKLVYRR--------FTEIYEFHKTLKEMFP 54 (118)
T ss_pred EEcCCcEEEEEee--------HHHHHHHHHHHHHhCC
Confidence 3345666654333 2568999999997753
No 34
>PF02751 TFIIA_gamma_C: Transcription initiation factor IIA, gamma subunit; InterPro: IPR015871 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the beta-barrel domain found at the C-terminal of the gamma subunit of transcription factor TFIIA. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=24.74 E-value=49 Score=21.35 Aligned_cols=9 Identities=22% Similarity=0.744 Sum_probs=7.3
Q ss_pred ceEEEEEec
Q 033353 2 GVFTYVCRK 10 (121)
Q Consensus 2 ~v~~fv~~~ 10 (121)
.|+|||+++
T Consensus 20 nVWTFi~kn 28 (52)
T PF02751_consen 20 NVWTFILKN 28 (52)
T ss_dssp TEEEEEEEE
T ss_pred cEEEEEEcC
Confidence 489999886
No 35
>PF08228 RNase_P_pop3: RNase P subunit Pop3; InterPro: IPR013241 This family of fungal proteins form a subunit of RNase P, the ribonucleoprotein enzyme that cleaves the leader sequence of precursor tRNAs to generate mature tRNAs. The structure of Pop3 has been assigned the L7Ae/L30e fold []. This RNA-binding fold is also present in human RNase P subunit Rpp38, raising the possibility that Pop3p and Rpp38 are functional homologues.
Probab=22.75 E-value=51 Score=25.47 Aligned_cols=9 Identities=44% Similarity=1.313 Sum_probs=7.8
Q ss_pred eEEEEEecC
Q 033353 3 VFTYVCRKN 11 (121)
Q Consensus 3 v~~fv~~~~ 11 (121)
+|.||||++
T Consensus 75 ~~vFVcr~D 83 (158)
T PF08228_consen 75 VYVFVCRSD 83 (158)
T ss_pred eEEEEECCC
Confidence 588999987
No 36
>cd06889 PX_NoxO1 The phosphoinositide binding Phox Homology domain of Nox Organizing protein 1. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Nox Organizing protein 1 (NoxO1) is a critical regulator of enzyme kinetics of the nonphagocytic NADPH oxidase Nox1, which catalyzes the transfer of electrons from NADPH to molecular oxygen to form superoxide. Nox1 is expressed in colon, stomach, uterus, prostate, and vascular smooth muscle cells. NoxO1, a homolog of the p47phox subunit of phagocytic NADPH oxidase, is involved in targeting activator subunits (such as NoxA1) to Nox1. It is co-localized with Nox1 in the membranes of resting cells and directs the subcellular localization of Nox1. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. The PX domain
Probab=22.67 E-value=1.1e+02 Score=22.71 Aligned_cols=18 Identities=17% Similarity=0.117 Sum_probs=13.7
Q ss_pred ccccchHHHHHHHHHHhh
Q 033353 27 ASAASTYELQRKLVQTSL 44 (121)
Q Consensus 27 ~~~~~~~~lq~~lv~~a~ 44 (121)
-+-...|+||++|...=-
T Consensus 38 R~y~eF~~lh~~L~~~FP 55 (121)
T cd06889 38 RSLEEFRKLHKQLKEKFP 55 (121)
T ss_pred EEHHHHHHHHHHHHHHCC
Confidence 344678999999987644
No 37
>KOG2240 consensus RNA polymerase II general transcription factor BTF3 and related proteins [Transcription]
Probab=22.65 E-value=78 Score=24.89 Aligned_cols=48 Identities=15% Similarity=0.176 Sum_probs=33.1
Q ss_pred EecCCCcccceeccCCcccccccchHHHHHHHHHHhhhccCCcchhhhh
Q 033353 8 CRKNGGEWSGKQIEGGDLEASAASTYELQRKLVQTSLSADSSGGVQSSF 56 (121)
Q Consensus 8 ~~~~g~~w~~k~~~~~~~~~~~~~~~~lq~~lv~~a~~~eVe~~w~slF 56 (121)
.+++||+||+++-.-+----++.+.--||..|..+-- +...++....|
T Consensus 17 ~~r~ggkGt~rrkk~~~~~~~~~ddkKlqs~lkkl~v-~~i~~i~evn~ 64 (162)
T KOG2240|consen 17 VVRIGGKGTARRKKKVVHKTATADDKKLQSSLKKLGV-NNIPGIEEVNM 64 (162)
T ss_pred eeeecCCCccccccCCCCCCCCcccchhhhhhhhhcc-ccccchhHhhh
Confidence 3678999999988634444667788889999887733 34455554444
Done!