Query psy10269
Match_columns 108
No_of_seqs 121 out of 879
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 22:08:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10269.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10269hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd05831 Ribosomal_P1 Ribosomal 100.0 1.1E-30 2.5E-35 175.5 6.6 99 2-107 4-103 (103)
2 cd04411 Ribosomal_P1_P2_L12p R 100.0 4.1E-30 8.9E-35 173.3 6.0 96 2-107 3-105 (105)
3 KOG1762|consensus 100.0 5.3E-30 1.2E-34 173.3 6.1 104 2-108 9-114 (114)
4 cd05833 Ribosomal_P2 Ribosomal 100.0 9.6E-29 2.1E-33 167.6 6.3 100 3-108 6-109 (109)
5 PTZ00373 60S Acidic ribosomal 100.0 1.4E-28 3E-33 167.3 6.5 100 3-108 8-112 (112)
6 PLN00138 large subunit ribosom 99.9 5.1E-28 1.1E-32 164.9 7.1 100 3-108 6-113 (113)
7 KOG3449|consensus 99.9 1.1E-25 2.4E-30 151.5 6.2 98 4-108 7-112 (112)
8 COG2058 RPP1A Ribosomal protei 99.9 1.6E-24 3.6E-29 145.6 5.6 104 2-108 3-109 (109)
9 PRK06402 rpl12p 50S ribosomal 99.9 4.6E-24 9.9E-29 143.9 4.4 57 2-60 3-59 (106)
10 PF00428 Ribosomal_60s: 60s Ac 99.8 5.9E-23 1.3E-27 134.2 -1.4 86 17-107 1-88 (88)
11 TIGR03685 L21P_arch 50S riboso 99.8 1.8E-20 3.9E-25 126.4 4.2 57 2-60 3-59 (105)
12 cd05832 Ribosomal_L12p Ribosom 99.8 3.6E-20 7.7E-25 125.0 4.2 57 2-60 3-59 (106)
13 PTZ00135 60S acidic ribosomal 99.6 5.4E-17 1.2E-21 126.8 0.5 95 2-108 199-310 (310)
14 PTZ00240 60S ribosomal protein 99.2 4E-12 8.6E-17 100.1 0.4 48 2-49 206-255 (323)
15 cd04411 Ribosomal_P1_P2_L12p R 97.1 0.00065 1.4E-08 45.8 3.4 28 8-37 25-53 (105)
16 PRK04019 rplP0 acidic ribosoma 95.9 0.0095 2.1E-07 47.1 3.5 38 21-58 243-291 (330)
17 KOG3449|consensus 94.4 0.1 2.3E-06 35.5 4.7 42 8-51 26-67 (112)
18 cd05833 Ribosomal_P2 Ribosomal 94.2 0.098 2.1E-06 35.5 4.2 31 8-40 26-56 (109)
19 PRK06402 rpl12p 50S ribosomal 93.0 0.067 1.5E-06 36.2 1.8 13 17-29 32-44 (106)
20 COG2058 RPP1A Ribosomal protei 92.1 0.062 1.3E-06 36.5 0.8 32 26-57 9-44 (109)
21 PTZ00240 60S ribosomal protein 90.0 0.52 1.1E-05 37.5 4.3 17 91-107 306-323 (323)
22 PRK04019 rplP0 acidic ribosoma 90.0 0.077 1.7E-06 42.0 -0.5 29 21-49 217-245 (330)
23 KOG0815|consensus 88.6 0.1 2.2E-06 39.7 -0.6 42 5-46 202-245 (245)
24 TIGR03685 L21P_arch 50S riboso 79.7 1.1 2.4E-05 30.1 1.4 17 28-44 11-27 (105)
25 PLN00138 large subunit ribosom 78.2 3.9 8.5E-05 27.8 3.7 23 8-32 26-48 (113)
26 PTZ00373 60S Acidic ribosomal 77.7 5.9 0.00013 27.0 4.5 28 8-37 28-55 (112)
27 cd05831 Ribosomal_P1 Ribosomal 76.2 2.7 5.8E-05 28.1 2.4 21 26-46 10-30 (103)
28 cd05832 Ribosomal_L12p Ribosom 76.0 2.9 6.4E-05 28.2 2.6 21 26-46 9-29 (106)
29 PF11116 DUF2624: Protein of u 75.0 3.8 8.2E-05 26.7 2.8 37 15-51 12-48 (85)
30 PF03948 Ribosomal_L9_C: Ribos 44.2 17 0.00037 23.2 1.7 29 12-40 26-55 (87)
31 PF02084 Bindin: Bindin; Inte 44.0 26 0.00056 26.8 2.9 51 4-58 89-147 (238)
32 PF13833 EF-hand_8: EF-hand do 32.7 45 0.00097 18.4 2.1 31 17-47 4-35 (54)
33 PF10017 Methyltransf_33: Hist 30.9 38 0.00083 22.9 1.8 24 17-40 95-118 (127)
34 PF07308 DUF1456: Protein of u 29.1 59 0.0013 20.0 2.3 29 17-45 13-41 (68)
35 PF05037 DUF669: Protein of un 28.8 65 0.0014 22.1 2.7 39 17-55 70-110 (141)
36 PF14788 EF-hand_10: EF hand; 28.2 59 0.0013 19.1 2.1 29 19-47 3-31 (51)
37 smart00874 B5 tRNA synthetase 27.8 63 0.0014 19.1 2.3 19 17-35 18-36 (71)
38 PF08339 RTX_C: RTX C-terminal 27.5 63 0.0014 23.0 2.5 48 17-64 60-116 (145)
39 PF03540 TFIID_30kDa: Transcri 24.3 1E+02 0.0022 18.1 2.6 37 21-57 6-42 (51)
40 KOG3981|consensus 23.9 86 0.0019 24.6 2.8 27 17-43 70-96 (326)
41 PRK00754 signal recognition pa 22.8 93 0.002 20.4 2.5 20 15-34 32-51 (95)
42 PF14091 DUF4269: Domain of un 22.6 57 0.0012 23.4 1.5 32 21-55 119-150 (152)
43 PF03484 B5: tRNA synthetase B 21.7 76 0.0016 19.1 1.8 21 17-37 18-38 (70)
44 PF10965 DUF2767: Protein of u 21.4 77 0.0017 19.8 1.8 23 5-29 21-43 (69)
45 PF02037 SAP: SAP domain; Int 21.2 1.4E+02 0.0031 15.5 3.2 29 16-44 2-30 (35)
46 PRK03745 signal recognition pa 21.1 1.1E+02 0.0023 20.4 2.5 20 15-34 29-48 (100)
47 PF14104 DUF4277: Domain of un 20.5 2.2E+02 0.0048 19.3 4.1 40 17-56 41-80 (115)
48 COG1400 SEC65 Signal recogniti 20.0 1.1E+02 0.0025 20.1 2.5 20 15-34 29-48 (93)
No 1
>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=99.97 E-value=1.1e-30 Score=175.51 Aligned_cols=99 Identities=66% Similarity=0.989 Sum_probs=76.0
Q ss_pred CccchhhcccCCCcCCCCHHHHHHHHHHhCCcccCchhHHHHHHhcCCCHHHHHHhcCCCCCc-ccccccchhhhcccch
Q psy10269 2 GPKCALFLHMSYIVGSEDGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGSGAGA-GPAAAAPAAAQAAAPA 80 (108)
Q Consensus 2 ~~~aaLiL~d~~~~~~it~e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i~~li~~~~a~~~~-a~~a~~~~~~~~~~~~ 80 (108)
.+||+|||||+++ +||++||++||+++|++|+++|+.+|++.|+||+|++||+++++++++ +|++++++++ ++
T Consensus 4 c~yAaLiL~d~~~--~~Tae~I~~ilkAaGveve~~~~~~f~~~L~gk~i~elIa~~~~~~~~aap~a~~a~~~--~~-- 77 (103)
T cd05831 4 CTYAALILHDDGI--EITADNINALLKAAGVNVEPYWPGLFAKALEGKDIKDLLSNVGGGGGGAAPAAAAAAAA--AA-- 77 (103)
T ss_pred HHHHHHHHccCCC--CCCHHHHHHHHHHcCCcccHHHHHHHHHHHcCCCHHHHhhccccccccccccccccccc--cc--
Confidence 3699999999999 999999999999999999999999999999999999999998765433 3332221111 11
Q ss_pred hhhhhhhhhhccccccccccCCCCCCC
Q psy10269 81 AAEAKEDKKKKEESDEGSDDDMGFGLF 107 (108)
Q Consensus 81 a~~~~~~~~~k~eeeeE~d~dmgfgLF 107 (108)
.++++++ ++|+|++||+|+|||||||
T Consensus 78 ~~~~~~~-~kk~e~eee~d~dmgfglF 103 (103)
T cd05831 78 AAEAKKE-EKKEEEEEESDDDMGFGLF 103 (103)
T ss_pred cccchhh-hcccccccccccccccccC
Confidence 1111233 4456666778999999999
No 2
>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=99.96 E-value=4.1e-30 Score=173.32 Aligned_cols=96 Identities=42% Similarity=0.582 Sum_probs=72.8
Q ss_pred CccchhhcccCCCcCCCCHHHHHHHHHHhCCcccCchhHHHHHHhcCCCHHHHHHhcCC-------CCCcccccccchhh
Q psy10269 2 GPKCALFLHMSYIVGSEDGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGS-------GAGAGPAAAAPAAA 74 (108)
Q Consensus 2 ~~~aaLiL~d~~~~~~it~e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i~~li~~~~a-------~~~~a~~a~~~~~~ 74 (108)
|.||.|||++.+. +||+++|++||+++|++|+++|+.+|++.|+|++|++||++... +|+ +++++ +
T Consensus 3 ~v~A~Lll~~~g~--~~ta~~I~~IL~aaGveVe~~~~~~~~~aLaGk~V~eli~~g~~kl~~~~~~~~-a~~~a----~ 75 (105)
T cd04411 3 YVAAYLLLHKGGK--ELTEDKIKELLSAAGAEIEPERVKLFLSALNGKNIDEVISKGKELMSSQAAAAA-APAAT----A 75 (105)
T ss_pred HHHHHHHHHhcCC--CCCHHHHHHHHHHcCCCcCHHHHHHHHHHHcCCCHHHHHHHHHhhccCCCCccc-ccccc----c
Confidence 7899999999998 89999999999999999999999999999999999999997532 221 11111 1
Q ss_pred hcccchhhhhhhhhhhccccccccccCCCCCCC
Q psy10269 75 QAAAPAAAEAKEDKKKKEESDEGSDDDMGFGLF 107 (108)
Q Consensus 75 ~~~~~~a~~~~~~~~~k~eeeeE~d~dmgfgLF 107 (108)
++++ ++.++++ ++|+|++||||||||||||
T Consensus 76 ~~~~--~~~~~~~-e~k~ee~eE~dddmgf~LF 105 (105)
T cd04411 76 AATA--EPAEKAE-EAKEEEEEEEDEDFGFGLF 105 (105)
T ss_pred cccc--cchhhhh-hhhcccccccccccCcccC
Confidence 1111 1111233 4455666888999999999
No 3
>KOG1762|consensus
Probab=99.96 E-value=5.3e-30 Score=173.33 Aligned_cols=104 Identities=63% Similarity=0.909 Sum_probs=80.6
Q ss_pred CccchhhcccCCCcCCCCHHHHHHHHHHhCCcccCchhHHHHHHhcCCCHHHHHHhcCCCCCcccc-cccchhhhcccch
Q psy10269 2 GPKCALFLHMSYIVGSEDGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGSGAGAGPA-AAAPAAAQAAAPA 80 (108)
Q Consensus 2 ~~~aaLiL~d~~~~~~it~e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i~~li~~~~a~~~~a~~-a~~~~~~~~~~~~ 80 (108)
.+|++|||+|+++ .+|.++|+++++++|++|+++||.+|+++|.+++|.+||+++++++++.++ +++++++++++++
T Consensus 9 c~yaalIL~d~~i--~it~dki~tl~kaa~v~ve~~Wp~lfakale~vni~~li~n~gag~~a~a~~~~~~~~aa~~~~a 86 (114)
T KOG1762|consen 9 CSYAALILHDDEI--EVTADKINTLTKAAGVNVEPYWPGLFAKALEGVNIKELICNVGAGGGALAAGAAAAGGAAAAGGA 86 (114)
T ss_pred Hhhhhhhccccce--eeehhhhhhHHHhccCcccccchhHHHHHhccCChHHHHHhcccCCccCCCcccccccccccccc
Confidence 4799999999999 999999999999999999999999999999999999999999876544321 1222222122211
Q ss_pred hh-hhhhhhhhccccccccccCCCCCCCC
Q psy10269 81 AA-EAKEDKKKKEESDEGSDDDMGFGLFD 108 (108)
Q Consensus 81 a~-~~~~~~~~k~eeeeE~d~dmgfgLFd 108 (108)
++ +++++ +.|+|+.||+||||||||||
T Consensus 87 A~~~Ekk~-eak~EeseesddDmgfGLfd 114 (114)
T KOG1762|consen 87 AAAEEKKE-EAKKEESEESDDDMGFGLFD 114 (114)
T ss_pred ccchHHHH-HhhhhhhcccccccccCCCC
Confidence 22 22333 55777789999999999998
No 4
>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=99.95 E-value=9.6e-29 Score=167.61 Aligned_cols=100 Identities=44% Similarity=0.536 Sum_probs=66.1
Q ss_pred ccchhhcccCCCcCCCCHHHHHHHHHHhCCcccCchhHHHHHHhcCCCHHHHHHhcCC--CC--Ccccccccchhhhccc
Q psy10269 3 PKCALFLHMSYIVGSEDGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGS--GA--GAGPAAAAPAAAQAAA 78 (108)
Q Consensus 3 ~~aaLiL~d~~~~~~it~e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i~~li~~~~a--~~--~~a~~a~~~~~~~~~~ 78 (108)
.|..+.|..+. +||++||++||+++|++|+++|+.+|++.|+||+|++||++... ++ +++.++++++++ +++
T Consensus 6 AylL~~l~g~~---~pTa~dI~~IL~AaGveVe~~~~~lf~~~L~GKdi~eLIa~g~~kl~s~~~~~~~aa~a~~~-~a~ 81 (109)
T cd05833 6 AYLLAVLGGNA---SPSAADVKKILGSVGVEVDDEKLNKVISELEGKDVEELIAAGKEKLASVPAGAGGAAPAAAA-AAA 81 (109)
T ss_pred HHHHHHHcCCC---CCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHhhhcCCCcccccccccccc-ccc
Confidence 34555555554 89999999999999999999999999999999999999997433 11 011111111111 111
Q ss_pred chhhhhhhhhhhccccccccccCCCCCCCC
Q psy10269 79 PAAAEAKEDKKKKEESDEGSDDDMGFGLFD 108 (108)
Q Consensus 79 ~~a~~~~~~~~~k~eeeeE~d~dmgfgLFd 108 (108)
++++++++ ++|+|++||+|+||||||||
T Consensus 82 -aa~~~~~e-~kkee~eee~ddDmGf~LFd 109 (109)
T cd05833 82 -AAAAAKKE-EKKEESEEESDDDMGFGLFD 109 (109)
T ss_pred -cccchhhh-hhccCCccccccccCCCCCC
Confidence 11111233 34445555669999999998
No 5
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=99.95 E-value=1.4e-28 Score=167.34 Aligned_cols=100 Identities=33% Similarity=0.453 Sum_probs=67.3
Q ss_pred ccchhhcccCCCcCCCCHHHHHHHHHHhCCcccCchhHHHHHHhcCCCHHHHHHh----c-CCCCCcccccccchhhhcc
Q psy10269 3 PKCALFLHMSYIVGSEDGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISN----V-GSGAGAGPAAAAPAAAQAA 77 (108)
Q Consensus 3 ~~aaLiL~d~~~~~~it~e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i~~li~~----~-~a~~~~a~~a~~~~~~~~~ 77 (108)
.|..+.|..++ +||++||++||+++|++|+++|+.+|++.|+||+|++||++ + +.||+++++++++++++++
T Consensus 8 AYlL~~lgG~~---~pTaddI~kIL~AaGveVd~~~~~l~~~~L~GKdI~ELIa~G~~kl~svgg~~~aa~a~a~~~~~~ 84 (112)
T PTZ00373 8 AYLMCVLGGNE---NPTKKEVKNVLSAVNADVEDDVLDNFFKSLEGKTPHELIAAGMKKLQNIGGGVAAAAAPAAGAATA 84 (112)
T ss_pred HHHHHHHcCCC---CCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHHHHhcccCccccccccccccccc
Confidence 35555555555 79999999999999999999999999999999999999984 1 1133221111111111011
Q ss_pred cchhhhhhhhhhhccccccccccCCCCCCCC
Q psy10269 78 APAAAEAKEDKKKKEESDEGSDDDMGFGLFD 108 (108)
Q Consensus 78 ~~~a~~~~~~~~~k~eeeeE~d~dmgfgLFd 108 (108)
.+ +++ +++ ++|+||+|||||||||||||
T Consensus 85 ~~-~~~-~~~-e~k~ee~ee~ddDmgf~LFd 112 (112)
T PTZ00373 85 GA-KAE-AKK-EEKKEEEEEEEDDLGFSLFG 112 (112)
T ss_pred cc-chh-hhh-hhcccccccccccccccccC
Confidence 11 112 233 44566678889999999998
No 6
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=99.95 E-value=5.1e-28 Score=164.94 Aligned_cols=100 Identities=38% Similarity=0.529 Sum_probs=69.7
Q ss_pred ccchhhcccCCCcCCCCHHHHHHHHHHhCCcccCchhHHHHHHhcCCCHHHHHHh-------cCCCCCcccccccch-hh
Q psy10269 3 PKCALFLHMSYIVGSEDGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISN-------VGSGAGAGPAAAAPA-AA 74 (108)
Q Consensus 3 ~~aaLiL~d~~~~~~it~e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i~~li~~-------~~a~~~~a~~a~~~~-~~ 74 (108)
.|..+.|..++ .||+++|++||+++|++|+++|+++|++.|+||+|++||++ ++++|++++++++++ ++
T Consensus 6 Ayll~~l~g~~---~pta~dI~~IL~AaGvevd~~~~~~f~~~L~gK~i~eLIa~G~~kl~sv~~gg~aa~a~a~a~~~~ 82 (113)
T PLN00138 6 AYLLAVLGGNT---CPSAEDLKDILGSVGADADDDRIELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAAAPAAG 82 (113)
T ss_pred HHHHHHhcCCC---CCCHHHHHHHHHHcCCcccHHHHHHHHHHHcCCCHHHHHHhchhccccCCCCCccccccccccccc
Confidence 35556666655 89999999999999999999999999999999999999964 666554322111111 11
Q ss_pred hcccchhhhhhhhhhhccccccccccCCCCCCCC
Q psy10269 75 QAAAPAAAEAKEDKKKKEESDEGSDDDMGFGLFD 108 (108)
Q Consensus 75 ~~~~~~a~~~~~~~~~k~eeeeE~d~dmgfgLFd 108 (108)
+++.+ +++ +++ ++|+|++||+|+||||||||
T Consensus 83 ~~~~~-~~~-~~~-e~k~e~eeE~ddDmGfgLFd 113 (113)
T PLN00138 83 GAAAP-AAE-AKK-EEKVEEKEESDDDMGFSLFD 113 (113)
T ss_pred ccccc-ccc-hhh-hhhccccccccccccccccC
Confidence 01111 111 222 34456667889999999998
No 7
>KOG3449|consensus
Probab=99.92 E-value=1.1e-25 Score=151.53 Aligned_cols=98 Identities=38% Similarity=0.542 Sum_probs=69.7
Q ss_pred cchhhcccCCCcCCCCHHHHHHHHHHhCCcccCchhHHHHHHhcCCCHHHHHHh-------cCCCCCccccccc-chhhh
Q psy10269 4 KCALFLHMSYIVGSEDGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISN-------VGSGAGAGPAAAA-PAAAQ 75 (108)
Q Consensus 4 ~aaLiL~d~~~~~~it~e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i~~li~~-------~~a~~~~a~~a~~-~~~~~ 75 (108)
|--+.|..+. .++..+|++||.++|++++..|+++|++.|+||+|.+||+. +++||+++.++++ +++++
T Consensus 7 YLL~~lgGn~---~psa~DikkIl~sVG~E~d~e~i~~visel~GK~i~ElIA~G~eklAsvpsGGa~~aaa~~aaggaa 83 (112)
T KOG3449|consen 7 YLLAVLGGNA---SPSASDIKKILESVGAEIDDERINLVLSELKGKDIEELIAAGREKLASVPSGGAVAAAAAPAAGGAA 83 (112)
T ss_pred HHHHHhcCCC---CCCHHHHHHHHHHhCcccCHHHHHHHHHHhcCCCHHHHHHHhHHHHhcCCCCCccccccCcCCCCCc
Confidence 3334444444 89999999999999999999999999999999999999984 6777663222222 11111
Q ss_pred cccchhhhhhhhhhhccccccccccCCCCCCCC
Q psy10269 76 AAAPAAAEAKEDKKKKEESDEGSDDDMGFGLFD 108 (108)
Q Consensus 76 ~~~~~a~~~~~~~~~k~eeeeE~d~dmgfgLFd 108 (108)
+++ +...++ ++|+||+||+||||||+|||
T Consensus 84 ~aa---~~a~~~-e~keEe~eesddDmgf~lFd 112 (112)
T KOG3449|consen 84 GAA---PAAAKE-EEKEEEKEESDDDMGFGLFD 112 (112)
T ss_pred cCC---ccchhh-hhhhhhcccccccccccccC
Confidence 121 121233 44556668999999999998
No 8
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=1.6e-24 Score=145.63 Aligned_cols=104 Identities=44% Similarity=0.569 Sum_probs=73.3
Q ss_pred CccchhhcccCCCcCCCCHHHHHHHHHHhCCcccCchhHHHHHHhcCCCHHHHHHhcCCCC-Ccc--cccccchhhhccc
Q psy10269 2 GPKCALFLHMSYIVGSEDGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGSGA-GAG--PAAAAPAAAQAAA 78 (108)
Q Consensus 2 ~~~aaLiL~d~~~~~~it~e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i~~li~~~~a~~-~~a--~~a~~~~~~~~~~ 78 (108)
|.|+.|+||-.+. +||++||.+|++++|++|++.|.+.|+++|+|+||+++|.+....- +++ +++++++++++.+
T Consensus 3 Yi~a~llL~~agk--ei~e~~l~~vl~aaGveve~~r~k~lvaaLeg~~idE~i~~~~~~~~a~a~a~aaaa~~A~~~~a 80 (109)
T COG2058 3 YIYAYLLLHLAGK--EITEDNLKSVLEAAGVEVEEARAKALVAALEGVDIDEVIKNAAEAPAAAAAAGAAAAAAAGAEAA 80 (109)
T ss_pred HHHHHHHHHHccC--cCCHHHHHHHHHHcCCCccHHHHHHHHHHhcCCCHHHHHHHhcccccccCCcccccccccccccc
Confidence 7899999999998 9999999999999999999999999999999999999999854321 111 1111110111111
Q ss_pred chhhhhhhhhhhccccccccccCCCCCCCC
Q psy10269 79 PAAAEAKEDKKKKEESDEGSDDDMGFGLFD 108 (108)
Q Consensus 79 ~~a~~~~~~~~~k~eeeeE~d~dmgfgLFd 108 (108)
....+++++ +++++.+||+++||||+|||
T Consensus 81 ~~~~ea~eE-e~eEe~~EE~~~~~lf~LF~ 109 (109)
T COG2058 81 AEADEAEEE-EKEEEAEEESDDDMLFGLFG 109 (109)
T ss_pred cchhhHHHH-HhhhchhhcccccchhhccC
Confidence 001011222 23455667888999999998
No 9
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=99.89 E-value=4.6e-24 Score=143.88 Aligned_cols=57 Identities=33% Similarity=0.397 Sum_probs=54.8
Q ss_pred CccchhhcccCCCcCCCCHHHHHHHHHHhCCcccCchhHHHHHHhcCCCHHHHHHhcCC
Q psy10269 2 GPKCALFLHMSYIVGSEDGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGS 60 (108)
Q Consensus 2 ~~~aaLiL~d~~~~~~it~e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i~~li~~~~a 60 (108)
|.||+|||++.+. +||++||++||+++|++|+++|+++|+++|+|++|++||.+.++
T Consensus 3 yiyAaLLL~~~g~--~it~e~I~~IL~AAGveVee~~~k~~v~aL~GkdIeElI~~a~~ 59 (106)
T PRK06402 3 YIYAALLLHSAGK--EINEDNLKKVLEAAGVEVDEARVKALVAALEDVNIEEAIKKAAA 59 (106)
T ss_pred HHHHHHHHHhcCC--CCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHhccc
Confidence 7899999999999 99999999999999999999999999999999999999988654
No 10
>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=99.84 E-value=5.9e-23 Score=134.20 Aligned_cols=86 Identities=64% Similarity=0.878 Sum_probs=56.4
Q ss_pred CCCHHHHHHHHHHhCCcccCchhHHHHHHhcCCCHHHHHHhcCCCCCc-ccccccchhhhcccchhhhhhhhhhhccccc
Q psy10269 17 SEDGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGSGAGA-GPAAAAPAAAQAAAPAAAEAKEDKKKKEESD 95 (108)
Q Consensus 17 ~it~e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i~~li~~~~a~~~~-a~~a~~~~~~~~~~~~a~~~~~~~~~k~eee 95 (108)
.||.++|.+||+++|++|+++|+.+|++.|++++|++||++++.++++ ++++++++++ .+ ++++ +++ ++|++++
T Consensus 1 ~pT~~~i~~vl~aag~~v~~~~~~~~~~~l~~~~i~~li~~~~~~~~~~aaa~aaa~aa--~~-~a~a-~~e-~kkEeee 75 (88)
T PF00428_consen 1 EPTAENIKKVLKAAGVEVEAIWLELFAKALEGKDIKELIANGSAGMAAAAAAAAAAAAA--AA-AAAA-AEE-EKKEEEE 75 (88)
T ss_dssp S-SCCCHHHHHHHHTHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHTTSSHHH--HH-HHHH-HST-THHHHT-
T ss_pred CCCHHHHHHHHHHhCCchhHHHHHHHHHHHcCCcHHHHHhccccccccccccccccccc--cc-cccc-chh-ccccccc
Confidence 478999999999999999999999999999999999999987654221 1111111111 11 1111 222 2222222
Q ss_pred -cccccCCCCCCC
Q psy10269 96 -EGSDDDMGFGLF 107 (108)
Q Consensus 96 -eE~d~dmgfgLF 107 (108)
||+|+|||||||
T Consensus 76 eEEed~dmGf~LF 88 (88)
T PF00428_consen 76 EEEEDDDMGFGLF 88 (88)
T ss_dssp -SS-SSSSSTTTT
T ss_pred ccccccccCcCCC
Confidence 688999999999
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=99.81 E-value=1.8e-20 Score=126.37 Aligned_cols=57 Identities=37% Similarity=0.443 Sum_probs=54.6
Q ss_pred CccchhhcccCCCcCCCCHHHHHHHHHHhCCcccCchhHHHHHHhcCCCHHHHHHhcCC
Q psy10269 2 GPKCALFLHMSYIVGSEDGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGS 60 (108)
Q Consensus 2 ~~~aaLiL~d~~~~~~it~e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i~~li~~~~a 60 (108)
|.||+|||++.++ +||.++|++||+++|++|+++|+.+|++.|+|++|.++|.++..
T Consensus 3 yvyA~Lll~~~g~--~iT~e~I~~IL~AAGv~ve~~~~~~la~~L~gk~i~eli~~~~~ 59 (105)
T TIGR03685 3 YIYAALLLHSAGK--EINEENLKAVLEAAGVEVDEARVKALVAALEGVNIEEAIKKAAA 59 (105)
T ss_pred HHHHHHHHHhcCC--CCCHHHHHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHHhhhc
Confidence 7899999999999 99999999999999999999999999999999999999987653
No 12
>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=99.80 E-value=3.6e-20 Score=124.98 Aligned_cols=57 Identities=33% Similarity=0.385 Sum_probs=54.8
Q ss_pred CccchhhcccCCCcCCCCHHHHHHHHHHhCCcccCchhHHHHHHhcCCCHHHHHHhcCC
Q psy10269 2 GPKCALFLHMSYIVGSEDGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISNVGS 60 (108)
Q Consensus 2 ~~~aaLiL~d~~~~~~it~e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i~~li~~~~a 60 (108)
|.||+|||++.+. +||.++|++||+++|++|+++|+.+|++.|+|++|+++|.+++.
T Consensus 3 yvyAaLLL~~~G~--eITae~I~~IL~AAGveVd~~~~~ala~aL~gkdIeElIa~~~~ 59 (106)
T cd05832 3 YIYAALLLHYAGK--EINEENLKKVLEAAGIEVDEARVKALVAALEEVNIDEAIKKAAV 59 (106)
T ss_pred HHHHHHHHHhcCC--CCCHHHHHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHHhccc
Confidence 7899999999999 99999999999999999999999999999999999999998754
No 13
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=99.62 E-value=5.4e-17 Score=126.81 Aligned_cols=95 Identities=33% Similarity=0.409 Sum_probs=66.1
Q ss_pred CccchhhcccCCCcCCCCH--HHHHHHHHHhCCcccCchhHHHHHHhcCC---------------CHHHHHHhcCCCCCc
Q psy10269 2 GPKCALFLHMSYIVGSEDG--EKIQTVLKAAGVEVEPYWPGLFAKALEGV---------------NVKELISNVGSGAGA 64 (108)
Q Consensus 2 ~~~aaLiL~d~~~~~~it~--e~I~~vl~aaG~~v~~~~~~~f~~alkgk---------------~i~~li~~~~a~~~~ 64 (108)
|+-..|.++++++.+.+.. .+|.+|+.++|++|.++|+|+|+++|++. +++..++++++..+
T Consensus 199 ~~~~vL~i~~e~~~~~~~~~~~~i~als~aag~pt~~s~p~~ia~a~k~~~a~a~~~~~~~~~~~~~~~~~a~~~~~~~- 277 (310)
T PTZ00135 199 YDAKVLDITDEDIVAKFQEGVQNVAAISLAAGYPTEASAPHSILNAFKNLAAIGLESGFTFPLAEKIKEALANPSAAAA- 277 (310)
T ss_pred eCHHHcCCCHHHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHhhcCCCChhhHHHHHhhcCchhhcc-
Confidence 3444577777777666665 89999999999999999999999999998 45555566665543
Q ss_pred ccccccchhhhcccchhhhhhhhhhhccccccccccCCCCCCCC
Q psy10269 65 GPAAAAPAAAQAAAPAAAEAKEDKKKKEESDEGSDDDMGFGLFD 108 (108)
Q Consensus 65 a~~a~~~~~~~~~~~~a~~~~~~~~~k~eeeeE~d~dmgfgLFd 108 (108)
+|+++ + + ++ + + + + ++++|||||||+||||||||
T Consensus 278 ~~~~~-~-~---~~--~-~-~-~-~~~~~~~ee~~~~~g~~lf~ 310 (310)
T PTZ00135 278 AAAAA-A-A---AA--A-A-A-A-AAPAEEEEEEEDDMGFGLFD 310 (310)
T ss_pred Ccccc-C-c---cc--c-c-c-c-ccccccccCcchhccccCCC
Confidence 22211 1 1 11 1 1 1 2 33456778889999999998
No 14
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=99.18 E-value=4e-12 Score=100.05 Aligned_cols=48 Identities=8% Similarity=0.059 Sum_probs=39.1
Q ss_pred CccchhhcccCCCcCCCCH--HHHHHHHHHhCCcccCchhHHHHHHhcCC
Q psy10269 2 GPKCALFLHMSYIVGSEDG--EKIQTVLKAAGVEVEPYWPGLFAKALEGV 49 (108)
Q Consensus 2 ~~~aaLiL~d~~~~~~it~--e~I~~vl~aaG~~v~~~~~~~f~~alkgk 49 (108)
|+-..|.|+++++.+.+.. .++.++...+|+++..+.+|++++++++.
T Consensus 206 ~~~~vL~i~~e~~~~~~~~a~~~~~~lsl~~~~pt~~si~~~i~~a~~~~ 255 (323)
T PTZ00240 206 FTREDLSMTEDVVEKMLMEGLSNVAAMSLGAGIPTAATIGPMLVDAFKNL 255 (323)
T ss_pred cCHHHcCCCHHHHHHHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHHH
Confidence 3344566777766666664 78999999999999999999999999987
No 15
>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=97.08 E-value=0.00065 Score=45.82 Aligned_cols=28 Identities=18% Similarity=0.310 Sum_probs=23.4
Q ss_pred hcccCCCcCCCCHHHHHHHHHH-hCCcccCc
Q psy10269 8 FLHMSYIVGSEDGEKIQTVLKA-AGVEVEPY 37 (108)
Q Consensus 8 iL~d~~~~~~it~e~I~~vl~a-aG~~v~~~ 37 (108)
||+..++ +++.+++..++++ .|.+++.-
T Consensus 25 IL~aaGv--eVe~~~~~~~~~aLaGk~V~el 53 (105)
T cd04411 25 LLSAAGA--EIEPERVKLFLSALNGKNIDEV 53 (105)
T ss_pred HHHHcCC--CcCHHHHHHHHHHHcCCCHHHH
Confidence 6788888 9999999999999 77776543
No 16
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=95.85 E-value=0.0095 Score=47.13 Aligned_cols=38 Identities=18% Similarity=0.244 Sum_probs=20.6
Q ss_pred HHHHHHHHHhCCcccCchhHHHHHH----------hcC-CCHHHHHHhc
Q psy10269 21 EKIQTVLKAAGVEVEPYWPGLFAKA----------LEG-VNVKELISNV 58 (108)
Q Consensus 21 e~I~~vl~aaG~~v~~~~~~~f~~a----------lkg-k~i~~li~~~ 58 (108)
.+..+|...+|+++.....+++.++ +.+ .++.+-|.+.
T Consensus 243 ~~a~aLa~~~~~~t~e~~~~il~kA~~~~~ala~~~~~~~~~~~~~~~~ 291 (330)
T PRK04019 243 REAKALAVEAGIVTPETADDILSKAVAQALALAAALADKDALDEELKEV 291 (330)
T ss_pred HHHHHHHHHcCCCChhhHHHHHHHHHHHHHHHHHHhcCcccccHHHHhh
Confidence 3444455555565555555555444 455 5666666554
No 17
>KOG3449|consensus
Probab=94.43 E-value=0.1 Score=35.53 Aligned_cols=42 Identities=19% Similarity=0.014 Sum_probs=28.3
Q ss_pred hcccCCCcCCCCHHHHHHHHHHhCCcccCchhHHHHHHhcCCCH
Q psy10269 8 FLHMSYIVGSEDGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNV 51 (108)
Q Consensus 8 iL~d~~~~~~it~e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i 51 (108)
||..-++ ++..+.|+.|++.+..+....++..=...|..+..
T Consensus 26 Il~sVG~--E~d~e~i~~visel~GK~i~ElIA~G~eklAsvps 67 (112)
T KOG3449|consen 26 ILESVGA--EIDDERINLVLSELKGKDIEELIAAGREKLASVPS 67 (112)
T ss_pred HHHHhCc--ccCHHHHHHHHHHhcCCCHHHHHHHhHHHHhcCCC
Confidence 4555567 88999999999999988555555443334444433
No 18
>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=94.15 E-value=0.098 Score=35.47 Aligned_cols=31 Identities=16% Similarity=0.058 Sum_probs=21.4
Q ss_pred hcccCCCcCCCCHHHHHHHHHHhCCcccCchhH
Q psy10269 8 FLHMSYIVGSEDGEKIQTVLKAAGVEVEPYWPG 40 (108)
Q Consensus 8 iL~d~~~~~~it~e~I~~vl~aaG~~v~~~~~~ 40 (108)
||...++ ++....+..+++.........++.
T Consensus 26 IL~AaGv--eVe~~~~~lf~~~L~GKdi~eLIa 56 (109)
T cd05833 26 ILGSVGV--EVDDEKLNKVISELEGKDVEELIA 56 (109)
T ss_pred HHHHcCC--CccHHHHHHHHHHHcCCCHHHHHH
Confidence 4555677 888899999999886654443333
No 19
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=92.96 E-value=0.067 Score=36.20 Aligned_cols=13 Identities=15% Similarity=0.404 Sum_probs=6.8
Q ss_pred CCCHHHHHHHHHH
Q psy10269 17 SEDGEKIQTVLKA 29 (108)
Q Consensus 17 ~it~e~I~~vl~a 29 (108)
++....++.++++
T Consensus 32 eVee~~~k~~v~a 44 (106)
T PRK06402 32 EVDEARVKALVAA 44 (106)
T ss_pred CccHHHHHHHHHH
Confidence 4555555555555
No 20
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=92.14 E-value=0.062 Score=36.50 Aligned_cols=32 Identities=25% Similarity=0.235 Sum_probs=18.6
Q ss_pred HHHHhCCcccCchhHHHHHHh----cCCCHHHHHHh
Q psy10269 26 VLKAAGVEVEPYWPGLFAKAL----EGVNVKELISN 57 (108)
Q Consensus 26 vl~aaG~~v~~~~~~~f~~al----kgk~i~~li~~ 57 (108)
+|..+|-++...-+..+.++. ....++.|++.
T Consensus 9 lL~~agkei~e~~l~~vl~aaGveve~~r~k~lvaa 44 (109)
T COG2058 9 LLHLAGKEITEDNLKSVLEAAGVEVEEARAKALVAA 44 (109)
T ss_pred HHHHccCcCCHHHHHHHHHHcCCCccHHHHHHHHHH
Confidence 566677777777777666543 22244555554
No 21
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=90.05 E-value=0.52 Score=37.51 Aligned_cols=17 Identities=59% Similarity=1.122 Sum_probs=13.2
Q ss_pred ccccccccccCCCCC-CC
Q psy10269 91 KEESDEGSDDDMGFG-LF 107 (108)
Q Consensus 91 k~eeeeE~d~dmgfg-LF 107 (108)
++|+|||+|+||||| ||
T Consensus 306 ~~~~~e~~~~d~~~~~~~ 323 (323)
T PTZ00240 306 KEEEEESDEDDFGMGALF 323 (323)
T ss_pred ccCCccCcccccCccccC
Confidence 356677888999998 66
No 22
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=89.95 E-value=0.077 Score=42.00 Aligned_cols=29 Identities=14% Similarity=0.076 Sum_probs=22.7
Q ss_pred HHHHHHHHHhCCcccCchhHHHHHHhcCC
Q psy10269 21 EKIQTVLKAAGVEVEPYWPGLFAKALEGV 49 (108)
Q Consensus 21 e~I~~vl~aaG~~v~~~~~~~f~~alkgk 49 (108)
.+..+|...+++++....++++.+++++.
T Consensus 217 ~~a~~Ls~~~~~pt~~tl~~~i~kA~~~a 245 (330)
T PRK04019 217 QNAFNLAVNAAYPTPETLETLIQKAFREA 245 (330)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHHHHHHHH
Confidence 34444455559999999999999999877
No 23
>KOG0815|consensus
Probab=88.56 E-value=0.1 Score=39.70 Aligned_cols=42 Identities=19% Similarity=0.092 Sum_probs=32.8
Q ss_pred chhhcccCCCcCCCCH--HHHHHHHHHhCCcccCchhHHHHHHh
Q psy10269 5 CALFLHMSYIVGSEDG--EKIQTVLKAAGVEVEPYWPGLFAKAL 46 (108)
Q Consensus 5 aaLiL~d~~~~~~it~--e~I~~vl~aaG~~v~~~~~~~f~~al 46 (108)
-.|+++++++.+++-+ .+|.+++.++|+++.++.+|.|++++
T Consensus 202 evLDiteE~l~~~f~~~vs~va~~sL~~~ypt~asv~h~~~n~~ 245 (245)
T KOG0815|consen 202 EVLDITEEDLFSKFLSGVSNVASVSLAAGYPTLASVPHSFINAY 245 (245)
T ss_pred hhcCCcHHHHHHHHHHHHHHHHHHHHhcCCCcccccchhhhhcC
Confidence 3566666665444444 78999999999999999999999864
No 24
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=79.74 E-value=1.1 Score=30.12 Aligned_cols=17 Identities=18% Similarity=0.106 Sum_probs=7.7
Q ss_pred HHhCCcccCchhHHHHH
Q psy10269 28 KAAGVEVEPYWPGLFAK 44 (108)
Q Consensus 28 ~aaG~~v~~~~~~~f~~ 44 (108)
.-.|.++...-+..+++
T Consensus 11 ~~~g~~iT~e~I~~IL~ 27 (105)
T TIGR03685 11 HSAGKEINEENLKAVLE 27 (105)
T ss_pred HhcCCCCCHHHHHHHHH
Confidence 33444444444444444
No 25
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=78.22 E-value=3.9 Score=27.84 Aligned_cols=23 Identities=17% Similarity=0.192 Sum_probs=15.7
Q ss_pred hcccCCCcCCCCHHHHHHHHHHhCC
Q psy10269 8 FLHMSYIVGSEDGEKIQTVLKAAGV 32 (108)
Q Consensus 8 iL~d~~~~~~it~e~I~~vl~aaG~ 32 (108)
||...++ ++..+.++.+++...-
T Consensus 26 IL~AaGv--evd~~~~~~f~~~L~g 48 (113)
T PLN00138 26 ILGSVGA--DADDDRIELLLSEVKG 48 (113)
T ss_pred HHHHcCC--cccHHHHHHHHHHHcC
Confidence 4445566 7777788888877754
No 26
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=77.71 E-value=5.9 Score=27.00 Aligned_cols=28 Identities=7% Similarity=0.057 Sum_probs=19.9
Q ss_pred hcccCCCcCCCCHHHHHHHHHHhCCcccCc
Q psy10269 8 FLHMSYIVGSEDGEKIQTVLKAAGVEVEPY 37 (108)
Q Consensus 8 iL~d~~~~~~it~e~I~~vl~aaG~~v~~~ 37 (108)
||...++ ++....+..+++.....-...
T Consensus 28 IL~AaGv--eVd~~~~~l~~~~L~GKdI~E 55 (112)
T PTZ00373 28 VLSAVNA--DVEDDVLDNFFKSLEGKTPHE 55 (112)
T ss_pred HHHHcCC--CccHHHHHHHHHHHcCCCHHH
Confidence 4555677 888889999999886544333
No 27
>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=76.17 E-value=2.7 Score=28.08 Aligned_cols=21 Identities=24% Similarity=0.305 Sum_probs=12.7
Q ss_pred HHHHhCCcccCchhHHHHHHh
Q psy10269 26 VLKAAGVEVEPYWPGLFAKAL 46 (108)
Q Consensus 26 vl~aaG~~v~~~~~~~f~~al 46 (108)
||...|.++...-+..+.++.
T Consensus 10 iL~d~~~~~Tae~I~~ilkAa 30 (103)
T cd05831 10 ILHDDGIEITADNINALLKAA 30 (103)
T ss_pred HHccCCCCCCHHHHHHHHHHc
Confidence 455566666666666666544
No 28
>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=76.02 E-value=2.9 Score=28.22 Aligned_cols=21 Identities=24% Similarity=0.131 Sum_probs=11.6
Q ss_pred HHHHhCCcccCchhHHHHHHh
Q psy10269 26 VLKAAGVEVEPYWPGLFAKAL 46 (108)
Q Consensus 26 vl~aaG~~v~~~~~~~f~~al 46 (108)
+|.-.|.++...-+..+++.-
T Consensus 9 LL~~~G~eITae~I~~IL~AA 29 (106)
T cd05832 9 LLHYAGKEINEENLKKVLEAA 29 (106)
T ss_pred HHHhcCCCCCHHHHHHHHHHh
Confidence 444555666666666555543
No 29
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=74.95 E-value=3.8 Score=26.69 Aligned_cols=37 Identities=14% Similarity=0.191 Sum_probs=34.1
Q ss_pred cCCCCHHHHHHHHHHhCCcccCchhHHHHHHhcCCCH
Q psy10269 15 VGSEDGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNV 51 (108)
Q Consensus 15 ~~~it~e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i 51 (108)
++.+|.+++-+.++.-|+++.....+.+++.|+|+++
T Consensus 12 ln~iT~~eLlkyskqy~i~it~~QA~~I~~~lr~k~i 48 (85)
T PF11116_consen 12 LNNITAKELLKYSKQYNISITKKQAEQIANILRGKNI 48 (85)
T ss_pred HhcCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCC
Confidence 3578999999999999999999999999999999954
No 30
>PF03948 Ribosomal_L9_C: Ribosomal protein L9, C-terminal domain; InterPro: IPR020069 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 [, ]. Ribosomal protein L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
Probab=44.23 E-value=17 Score=23.21 Aligned_cols=29 Identities=24% Similarity=0.354 Sum_probs=24.9
Q ss_pred CCCcCCCCHHHHHHHHHHh-CCcccCchhH
Q psy10269 12 SYIVGSEDGEKIQTVLKAA-GVEVEPYWPG 40 (108)
Q Consensus 12 ~~~~~~it~e~I~~vl~aa-G~~v~~~~~~ 40 (108)
+.+.+++|..+|...|+.. |++++..+..
T Consensus 26 gklfGSVt~~dIa~~l~~~~g~~Idk~~I~ 55 (87)
T PF03948_consen 26 GKLFGSVTSKDIAKALKEQTGIEIDKKKIE 55 (87)
T ss_dssp SSBSSEBSHHHHHHHHHHCCSSSSSSSSBC
T ss_pred cceecCcCHHHHHHHHHHhhCCeEeccEEE
Confidence 4567799999999999999 9999987764
No 31
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=44.04 E-value=26 Score=26.85 Aligned_cols=51 Identities=25% Similarity=0.369 Sum_probs=37.7
Q ss_pred cchhhcccCCCcCCCCH---HHHHHHHHHhCC--cc---cCchhHHHHHHhcCCCHHHHHHhc
Q psy10269 4 KCALFLHMSYIVGSEDG---EKIQTVLKAAGV--EV---EPYWPGLFAKALEGVNVKELISNV 58 (108)
Q Consensus 4 ~aaLiL~d~~~~~~it~---e~I~~vl~aaG~--~v---~~~~~~~f~~alkgk~i~~li~~~ 58 (108)
|...+..+++. .|++ ++|++||-+..| +| |+|-+-++.+-|+.. ..||+++
T Consensus 89 YSSss~~EEet--TISAKvm~~ikavLgaTKiDLPVDINDPYDlGLLLRhLRHH--SNLLAnI 147 (238)
T PF02084_consen 89 YSSSSVDEEET--TISAKVMEDIKAVLGATKIDLPVDINDPYDLGLLLRHLRHH--SNLLANI 147 (238)
T ss_pred cccccccCCCc--cccHHHHHHHHHHhcccccccccccCChhhHHHHHHHHHHH--HHHHhhc
Confidence 55555555666 8888 999999999987 44 577777888877664 3578776
No 32
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=32.68 E-value=45 Score=18.40 Aligned_cols=31 Identities=10% Similarity=0.160 Sum_probs=25.2
Q ss_pred CCCHHHHHHHHHHhCCc-ccCchhHHHHHHhc
Q psy10269 17 SEDGEKIQTVLKAAGVE-VEPYWPGLFAKALE 47 (108)
Q Consensus 17 ~it~e~I~~vl~aaG~~-v~~~~~~~f~~alk 47 (108)
.||.+++..++...|++ ..+...+.+++.+.
T Consensus 4 ~i~~~~~~~~l~~~g~~~~s~~e~~~l~~~~D 35 (54)
T PF13833_consen 4 KITREEFRRALSKLGIKDLSEEEVDRLFREFD 35 (54)
T ss_dssp EEEHHHHHHHHHHTTSSSSCHHHHHHHHHHHT
T ss_pred EECHHHHHHHHHHhCCCCCCHHHHHHHHHhcc
Confidence 57889999999888998 88888887777773
No 33
>PF10017 Methyltransf_33: Histidine-specific methyltransferase, SAM-dependent; InterPro: IPR019257 This domain is found in methyltransferases and various hypothetical proteins.
Probab=30.85 E-value=38 Score=22.88 Aligned_cols=24 Identities=29% Similarity=0.548 Sum_probs=21.9
Q ss_pred CCCHHHHHHHHHHhCCcccCchhH
Q psy10269 17 SEDGEKIQTVLKAAGVEVEPYWPG 40 (108)
Q Consensus 17 ~it~e~I~~vl~aaG~~v~~~~~~ 40 (108)
+.|.+.+..++..+|+.+...|.+
T Consensus 95 Ky~~~~~~~l~~~aGl~~~~~w~d 118 (127)
T PF10017_consen 95 KYSPEEFEALAEQAGLEVEKRWTD 118 (127)
T ss_pred CcCHHHHHHHHHHCCCeeEEEEEC
Confidence 789999999999999999988864
No 34
>PF07308 DUF1456: Protein of unknown function (DUF1456); InterPro: IPR009921 This domain occurs in several hypothetical bacterial proteins of around 150 residues in length. The function of this domain is unknown.
Probab=29.15 E-value=59 Score=19.98 Aligned_cols=29 Identities=14% Similarity=0.189 Sum_probs=22.2
Q ss_pred CCCHHHHHHHHHHhCCcccCchhHHHHHH
Q psy10269 17 SEDGEKIQTVLKAAGVEVEPYWPGLFAKA 45 (108)
Q Consensus 17 ~it~e~I~~vl~aaG~~v~~~~~~~f~~a 45 (108)
.++.+++..+++.+|++|.+.-...|.+.
T Consensus 13 ~l~d~~m~~if~l~~~~vs~~el~a~lrk 41 (68)
T PF07308_consen 13 DLKDDDMIEIFALAGFEVSKAELSAWLRK 41 (68)
T ss_pred cCChHHHHHHHHHcCCccCHHHHHHHHCC
Confidence 45667888888888888888877777543
No 35
>PF05037 DUF669: Protein of unknown function (DUF669); InterPro: IPR007731 This entry is represented by Streptococcus phage Sfi11, Gp151. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=28.78 E-value=65 Score=22.12 Aligned_cols=39 Identities=18% Similarity=0.214 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHhCCc--ccCchhHHHHHHhcCCCHHHHH
Q psy10269 17 SEDGEKIQTVLKAAGVE--VEPYWPGLFAKALEGVNVKELI 55 (108)
Q Consensus 17 ~it~e~I~~vl~aaG~~--v~~~~~~~f~~alkgk~i~~li 55 (108)
+.+...+..+++++|++ .+..-++-|++.|.|+.+.=.+
T Consensus 70 ~~~~~~l~~i~~a~G~~~~~~~~sl~~~~~~l~gk~l~V~v 110 (141)
T PF05037_consen 70 EYSIKRLNAIAKAAGIPEGTDFESLEQFLNQLLGKPLRVTV 110 (141)
T ss_pred hhhHHHHHHHHHHhCCCCCCCcccHHHHHHHHcCCeeEEEe
Confidence 56678999999999986 4455578899999988775444
No 36
>PF14788 EF-hand_10: EF hand; PDB: 1DJW_B 1DJI_B 1DJG_B 1QAS_B 2ISD_B 1DJZ_B 1DJY_B 1DJX_B 1QAT_A 1DJH_A ....
Probab=28.16 E-value=59 Score=19.09 Aligned_cols=29 Identities=10% Similarity=0.257 Sum_probs=19.8
Q ss_pred CHHHHHHHHHHhCCcccCchhHHHHHHhc
Q psy10269 19 DGEKIQTVLKAAGVEVEPYWPGLFAKALE 47 (108)
Q Consensus 19 t~e~I~~vl~aaG~~v~~~~~~~f~~alk 47 (108)
+-..|+++|+-.+|.++..+...+....+
T Consensus 3 sf~Evk~lLk~~NI~~~~~yA~~LFq~~D 31 (51)
T PF14788_consen 3 SFKEVKKLLKMMNIEMDDEYARQLFQECD 31 (51)
T ss_dssp EHHHHHHHHHHTT----HHHHHHHHHHH-
T ss_pred CHHHHHHHHHHHccCcCHHHHHHHHHHhc
Confidence 45789999999999999999887766554
No 37
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=27.80 E-value=63 Score=19.08 Aligned_cols=19 Identities=42% Similarity=0.613 Sum_probs=15.8
Q ss_pred CCCHHHHHHHHHHhCCccc
Q psy10269 17 SEDGEKIQTVLKAAGVEVE 35 (108)
Q Consensus 17 ~it~e~I~~vl~aaG~~v~ 35 (108)
+++.+.|..+|+..|++++
T Consensus 18 ~i~~~ei~~~L~~lg~~~~ 36 (71)
T smart00874 18 DLSAEEIEEILKRLGFEVE 36 (71)
T ss_pred CCCHHHHHHHHHHCCCeEE
Confidence 6788889999999998764
No 38
>PF08339 RTX_C: RTX C-terminal domain; InterPro: IPR013550 This domain describes the C-terminal region of various bacterial haemolysins and leukotoxins, which belong to the RTX family of toxins. These are produced by various Gram negative bacteria, such as Escherichia coli (P09983 from SWISSPROT) and Actinobacillus pleuropneumoniae (P15377 from SWISSPROT). RTX toxins may interact with lipopolysaccharide (LPS) to functionally impair and eventually kill leukocytes []. This region is found in association with the RTX N-terminal domain (IPR003995 from INTERPRO) and multiple hemolysin-type calcium-binding repeats (IPR001343 from INTERPRO).
Probab=27.46 E-value=63 Score=23.00 Aligned_cols=48 Identities=15% Similarity=0.243 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHH-HhCCcccCchhHHHHHHhcCC--------CHHHHHHhcCCCCCc
Q psy10269 17 SEDGEKIQTVLK-AAGVEVEPYWPGLFAKALEGV--------NVKELISNVGSGAGA 64 (108)
Q Consensus 17 ~it~e~I~~vl~-aaG~~v~~~~~~~f~~alkgk--------~i~~li~~~~a~~~~ 64 (108)
.||.++|.+++. .-......+...-.+..++.+ +|..+|++.++++..
T Consensus 60 ~ITs~qld~l~~~~~~g~i~~~~l~~~a~~y~~~~~~~~l~n~i~KIISS~~~F~s~ 116 (145)
T PF08339_consen 60 RITSDQLDKLLEDKGKGKITSYQLSNNAENYKSKKNLSNLANEINKIISSAGSFTSS 116 (145)
T ss_pred EEcHhHHHHHhcccccCcchHHHHHHHHHhhcchhhhHHHHHHHHHHHHHhhccccc
Confidence 789999999998 433456666666666666522 677888887776544
No 39
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=24.27 E-value=1e+02 Score=18.07 Aligned_cols=37 Identities=8% Similarity=0.074 Sum_probs=29.0
Q ss_pred HHHHHHHHHhCCcccCchhHHHHHHhcCCCHHHHHHh
Q psy10269 21 EKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELISN 57 (108)
Q Consensus 21 e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i~~li~~ 57 (108)
+=+.-.|..+|+++..-....+++....|=+.+++.+
T Consensus 6 ~v~~~yL~~~G~~~~D~rv~RLvSLaaQKFisdI~~d 42 (51)
T PF03540_consen 6 EVTDYYLERSGFQTSDPRVKRLVSLAAQKFISDIAND 42 (51)
T ss_pred HHHHHHHHHCCCCCCCHhHHHHHHHHHHHHHHHHHHH
Confidence 4567789999999988888888887777767776653
No 40
>KOG3981|consensus
Probab=23.88 E-value=86 Score=24.62 Aligned_cols=27 Identities=22% Similarity=0.257 Sum_probs=23.6
Q ss_pred CCCHHHHHHHHHHhCCcccCchhHHHH
Q psy10269 17 SEDGEKIQTVLKAAGVEVEPYWPGLFA 43 (108)
Q Consensus 17 ~it~e~I~~vl~aaG~~v~~~~~~~f~ 43 (108)
.=|+.||..+++-+-+|+++.+.+.|.
T Consensus 70 DDTasnv~rLc~rA~yP~~p~~~~~~~ 96 (326)
T KOG3981|consen 70 DDTASNVVRLCKRAIYPVEPQFFDKFF 96 (326)
T ss_pred CccHHHHHHHHHHhcCCCCHHHHHHHh
Confidence 448999999999999999988777775
No 41
>PRK00754 signal recognition particle protein Srp19; Provisional
Probab=22.81 E-value=93 Score=20.41 Aligned_cols=20 Identities=20% Similarity=0.170 Sum_probs=17.3
Q ss_pred cCCCCHHHHHHHHHHhCCcc
Q psy10269 15 VGSEDGEKIQTVLKAAGVEV 34 (108)
Q Consensus 15 ~~~it~e~I~~vl~aaG~~v 34 (108)
+..||.++|..+++..|+++
T Consensus 32 V~~P~~~EI~~a~~~lgl~~ 51 (95)
T PRK00754 32 VKEPRLEEIIEAAEKLGLNP 51 (95)
T ss_pred ccCCCHHHHHHHHHHcCCCe
Confidence 35789999999999999974
No 42
>PF14091 DUF4269: Domain of unknown function (DUF4269)
Probab=22.57 E-value=57 Score=23.39 Aligned_cols=32 Identities=38% Similarity=0.629 Sum_probs=25.1
Q ss_pred HHHHHHHHHhCCcccCchhHHHHHHhcCCCHHHHH
Q psy10269 21 EKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELI 55 (108)
Q Consensus 21 e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i~~li 55 (108)
+.|.. ||..|++++|.+.+++- |.|-....||
T Consensus 119 ~~Ii~-LK~~GlKTEPAFa~lLg--L~GDPY~~LL 150 (152)
T PF14091_consen 119 EEIIE-LKESGLKTEPAFAKLLG--LEGDPYEALL 150 (152)
T ss_pred HHHHH-HHHcCCcchHHHHHHhC--CCCChHHHHh
Confidence 34443 57999999999999985 8887777776
No 43
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=21.67 E-value=76 Score=19.05 Aligned_cols=21 Identities=33% Similarity=0.411 Sum_probs=14.2
Q ss_pred CCCHHHHHHHHHHhCCcccCc
Q psy10269 17 SEDGEKIQTVLKAAGVEVEPY 37 (108)
Q Consensus 17 ~it~e~I~~vl~aaG~~v~~~ 37 (108)
.++.+.|.++|+..|+.+...
T Consensus 18 ~i~~~~i~~~L~~lg~~~~~~ 38 (70)
T PF03484_consen 18 DISPEEIIKILKRLGFKVEKI 38 (70)
T ss_dssp ---HHHHHHHHHHTT-EEEE-
T ss_pred CCCHHHHHHHHHHCCCEEEEC
Confidence 678899999999999987764
No 44
>PF10965 DUF2767: Protein of unknown function (DUF2767); InterPro: IPR024493 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=21.44 E-value=77 Score=19.83 Aligned_cols=23 Identities=22% Similarity=0.036 Sum_probs=20.0
Q ss_pred chhhcccCCCcCCCCHHHHHHHHHH
Q psy10269 5 CALFLHMSYIVGSEDGEKIQTVLKA 29 (108)
Q Consensus 5 aaLiL~d~~~~~~it~e~I~~vl~a 29 (108)
+.|.|++.++ +++..+|..+|+.
T Consensus 21 ~Vl~L~~~G~--etk~~~Ia~~LrT 43 (69)
T PF10965_consen 21 AVLELADLGH--ETKRIVIADVLRT 43 (69)
T ss_pred HHHHHHHcCC--CchhhHHHHHHHH
Confidence 4688999998 9899999999977
No 45
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=21.25 E-value=1.4e+02 Score=15.54 Aligned_cols=29 Identities=14% Similarity=0.155 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHHHHhCCcccCchhHHHHH
Q psy10269 16 GSEDGEKIQTVLKAAGVEVEPYWPGLFAK 44 (108)
Q Consensus 16 ~~it~e~I~~vl~aaG~~v~~~~~~~f~~ 44 (108)
+..|..+++.+|+.-|+++.-....++.+
T Consensus 2 ~~l~v~eLk~~l~~~gL~~~G~K~~Li~R 30 (35)
T PF02037_consen 2 SKLTVAELKEELKERGLSTSGKKAELIER 30 (35)
T ss_dssp TTSHHHHHHHHHHHTTS-STSSHHHHHHH
T ss_pred CcCcHHHHHHHHHHCCCCCCCCHHHHHHH
Confidence 35678899999999999998887766654
No 46
>PRK03745 signal recognition particle protein Srp19; Provisional
Probab=21.10 E-value=1.1e+02 Score=20.40 Aligned_cols=20 Identities=30% Similarity=0.292 Sum_probs=18.0
Q ss_pred cCCCCHHHHHHHHHHhCCcc
Q psy10269 15 VGSEDGEKIQTVLKAAGVEV 34 (108)
Q Consensus 15 ~~~it~e~I~~vl~aaG~~v 34 (108)
++.||...|..++++.|+++
T Consensus 29 V~~P~~~EI~~a~~~lgl~~ 48 (100)
T PRK03745 29 VERPTLEEIVDAAEALGFKV 48 (100)
T ss_pred ccCCCHHHHHHHHHHcCCCc
Confidence 45789999999999999987
No 47
>PF14104 DUF4277: Domain of unknown function (DUF4277)
Probab=20.52 E-value=2.2e+02 Score=19.34 Aligned_cols=40 Identities=15% Similarity=0.146 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHhCCcccCchhHHHHHHhcCCCHHHHHH
Q psy10269 17 SEDGEKIQTVLKAAGVEVEPYWPGLFAKALEGVNVKELIS 56 (108)
Q Consensus 17 ~it~e~I~~vl~aaG~~v~~~~~~~f~~alkgk~i~~li~ 56 (108)
++|.-.+-+.+---|.-.......+|-..|++++++.||-
T Consensus 41 ~vs~G~~vkamilN~Lg~~~~pLyl~~~ff~~~~~E~L~g 80 (115)
T PF14104_consen 41 KVSHGQVVKAMILNGLGFVSRPLYLFEEFFEDKPVERLLG 80 (115)
T ss_pred cccHHHHHHHHHHHhcCCCCcchhhhHHHHccCCHHHHhc
Confidence 6777666666666667777788899999999999999993
No 48
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=20.03 E-value=1.1e+02 Score=20.07 Aligned_cols=20 Identities=25% Similarity=0.351 Sum_probs=17.9
Q ss_pred cCCCCHHHHHHHHHHhCCcc
Q psy10269 15 VGSEDGEKIQTVLKAAGVEV 34 (108)
Q Consensus 15 ~~~it~e~I~~vl~aaG~~v 34 (108)
+..|+.++|..+++..|+++
T Consensus 29 V~~P~~~ei~~a~~~LGl~~ 48 (93)
T COG1400 29 VENPSLEEIAEALRELGLKP 48 (93)
T ss_pred ccCCCHHHHHHHHHHcCCCe
Confidence 45889999999999999976
Done!