Query psy2830
Match_columns 183
No_of_seqs 137 out of 817
Neff 4.3
Searched_HMMs 46136
Date Fri Aug 16 18:00:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2830.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2830hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00373 60S Acidic ribosomal 100.0 3.4E-40 7.3E-45 255.9 10.6 111 38-152 2-112 (112)
2 PLN00138 large subunit ribosom 100.0 4.1E-39 8.9E-44 250.0 10.6 113 39-152 1-113 (113)
3 cd05833 Ribosomal_P2 Ribosomal 100.0 5E-38 1.1E-42 242.4 10.6 109 39-152 1-109 (109)
4 KOG3449|consensus 100.0 6.7E-38 1.5E-42 242.2 10.3 112 39-152 1-112 (112)
5 cd04411 Ribosomal_P1_P2_L12p R 100.0 8.6E-35 1.9E-39 223.0 10.5 105 39-151 1-105 (105)
6 cd05831 Ribosomal_P1 Ribosomal 100.0 3.7E-28 7.9E-33 185.6 9.2 101 39-151 3-103 (103)
7 COG2058 RPP1A Ribosomal protei 99.9 1.2E-27 2.5E-32 184.9 9.6 109 39-152 1-109 (109)
8 KOG1762|consensus 99.9 1.6E-26 3.5E-31 179.7 6.6 105 39-152 8-114 (114)
9 PRK06402 rpl12p 50S ribosomal 99.9 1E-24 2.2E-29 168.1 8.4 55 39-94 1-55 (106)
10 TIGR03685 L21P_arch 50S riboso 99.9 1.6E-21 3.4E-26 149.9 8.0 56 39-95 1-56 (105)
11 PF00428 Ribosomal_60s: 60s Ac 99.9 1.2E-22 2.6E-27 149.9 1.8 87 55-151 1-88 (88)
12 cd05832 Ribosomal_L12p Ribosom 99.9 1.7E-21 3.7E-26 150.2 7.9 56 39-95 1-56 (106)
13 PTZ00135 60S acidic ribosomal 98.8 3.5E-09 7.5E-14 94.4 4.2 27 60-86 221-247 (310)
14 PTZ00240 60S ribosomal protein 97.8 3.1E-05 6.7E-10 69.9 5.3 17 135-151 306-323 (323)
15 PRK04019 rplP0 acidic ribosoma 96.9 0.0022 4.8E-08 57.6 6.2 48 41-95 242-290 (330)
16 COG2058 RPP1A Ribosomal protei 96.5 0.0049 1.1E-07 48.3 4.7 27 64-91 9-35 (109)
17 KOG3449|consensus 94.6 0.15 3.2E-06 40.3 6.5 24 54-77 32-55 (112)
18 cd04411 Ribosomal_P1_P2_L12p R 93.5 0.2 4.3E-06 38.7 5.4 30 54-84 31-61 (105)
19 PRK06402 rpl12p 50S ribosomal 89.0 0.75 1.6E-05 35.9 4.4 26 64-90 9-34 (106)
20 TIGR03685 L21P_arch 50S riboso 85.9 1.7 3.6E-05 33.6 4.7 27 64-91 9-35 (105)
21 cd05833 Ribosomal_P2 Ribosomal 85.6 2.8 6.1E-05 32.6 5.9 18 54-71 32-49 (109)
22 cd05831 Ribosomal_P1 Ribosomal 84.3 2.4 5.3E-05 32.5 4.9 27 64-91 10-36 (103)
23 cd05832 Ribosomal_L12p Ribosom 83.2 2.6 5.5E-05 32.9 4.7 27 64-91 9-35 (106)
24 PTZ00373 60S Acidic ribosomal 80.1 0.95 2.1E-05 35.6 1.3 18 54-71 34-51 (112)
25 KOG1762|consensus 76.4 2.7 5.9E-05 33.4 2.9 32 64-96 15-50 (114)
26 PTZ00240 60S ribosomal protein 76.0 4 8.6E-05 37.3 4.2 24 39-66 226-249 (323)
27 PLN00138 large subunit ribosom 73.9 2.1 4.7E-05 33.5 1.7 18 54-71 32-49 (113)
28 PF00428 Ribosomal_60s: 60s Ac 71.3 0.8 1.7E-05 33.7 -1.1 13 130-142 70-82 (88)
29 PF11116 DUF2624: Protein of u 50.8 29 0.00063 26.2 4.0 36 55-90 14-49 (85)
30 PTZ00135 60S acidic ribosomal 49.2 8.1 0.00018 34.9 1.0 19 134-152 292-310 (310)
31 PRK04019 rplP0 acidic ribosoma 46.8 7.3 0.00016 35.1 0.3 19 85-103 256-274 (330)
32 COG5465 Uncharacterized conser 45.8 26 0.00057 29.4 3.4 80 6-95 71-157 (166)
33 PF13405 EF-hand_6: EF-hand do 45.6 29 0.00063 20.1 2.7 27 43-69 4-31 (31)
34 cd05027 S-100B S-100B: S-100B 40.5 1E+02 0.0022 22.3 5.6 55 40-94 9-75 (88)
35 PF07308 DUF1456: Protein of u 39.3 44 0.00094 23.9 3.3 29 56-84 14-42 (68)
36 PF02885 Glycos_trans_3N: Glyc 39.3 65 0.0014 22.1 4.1 44 52-95 11-57 (66)
37 cd00051 EFh EF-hand, calcium b 37.0 91 0.002 18.4 5.3 40 45-84 6-45 (63)
38 PTZ00184 calmodulin; Provision 35.1 1.2E+02 0.0025 22.1 5.2 42 43-84 88-129 (149)
39 KOG1668|consensus 34.5 15 0.00032 32.4 0.3 19 140-160 101-119 (231)
40 PF13833 EF-hand_8: EF-hand do 32.1 77 0.0017 20.0 3.4 30 55-84 4-34 (54)
41 KOG0027|consensus 30.9 2.5E+02 0.0054 21.6 6.7 55 40-94 9-68 (151)
42 KOG0031|consensus 26.6 3.1E+02 0.0068 23.3 6.8 48 47-96 58-106 (171)
43 cd05022 S-100A13 S-100A13: S-1 26.5 1.9E+02 0.0042 21.2 5.1 45 40-84 9-56 (89)
44 PF07462 MSP1_C: Merozoite sur 25.4 65 0.0014 31.9 3.0 12 146-157 334-345 (574)
45 cd05031 S-100A10_like S-100A10 25.1 2.6E+02 0.0056 19.9 5.8 54 40-93 9-74 (94)
46 PF13499 EF-hand_7: EF-hand do 23.8 1.8E+02 0.0039 18.8 4.1 38 43-80 4-41 (66)
47 COG5126 FRQ1 Ca2+-binding prot 23.1 3E+02 0.0066 22.8 6.1 55 40-94 21-79 (160)
48 PF07524 Bromo_TP: Bromodomain 22.8 1.7E+02 0.0036 20.4 4.0 25 49-73 52-76 (77)
49 PF01581 FARP: FMRFamide relat 22.3 48 0.0011 15.9 0.8 10 163-172 2-11 (11)
50 PF14658 EF-hand_9: EF-hand do 22.2 1.8E+02 0.0038 20.9 4.0 39 28-69 7-45 (66)
51 PF13897 GOLD_2: Golgi-dynamic 21.7 66 0.0014 26.3 1.9 10 142-151 27-36 (136)
52 PF14788 EF-hand_10: EF hand; 21.0 1.8E+02 0.004 19.9 3.7 29 57-85 3-31 (51)
53 PF03115 Astro_capsid: Astrovi 20.5 34 0.00073 35.0 0.0 13 146-158 690-702 (787)
54 PF11112 PyocinActivator: Pyoc 20.3 58 0.0013 23.8 1.2 29 17-46 40-68 (76)
No 1
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=100.00 E-value=3.4e-40 Score=255.93 Aligned_cols=111 Identities=45% Similarity=0.753 Sum_probs=87.9
Q ss_pred hhHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCCHHHHHHhhhhhhccCCCCCCccchhcccc
Q psy2830 38 IMRYVAAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIVLKELNGKNLEEIIAAGKEKLASMPSGGGAVSASAGAA 117 (183)
Q Consensus 38 ~M~ylAAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lFakaL~GKdI~ELIa~G~~KL~sv~sGG~aaaa~aaaa 117 (183)
+|||+|||||+.++||.+||++||++||+++|++|+++|+++|++.|+||||+|||++|++||+|| ||++++++++++
T Consensus 2 ~MkyvaAYlL~~lgG~~~pTaddI~kIL~AaGveVd~~~~~l~~~~L~GKdI~ELIa~G~~kl~sv--gg~~~aa~a~a~ 79 (112)
T PTZ00373 2 AMKYVAAYLMCVLGGNENPTKKEVKNVLSAVNADVEDDVLDNFFKSLEGKTPHELIAAGMKKLQNI--GGGVAAAAAPAA 79 (112)
T ss_pred chHHHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHHHHhcc--cCcccccccccc
Confidence 699999999999999999999999999999999999999999999999999999999999999999 333222112111
Q ss_pred CccccccccchHHHHhhhhhccccccCCcCccccc
Q psy2830 118 APAAAAEEGKKEEKKAEKKEESDASDDDMGFGVWE 152 (183)
Q Consensus 118 a~A~~~aaaaa~~~eeek~EeeEEsDdDMGFgLFD 152 (183)
++++ +++++++++++|+|++|||||||||||||
T Consensus 80 ~~~~--~~~~~~~~~e~k~ee~ee~ddDmgf~LFd 112 (112)
T PTZ00373 80 GAAT--AGAKAEAKKEEKKEEEEEEEDDLGFSLFG 112 (112)
T ss_pred cccc--cccchhhhhhhcccccccccccccccccC
Confidence 1111 11222334445566777889999999997
No 2
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=100.00 E-value=4.1e-39 Score=249.96 Aligned_cols=113 Identities=50% Similarity=0.829 Sum_probs=90.2
Q ss_pred hHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCCHHHHHHhhhhhhccCCCCCCccchhccccC
Q psy2830 39 MRYVAAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIVLKELNGKNLEEIIAAGKEKLASMPSGGGAVSASAGAAA 118 (183)
Q Consensus 39 M~ylAAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lFakaL~GKdI~ELIa~G~~KL~sv~sGG~aaaa~aaaaa 118 (183)
|||||||||+.++||++||++||++||+++|++|+++|+++|++.|+||+|+|||++|++||+++++||+++++++++++
T Consensus 1 mkyvaAyll~~l~g~~~pta~dI~~IL~AaGvevd~~~~~~f~~~L~gK~i~eLIa~G~~kl~sv~~gg~aa~a~a~a~~ 80 (113)
T PLN00138 1 MKVVAAYLLAVLGGNTCPSAEDLKDILGSVGADADDDRIELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAAAPA 80 (113)
T ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCcccHHHHHHHHHHHcCCCHHHHHHhchhccccCCCCCccccccccccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999998764431121111
Q ss_pred ccccccccchHHHHhhhhhccccccCCcCccccc
Q psy2830 119 PAAAAEEGKKEEKKAEKKEESDASDDDMGFGVWE 152 (183)
Q Consensus 119 ~A~~~aaaaa~~~eeek~EeeEEsDdDMGFgLFD 152 (183)
++ +++.+++++++++|+|++||+||||||||||
T Consensus 81 ~~-~~~~~~~~~~~e~k~e~eeE~ddDmGfgLFd 113 (113)
T PLN00138 81 AG-GAAAPAAEAKKEEKVEEKEESDDDMGFSLFD 113 (113)
T ss_pred cc-cccccccchhhhhhccccccccccccccccC
Confidence 11 1111122233444556667889999999997
No 3
>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=100.00 E-value=5e-38 Score=242.38 Aligned_cols=109 Identities=55% Similarity=0.905 Sum_probs=86.7
Q ss_pred hHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCCHHHHHHhhhhhhccCCCCCCccchhccccC
Q psy2830 39 MRYVAAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIVLKELNGKNLEEIIAAGKEKLASMPSGGGAVSASAGAAA 118 (183)
Q Consensus 39 M~ylAAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lFakaL~GKdI~ELIa~G~~KL~sv~sGG~aaaa~aaaaa 118 (183)
|||||||||++++||.+||++||++||+++|++|+++|+++|++.|+||||++||++|.+||++|++++++++++++ +
T Consensus 1 MkyvaAylL~~l~g~~~pTa~dI~~IL~AaGveVe~~~~~lf~~~L~GKdi~eLIa~g~~kl~s~~~~~~~aa~a~~--~ 78 (109)
T cd05833 1 MKYVAAYLLAVLGGNASPSAADVKKILGSVGVEVDDEKLNKVISELEGKDVEELIAAGKEKLASVPAGAGGAAPAAA--A 78 (109)
T ss_pred CHHHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHhhhcCCCccccccccccc--c
Confidence 89999999999999999999999999999999999999999999999999999999999999999854433221111 1
Q ss_pred ccccccccchHHHHhhhhhccccccCCcCccccc
Q psy2830 119 PAAAAEEGKKEEKKAEKKEESDASDDDMGFGVWE 152 (183)
Q Consensus 119 ~A~~~aaaaa~~~eeek~EeeEEsDdDMGFgLFD 152 (183)
++ +++++++++++|+|++||+||||||||||
T Consensus 79 ~a---~aa~~~~~e~kkee~eee~ddDmGf~LFd 109 (109)
T cd05833 79 AA---AAAAAAKKEEKKEESEEESDDDMGFGLFD 109 (109)
T ss_pred cc---ccccchhhhhhccCCccccccccCCCCCC
Confidence 11 11122234445555666679999999998
No 4
>KOG3449|consensus
Probab=100.00 E-value=6.7e-38 Score=242.19 Aligned_cols=112 Identities=57% Similarity=0.911 Sum_probs=92.5
Q ss_pred hHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCCHHHHHHhhhhhhccCCCCCCccchhccccC
Q psy2830 39 MRYVAAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIVLKELNGKNLEEIIAAGKEKLASMPSGGGAVSASAGAAA 118 (183)
Q Consensus 39 M~ylAAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lFakaL~GKdI~ELIa~G~~KL~sv~sGG~aaaa~aaaaa 118 (183)
|||+|||||++++||.+|++.||++||.++|++++++|+++|++.|+||+|+|||++|++||+|||+||++++++++++.
T Consensus 1 MkyvaAYLL~~lgGn~~psa~DikkIl~sVG~E~d~e~i~~visel~GK~i~ElIA~G~eklAsvpsGGa~~aaa~~aag 80 (112)
T KOG3449|consen 1 MKYVAAYLLAVLGGNASPSASDIKKILESVGAEIDDERINLVLSELKGKDIEELIAAGREKLASVPSGGAVAAAAAPAAG 80 (112)
T ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHHhCcccCHHHHHHHHHHhcCCCHHHHHHHhHHHHhcCCCCCccccccCcCCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999985432222222
Q ss_pred ccccccccchHHHHhhhhhccccccCCcCccccc
Q psy2830 119 PAAAAEEGKKEEKKAEKKEESDASDDDMGFGVWE 152 (183)
Q Consensus 119 ~A~~~aaaaa~~~eeek~EeeEEsDdDMGFgLFD 152 (183)
++++++ +..+++|+|+|++|||||||||+|||
T Consensus 81 gaa~aa--~~a~~~e~keEe~eesddDmgf~lFd 112 (112)
T KOG3449|consen 81 GAAGAA--PAAAKEEEKEEEKEESDDDMGFGLFD 112 (112)
T ss_pred CCccCC--ccchhhhhhhhhcccccccccccccC
Confidence 222212 22224555666669999999999997
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=100.00 E-value=8.6e-35 Score=223.04 Aligned_cols=105 Identities=41% Similarity=0.709 Sum_probs=86.6
Q ss_pred hHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCCHHHHHHhhhhhhccCCCCCCccchhccccC
Q psy2830 39 MRYVAAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIVLKELNGKNLEEIIAAGKEKLASMPSGGGAVSASAGAAA 118 (183)
Q Consensus 39 M~ylAAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lFakaL~GKdI~ELIa~G~~KL~sv~sGG~aaaa~aaaaa 118 (183)
|+|++||||++++|+. ||++||++||+++|++|+++|+++|+++|+||+|++||++|.+||+++|+||++++ + +
T Consensus 1 m~~v~A~Lll~~~g~~-~ta~~I~~IL~aaGveVe~~~~~~~~~aLaGk~V~eli~~g~~kl~~~~~~~~a~~--~-a-- 74 (105)
T cd04411 1 MEYVAAYLLLHKGGKE-LTEDKIKELLSAAGAEIEPERVKLFLSALNGKNIDEVISKGKELMSSQAAAAAAPA--A-T-- 74 (105)
T ss_pred CHHHHHHHHHHhcCCC-CCHHHHHHHHHHcCCCcCHHHHHHHHHHHcCCCHHHHHHHHHhhccCCCCcccccc--c-c--
Confidence 7999999999999987 99999999999999999999999999999999999999999999999998765422 1 1
Q ss_pred ccccccccchHHHHhhhhhccccccCCcCcccc
Q psy2830 119 PAAAAEEGKKEEKKAEKKEESDASDDDMGFGVW 151 (183)
Q Consensus 119 ~A~~~aaaaa~~~eeek~EeeEEsDdDMGFgLF 151 (183)
++++ ++++++++++|+|++||||||||||||
T Consensus 75 ~~~~--~~~~~~~~e~k~ee~eE~dddmgf~LF 105 (105)
T cd04411 75 AAAT--AEPAEKAEEAKEEEEEEEDEDFGFGLF 105 (105)
T ss_pred cccc--ccchhhhhhhhcccccccccccCcccC
Confidence 1111 112233444556677888999999999
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=99.95 E-value=3.7e-28 Score=185.65 Aligned_cols=101 Identities=29% Similarity=0.517 Sum_probs=75.1
Q ss_pred hHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCCHHHHHHhhhhhhccCCCCCCccchhccccC
Q psy2830 39 MRYVAAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIVLKELNGKNLEEIIAAGKEKLASMPSGGGAVSASAGAAA 118 (183)
Q Consensus 39 M~ylAAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lFakaL~GKdI~ELIa~G~~KL~sv~sGG~aaaa~aaaaa 118 (183)
.|.|||++|++ .+.+||++||++||+++|++|+++|+++|++.|+||+|++||++ ++++|+++++++++ +
T Consensus 3 ac~yAaLiL~d--~~~~~Tae~I~~ilkAaGveve~~~~~~f~~~L~gk~i~elIa~-------~~~~~~~aap~a~~-a 72 (103)
T cd05831 3 ACTYAALILHD--DGIEITADNINALLKAAGVNVEPYWPGLFAKALEGKDIKDLLSN-------VGGGGGGAAPAAAA-A 72 (103)
T ss_pred HHHHHHHHHcc--CCCCCCHHHHHHHHHHcCCcccHHHHHHHHHHHcCCCHHHHhhc-------cccccccccccccc-c
Confidence 49999999999 56889999999999999999999999999999999999999974 44443322211111 1
Q ss_pred ccccccccchHHHHhhhhhccccccCCcCcccc
Q psy2830 119 PAAAAEEGKKEEKKAEKKEESDASDDDMGFGVW 151 (183)
Q Consensus 119 ~A~~~aaaaa~~~eeek~EeeEEsDdDMGFgLF 151 (183)
++ + ++.++++++++|+|++||+|||||||||
T Consensus 73 ~~-~-~~~~~~~~~~kk~e~eee~d~dmgfglF 103 (103)
T cd05831 73 AA-A-AAAAEAKKEEKKEEEEEESDDDMGFGLF 103 (103)
T ss_pred cc-c-cccccchhhhcccccccccccccccccC
Confidence 11 1 1112233455566777778999999999
No 7
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=1.2e-27 Score=184.86 Aligned_cols=109 Identities=34% Similarity=0.612 Sum_probs=84.3
Q ss_pred hHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCCHHHHHHhhhhhhccCCCCCCccchhccccC
Q psy2830 39 MRYVAAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIVLKELNGKNLEEIIAAGKEKLASMPSGGGAVSASAGAAA 118 (183)
Q Consensus 39 M~ylAAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lFakaL~GKdI~ELIa~G~~KL~sv~sGG~aaaa~aaaaa 118 (183)
|+|++||+|++++|+ +||+++|++||+++|++|++.|++.|++.|+||||+|+|.++..++.+++.++++++++++ +
T Consensus 1 MeYi~a~llL~~agk-ei~e~~l~~vl~aaGveve~~r~k~lvaaLeg~~idE~i~~~~~~~~a~a~a~aaaa~~A~--~ 77 (109)
T COG2058 1 MEYIYAYLLLHLAGK-EITEDNLKSVLEAAGVEVEEARAKALVAALEGVDIDEVIKNAAEAPAAAAAAGAAAAAAAG--A 77 (109)
T ss_pred ChHHHHHHHHHHccC-cCCHHHHHHHHHHcCCCccHHHHHHHHHHhcCCCHHHHHHHhcccccccCCcccccccccc--c
Confidence 789999999999988 6999999999999999999999999999999999999999998888777665544331011 1
Q ss_pred ccccccccchHHHHhhhhhccccccCCcCccccc
Q psy2830 119 PAAAAEEGKKEEKKAEKKEESDASDDDMGFGVWE 152 (183)
Q Consensus 119 ~A~~~aaaaa~~~eeek~EeeEEsDdDMGFgLFD 152 (183)
+++ +.+...++++++++.+||+|+||||+|||
T Consensus 78 ~~a--~~~~ea~eEe~eEe~~EE~~~~~lf~LF~ 109 (109)
T COG2058 78 EAA--AEADEAEEEEKEEEAEEESDDDMLFGLFG 109 (109)
T ss_pred ccc--cchhhHHHHHhhhchhhcccccchhhccC
Confidence 111 11012223334556678889999999997
No 8
>KOG1762|consensus
Probab=99.93 E-value=1.6e-26 Score=179.68 Aligned_cols=105 Identities=32% Similarity=0.530 Sum_probs=82.3
Q ss_pred hHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCCHHHHHHhhhhhhccCCCCCCccchhc-ccc
Q psy2830 39 MRYVAAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIVLKELNGKNLEEIIAAGKEKLASMPSGGGAVSASA-GAA 117 (183)
Q Consensus 39 M~ylAAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lFakaL~GKdI~ELIa~G~~KL~sv~sGG~aaaa~a-aaa 117 (183)
.|.|++++|++ ....+|.++|.+++|++|++|+++||.+|+++|.++||.+||+ ++++||+++++.+ +++
T Consensus 8 ac~yaalIL~d--~~i~it~dki~tl~kaa~v~ve~~Wp~lfakale~vni~~li~-------n~gag~~a~a~~~~~~~ 78 (114)
T KOG1762|consen 8 ACSYAALILHD--DEIEVTADKINTLTKAAGVNVEPYWPGLFAKALEGVNIKELIC-------NVGAGGGALAAGAAAAG 78 (114)
T ss_pred HHhhhhhhccc--cceeeehhhhhhHHHhccCcccccchhHHHHHhccCChHHHHH-------hcccCCccCCCcccccc
Confidence 59999999999 4478999999999999999999999999999999999999998 6777655543211 111
Q ss_pred Cccc-cccccchHHHHhhhhhccccccCCcCccccc
Q psy2830 118 APAA-AAEEGKKEEKKAEKKEESDASDDDMGFGVWE 152 (183)
Q Consensus 118 a~A~-~~aaaaa~~~eeek~EeeEEsDdDMGFgLFD 152 (183)
.+++ ++++++++++++.|+|+.||+||||||||||
T Consensus 79 ~aa~~~~aA~~~Ekk~eak~EeseesddDmgfGLfd 114 (114)
T KOG1762|consen 79 GAAAAGGAAAAEEKKEEAKKEESEESDDDMGFGLFD 114 (114)
T ss_pred ccccccccccchHHHHHhhhhhhcccccccccCCCC
Confidence 1221 1133345556667778889999999999997
No 9
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=99.91 E-value=1e-24 Score=168.12 Aligned_cols=55 Identities=33% Similarity=0.555 Sum_probs=53.7
Q ss_pred hHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCCHHHHHH
Q psy2830 39 MRYVAAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIVLKELNGKNLEEIIA 94 (183)
Q Consensus 39 M~ylAAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lFakaL~GKdI~ELIa 94 (183)
|+|++||||++++|+ +||++||++||+++|++|+++|+++|+++|+|+||++||.
T Consensus 1 M~yiyAaLLL~~~g~-~it~e~I~~IL~AAGveVee~~~k~~v~aL~GkdIeElI~ 55 (106)
T PRK06402 1 MEYIYAALLLHSAGK-EINEDNLKKVLEAAGVEVDEARVKALVAALEDVNIEEAIK 55 (106)
T ss_pred CHHHHHHHHHHhcCC-CCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHH
Confidence 799999999999988 7999999999999999999999999999999999999997
No 10
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=99.85 E-value=1.6e-21 Score=149.87 Aligned_cols=56 Identities=32% Similarity=0.555 Sum_probs=54.2
Q ss_pred hHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCCHHHHHHh
Q psy2830 39 MRYVAAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIVLKELNGKNLEEIIAA 95 (183)
Q Consensus 39 M~ylAAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lFakaL~GKdI~ELIa~ 95 (183)
|+|++||||++++|+ +||+++|++||+++||+|+++|+.+|++.|+|++|++||.+
T Consensus 1 M~yvyA~Lll~~~g~-~iT~e~I~~IL~AAGv~ve~~~~~~la~~L~gk~i~eli~~ 56 (105)
T TIGR03685 1 MEYIYAALLLHSAGK-EINEENLKAVLEAAGVEVDEARVKALVAALEGVNIEEAIKK 56 (105)
T ss_pred CHHHHHHHHHHhcCC-CCCHHHHHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHHh
Confidence 899999999999988 79999999999999999999999999999999999999973
No 11
>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=99.85 E-value=1.2e-22 Score=149.91 Aligned_cols=87 Identities=38% Similarity=0.661 Sum_probs=58.8
Q ss_pred CCCHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCCHHHHHHhhhhhhccCCCCCCccchhccccCccccccccchHHHHhh
Q psy2830 55 NPAQGDVEKILSSVGIESDAEKLKIVLKELNGKNLEEIIAAGKEKLASMPSGGGAVSASAGAAAPAAAAEEGKKEEKKAE 134 (183)
Q Consensus 55 spTaedI~kVLkAaGveVe~~~~~lFakaL~GKdI~ELIa~G~~KL~sv~sGG~aaaa~aaaaa~A~~~aaaaa~~~eee 134 (183)
+||+++|.+||+++|++|+++|+.+|++.|+|++|++||+.+..+|... ++ ++++++++. ++ ++++++++
T Consensus 1 ~pT~~~i~~vl~aag~~v~~~~~~~~~~~l~~~~i~~li~~~~~~~~~~------aa--a~aaa~aa~-~~-a~a~~e~k 70 (88)
T PF00428_consen 1 EPTAENIKKVLKAAGVEVEAIWLELFAKALEGKDIKELIANGSAGMAAA------AA--AAAAAAAAA-AA-AAAAEEEK 70 (88)
T ss_dssp S-SCCCHHHHHHHHTHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHH------HH--HTTSSHHHH-HH-HHHHSTTH
T ss_pred CCCHHHHHHHHHHhCCchhHHHHHHHHHHHcCCcHHHHHhccccccccc------cc--ccccccccc-cc-cccchhcc
Confidence 4899999999999999999999999999999999999999998887611 11 111011111 11 11112222
Q ss_pred hhhc-cccccCCcCcccc
Q psy2830 135 KKEE-SDASDDDMGFGVW 151 (183)
Q Consensus 135 k~Ee-eEEsDdDMGFgLF 151 (183)
|+++ +||+|+|||||||
T Consensus 71 kEeeeeEEed~dmGf~LF 88 (88)
T PF00428_consen 71 KEEEEEEEEDDDMGFGLF 88 (88)
T ss_dssp HHHT--SS-SSSSSTTTT
T ss_pred cccccccccccccCcCCC
Confidence 2222 2688999999999
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=99.85 E-value=1.7e-21 Score=150.24 Aligned_cols=56 Identities=32% Similarity=0.545 Sum_probs=54.2
Q ss_pred hHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCCHHHHHHh
Q psy2830 39 MRYVAAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIVLKELNGKNLEEIIAA 95 (183)
Q Consensus 39 M~ylAAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lFakaL~GKdI~ELIa~ 95 (183)
|+|++||||++++|+ +||+++|++||+++|++|+++|+.+|++.|+|++|++||++
T Consensus 1 M~yvyAaLLL~~~G~-eITae~I~~IL~AAGveVd~~~~~ala~aL~gkdIeElIa~ 56 (106)
T cd05832 1 MEYIYAALLLHYAGK-EINEENLKKVLEAAGIEVDEARVKALVAALEEVNIDEAIKK 56 (106)
T ss_pred CHHHHHHHHHHhcCC-CCCHHHHHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHHh
Confidence 899999999999988 79999999999999999999999999999999999999974
No 13
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=98.81 E-value=3.5e-09 Score=94.35 Aligned_cols=27 Identities=19% Similarity=0.318 Sum_probs=23.8
Q ss_pred HHHHHHHHcCCCcCHHHHHHHHHHhCC
Q psy2830 60 DVEKILSSVGIESDAEKLKIVLKELNG 86 (183)
Q Consensus 60 dI~kVLkAaGveVe~~~~~lFakaL~G 86 (183)
+|.+|..++|+.++++|+.+|+++++.
T Consensus 221 ~i~als~aag~pt~~s~p~~ia~a~k~ 247 (310)
T PTZ00135 221 NVAAISLAAGYPTEASAPHSILNAFKN 247 (310)
T ss_pred HHHHHHHHhCCCcHHHHHHHHHHHHHH
Confidence 567888999999999999999998843
No 14
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=97.80 E-value=3.1e-05 Score=69.91 Aligned_cols=17 Identities=41% Similarity=0.980 Sum_probs=12.6
Q ss_pred hhhccccccCCcCcc-cc
Q psy2830 135 KKEESDASDDDMGFG-VW 151 (183)
Q Consensus 135 k~EeeEEsDdDMGFg-LF 151 (183)
++|+|||+||||||| ||
T Consensus 306 ~~~~~e~~~~d~~~~~~~ 323 (323)
T PTZ00240 306 KEEEEESDEDDFGMGALF 323 (323)
T ss_pred ccCCccCcccccCccccC
Confidence 356677888999996 54
No 15
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=96.89 E-value=0.0022 Score=57.56 Aligned_cols=48 Identities=21% Similarity=0.234 Sum_probs=36.5
Q ss_pred HHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHhCC-CCHHHHHHh
Q psy2830 41 YVAAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIVLKELNG-KNLEEIIAA 95 (183)
Q Consensus 41 ylAAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lFakaL~G-KdI~ELIa~ 95 (183)
|--|+.|+.-.+ =||++.|..||..+ ......++..|.+ .++.+-|.+
T Consensus 242 ~~~a~aLa~~~~--~~t~e~~~~il~kA-----~~~~~ala~~~~~~~~~~~~~~~ 290 (330)
T PRK04019 242 FREAKALAVEAG--IVTPETADDILSKA-----VAQALALAAALADKDALDEELKE 290 (330)
T ss_pred HHHHHHHHHHcC--CCChhhHHHHHHHH-----HHHHHHHHHHhcCcccccHHHHh
Confidence 334555555442 48999999999998 5667789999999 999988874
No 16
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=96.48 E-value=0.0049 Score=48.32 Aligned_cols=27 Identities=37% Similarity=0.519 Sum_probs=22.7
Q ss_pred HHHHcCCCcCHHHHHHHHHHhCCCCHHH
Q psy2830 64 ILSSVGIESDAEKLKIVLKELNGKNLEE 91 (183)
Q Consensus 64 VLkAaGveVe~~~~~lFakaL~GKdI~E 91 (183)
+|..+|-++....++.+.++. |.+|++
T Consensus 9 lL~~agkei~e~~l~~vl~aa-Gveve~ 35 (109)
T COG2058 9 LLHLAGKEITEDNLKSVLEAA-GVEVEE 35 (109)
T ss_pred HHHHccCcCCHHHHHHHHHHc-CCCccH
Confidence 678899999999999988875 888775
No 17
>KOG3449|consensus
Probab=94.55 E-value=0.15 Score=40.30 Aligned_cols=24 Identities=13% Similarity=0.108 Sum_probs=18.8
Q ss_pred CCCCHHHHHHHHHHcCCCcCHHHH
Q psy2830 54 ENPAQGDVEKILSSVGIESDAEKL 77 (183)
Q Consensus 54 ~spTaedI~kVLkAaGveVe~~~~ 77 (183)
.++..+.|++||+....+--.+.+
T Consensus 32 ~E~d~e~i~~visel~GK~i~ElI 55 (112)
T KOG3449|consen 32 AEIDDERINLVLSELKGKDIEELI 55 (112)
T ss_pred cccCHHHHHHHHHHhcCCCHHHHH
Confidence 679999999999999886433333
No 18
>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=93.54 E-value=0.2 Score=38.74 Aligned_cols=30 Identities=17% Similarity=0.044 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHHHH-cCCCcCHHHHHHHHHHh
Q psy2830 54 ENPAQGDVEKILSS-VGIESDAEKLKIVLKEL 84 (183)
Q Consensus 54 ~spTaedI~kVLkA-aGveVe~~~~~lFakaL 84 (183)
.+++.+.+..++++ .|.+|+.-. ......|
T Consensus 31 veVe~~~~~~~~~aLaGk~V~eli-~~g~~kl 61 (105)
T cd04411 31 AEIEPERVKLFLSALNGKNIDEVI-SKGKELM 61 (105)
T ss_pred CCcCHHHHHHHHHHHcCCCHHHHH-HHHHhhc
Confidence 57999999999999 888887654 3333334
No 19
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=88.98 E-value=0.75 Score=35.86 Aligned_cols=26 Identities=35% Similarity=0.561 Sum_probs=13.1
Q ss_pred HHHHcCCCcCHHHHHHHHHHhCCCCHH
Q psy2830 64 ILSSVGIESDAEKLKIVLKELNGKNLE 90 (183)
Q Consensus 64 VLkAaGveVe~~~~~lFakaL~GKdI~ 90 (183)
||.-.|.++...-++.++++. |.+|+
T Consensus 9 LL~~~g~~it~e~I~~IL~AA-GveVe 34 (106)
T PRK06402 9 LLHSAGKEINEDNLKKVLEAA-GVEVD 34 (106)
T ss_pred HHHhcCCCCCHHHHHHHHHHc-CCCcc
Confidence 344455555555555555543 44444
No 20
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=85.89 E-value=1.7 Score=33.65 Aligned_cols=27 Identities=41% Similarity=0.612 Sum_probs=17.7
Q ss_pred HHHHcCCCcCHHHHHHHHHHhCCCCHHH
Q psy2830 64 ILSSVGIESDAEKLKIVLKELNGKNLEE 91 (183)
Q Consensus 64 VLkAaGveVe~~~~~lFakaL~GKdI~E 91 (183)
||.-.|.++....++.++++- |.+|++
T Consensus 9 ll~~~g~~iT~e~I~~IL~AA-Gv~ve~ 35 (105)
T TIGR03685 9 LLHSAGKEINEENLKAVLEAA-GVEVDE 35 (105)
T ss_pred HHHhcCCCCCHHHHHHHHHHh-CCcccH
Confidence 456667777777777777764 555554
No 21
>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=85.65 E-value=2.8 Score=32.58 Aligned_cols=18 Identities=11% Similarity=0.176 Sum_probs=10.9
Q ss_pred CCCCHHHHHHHHHHcCCC
Q psy2830 54 ENPAQGDVEKILSSVGIE 71 (183)
Q Consensus 54 ~spTaedI~kVLkAaGve 71 (183)
.++..+.+..++++....
T Consensus 32 veVe~~~~~lf~~~L~GK 49 (109)
T cd05833 32 VEVDDEKLNKVISELEGK 49 (109)
T ss_pred CCccHHHHHHHHHHHcCC
Confidence 356666666666666543
No 22
>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=84.29 E-value=2.4 Score=32.50 Aligned_cols=27 Identities=41% Similarity=0.592 Sum_probs=21.7
Q ss_pred HHHHcCCCcCHHHHHHHHHHhCCCCHHH
Q psy2830 64 ILSSVGIESDAEKLKIVLKELNGKNLEE 91 (183)
Q Consensus 64 VLkAaGveVe~~~~~lFakaL~GKdI~E 91 (183)
||...|.++....+...+++. |.++++
T Consensus 10 iL~d~~~~~Tae~I~~ilkAa-Gveve~ 36 (103)
T cd05831 10 ILHDDGIEITADNINALLKAA-GVNVEP 36 (103)
T ss_pred HHccCCCCCCHHHHHHHHHHc-CCcccH
Confidence 678888999999999888875 677764
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=83.16 E-value=2.6 Score=32.91 Aligned_cols=27 Identities=37% Similarity=0.540 Sum_probs=20.4
Q ss_pred HHHHcCCCcCHHHHHHHHHHhCCCCHHH
Q psy2830 64 ILSSVGIESDAEKLKIVLKELNGKNLEE 91 (183)
Q Consensus 64 VLkAaGveVe~~~~~lFakaL~GKdI~E 91 (183)
||...|.++....++.++++- |.++++
T Consensus 9 LL~~~G~eITae~I~~IL~AA-GveVd~ 35 (106)
T cd05832 9 LLHYAGKEINEENLKKVLEAA-GIEVDE 35 (106)
T ss_pred HHHhcCCCCCHHHHHHHHHHh-CCcccH
Confidence 567788888888888888864 666654
No 24
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=80.13 E-value=0.95 Score=35.58 Aligned_cols=18 Identities=6% Similarity=0.128 Sum_probs=14.6
Q ss_pred CCCCHHHHHHHHHHcCCC
Q psy2830 54 ENPAQGDVEKILSSVGIE 71 (183)
Q Consensus 54 ~spTaedI~kVLkAaGve 71 (183)
.++..+.+..++++....
T Consensus 34 veVd~~~~~l~~~~L~GK 51 (112)
T PTZ00373 34 ADVEDDVLDNFFKSLEGK 51 (112)
T ss_pred CCccHHHHHHHHHHHcCC
Confidence 568999999999988653
No 25
>KOG1762|consensus
Probab=76.37 E-value=2.7 Score=33.37 Aligned_cols=32 Identities=34% Similarity=0.466 Sum_probs=23.7
Q ss_pred HHHHcCCCcCHHHHHHHHHHhCCCCHH----HHHHhh
Q psy2830 64 ILSSVGIESDAEKLKIVLKELNGKNLE----EIIAAG 96 (183)
Q Consensus 64 VLkAaGveVe~~~~~lFakaL~GKdI~----ELIa~G 96 (183)
||.-.+++|..+.+..+.++. |.+++ .|++..
T Consensus 15 IL~d~~i~it~dki~tl~kaa-~v~ve~~Wp~lfaka 50 (114)
T KOG1762|consen 15 ILHDDEIEVTADKINTLTKAA-GVNVEPYWPGLFAKA 50 (114)
T ss_pred hccccceeeehhhhhhHHHhc-cCcccccchhHHHHH
Confidence 667788999999999998875 55655 455543
No 26
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=75.97 E-value=4 Score=37.27 Aligned_cols=24 Identities=29% Similarity=0.364 Sum_probs=14.1
Q ss_pred hHHHHHHHHHHhCCCCCCCHHHHHHHHH
Q psy2830 39 MRYVAAYLLAALGGKENPAQGDVEKILS 66 (183)
Q Consensus 39 M~ylAAylL~~lgGn~spTaedI~kVLk 66 (183)
.+.++++.|.. .-||.+-|..+|.
T Consensus 226 ~~~~~~lsl~~----~~pt~~si~~~i~ 249 (323)
T PTZ00240 226 LSNVAAMSLGA----GIPTAATIGPMLV 249 (323)
T ss_pred HHHHHHHHHhh----CCCcHHHHHHHHH
Confidence 44555544433 2489888876663
No 27
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=73.87 E-value=2.1 Score=33.52 Aligned_cols=18 Identities=22% Similarity=0.292 Sum_probs=13.3
Q ss_pred CCCCHHHHHHHHHHcCCC
Q psy2830 54 ENPAQGDVEKILSSVGIE 71 (183)
Q Consensus 54 ~spTaedI~kVLkAaGve 71 (183)
.++..+.++.+++.....
T Consensus 32 vevd~~~~~~f~~~L~gK 49 (113)
T PLN00138 32 ADADDDRIELLLSEVKGK 49 (113)
T ss_pred CcccHHHHHHHHHHHcCC
Confidence 468888888888877553
No 28
>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=71.27 E-value=0.8 Score=33.67 Aligned_cols=13 Identities=38% Similarity=0.614 Sum_probs=4.4
Q ss_pred HHHhhhhhccccc
Q psy2830 130 EKKAEKKEESDAS 142 (183)
Q Consensus 130 ~~eeek~EeeEEs 142 (183)
+++++++||+|++
T Consensus 70 kkEeeeeEEed~d 82 (88)
T PF00428_consen 70 KKEEEEEEEEDDD 82 (88)
T ss_dssp HHHHT--SS-SSS
T ss_pred ccccccccccccc
Confidence 3444443444443
No 29
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=50.80 E-value=29 Score=26.21 Aligned_cols=36 Identities=19% Similarity=0.248 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCCHH
Q psy2830 55 NPAQGDVEKILSSVGIESDAEKLKIVLKELNGKNLE 90 (183)
Q Consensus 55 spTaedI~kVLkAaGveVe~~~~~lFakaL~GKdI~ 90 (183)
.+|.+++.+.-+.-|+.+....++..+..|.|+++.
T Consensus 14 ~iT~~eLlkyskqy~i~it~~QA~~I~~~lr~k~in 49 (85)
T PF11116_consen 14 NITAKELLKYSKQYNISITKKQAEQIANILRGKNIN 49 (85)
T ss_pred cCCHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCCC
Confidence 589999999999999999999999999999999874
No 30
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=49.23 E-value=8.1 Score=34.86 Aligned_cols=19 Identities=42% Similarity=0.947 Sum_probs=15.6
Q ss_pred hhhhccccccCCcCccccc
Q psy2830 134 EKKEESDASDDDMGFGVWE 152 (183)
Q Consensus 134 ek~EeeEEsDdDMGFgLFD 152 (183)
+++|+||||||||||||||
T Consensus 292 ~~~~~~ee~~~~~g~~lf~ 310 (310)
T PTZ00135 292 APAEEEEEEEDDMGFGLFD 310 (310)
T ss_pred cccccccCcchhccccCCC
Confidence 3356778889999999997
No 31
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=46.81 E-value=7.3 Score=35.13 Aligned_cols=19 Identities=5% Similarity=0.249 Sum_probs=12.1
Q ss_pred CCCCHHHHHHhhhhhhccC
Q psy2830 85 NGKNLEEIIAAGKEKLASM 103 (183)
Q Consensus 85 ~GKdI~ELIa~G~~KL~sv 103 (183)
.-.++..+|..+-.++..+
T Consensus 256 t~e~~~~il~kA~~~~~al 274 (330)
T PRK04019 256 TPETADDILSKAVAQALAL 274 (330)
T ss_pred ChhhHHHHHHHHHHHHHHH
Confidence 4566777777766666554
No 32
>COG5465 Uncharacterized conserved protein [Function unknown]
Probab=45.82 E-value=26 Score=29.42 Aligned_cols=80 Identities=25% Similarity=0.243 Sum_probs=52.6
Q ss_pred CCCCcchhh------hhhhhhccCCCCCcccccchhhhhhHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHH-
Q psy2830 6 RPNSANAEV------YFGLILIPTSNPGLQSQAGGYLRIMRYVAAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLK- 78 (183)
Q Consensus 6 ~~~~~~~~~------~~~~~~~~~~~~~~~~q~~~~~~~M~ylAAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~- 78 (183)
-|+|...|+ +=+.|+++|+ ++.+|-+..+. + ..|..++ +.+||...+.-.|.++---+|.|...
T Consensus 71 vpes~~~~~~rLL~liN~~v~~ghF--~lweeeg~I~f--R----~~L~l~~-G~ep~~~q~~v~idta~eacdsff~Af 141 (166)
T COG5465 71 VPESRRAEVARLLSLINRDVLIGHF--DLWEEEGAIFF--R----QSLLLAG-GVEPTSQQVEVLIDTALEACDSFFQAF 141 (166)
T ss_pred CchhHHHHHHHHHHHhhcccccCCc--CcccccCeeee--e----eehhccC-CCCccHHHHHHHHHHHHHHHHHHHHHH
Confidence 355665554 5688999999 89999888431 1 1233344 45799999999999885444554443
Q ss_pred HHHHHhCCCCHHHHHHh
Q psy2830 79 IVLKELNGKNLEEIIAA 95 (183)
Q Consensus 79 lFakaL~GKdI~ELIa~ 95 (183)
.|+. -.|++..+++.+
T Consensus 142 ~fv~-~g~~~~dea~~~ 157 (166)
T COG5465 142 QFVV-WGGMDADEALAA 157 (166)
T ss_pred HHhh-cCCCCHHHHHHH
Confidence 2222 378888888874
No 33
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=45.57 E-value=29 Score=20.08 Aligned_cols=27 Identities=22% Similarity=0.291 Sum_probs=20.9
Q ss_pred HHHHHHHhCCCCCCCHHHHHHHHH-HcC
Q psy2830 43 AAYLLAALGGKENPAQGDVEKILS-SVG 69 (183)
Q Consensus 43 AAylL~~lgGn~spTaedI~kVLk-AaG 69 (183)
.++-+++..++-.||.+++..+|+ +.|
T Consensus 4 ~~F~~~D~d~dG~I~~~el~~~l~~~lG 31 (31)
T PF13405_consen 4 EAFKMFDKDGDGFIDFEELRAILRKSLG 31 (31)
T ss_dssp HHHHHH-TTSSSEEEHHHHHHHHHHHTT
T ss_pred HHHHHHCCCCCCcCcHHHHHHHHHHhcC
Confidence 455667777778899999999999 765
No 34
>cd05027 S-100B S-100B: S-100B domain found in proteins similar to S100B. S100B is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100B group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100B is most abundant in glial cells of the central nervous system, predominately in astrocytes. S100B is involved in signal transduction via the inhibition of protein phoshorylation, regulation of enzyme activity and by affecting the calcium homeostasis. Upon calcium binding the S100B homodimer changes conformation to expose a hydrophobic cleft, which represents the interaction site of S100B with its more than 20 known target proteins. These target proteins include several cellular architecture proteins such as tubulin and GFAP; S100B can inhibit polymerization of these oligomeric molecules. Furthermore, S100B i
Probab=40.50 E-value=1e+02 Score=22.35 Aligned_cols=55 Identities=11% Similarity=0.300 Sum_probs=41.5
Q ss_pred HHHHHHHHHH-hCCCC-CCCHHHHHHHHHH-----cCCCcCHHHHHHHHHHhCC-----CCHHHHHH
Q psy2830 40 RYVAAYLLAA-LGGKE-NPAQGDVEKILSS-----VGIESDAEKLKIVLKELNG-----KNLEEIIA 94 (183)
Q Consensus 40 ~ylAAylL~~-lgGn~-spTaedI~kVLkA-----aGveVe~~~~~lFakaL~G-----KdI~ELIa 94 (183)
....+|-+++ ..|+- .|+.++++.+|++ .|-...+..++.+++.+.. .++++.+.
T Consensus 9 ~l~~aF~~fD~~dgdG~~I~~~eL~~ll~~~~~~~lg~~~~~~~v~~~i~~~D~n~dG~v~f~eF~~ 75 (88)
T cd05027 9 ALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMA 75 (88)
T ss_pred HHHHHHHHhcccCCCcCEECHHHHHHHHHHHhHHHhcCCCCHHHHHHHHHHhCCCCCCcCcHHHHHH
Confidence 5667777776 45565 4999999999999 8888888888888888832 45666653
No 35
>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=39.35 E-value=44 Score=23.88 Aligned_cols=29 Identities=21% Similarity=0.295 Sum_probs=22.3
Q ss_pred CCHHHHHHHHHHcCCCcCHHHHHHHHHHh
Q psy2830 56 PAQGDVEKILSSVGIESDAEKLKIVLKEL 84 (183)
Q Consensus 56 pTaedI~kVLkAaGveVe~~~~~lFakaL 84 (183)
++.++|..|++.+|.+|.+..+..|.+.=
T Consensus 14 l~d~~m~~if~l~~~~vs~~el~a~lrke 42 (68)
T PF07308_consen 14 LKDDDMIEIFALAGFEVSKAELSAWLRKE 42 (68)
T ss_pred CChHHHHHHHHHcCCccCHHHHHHHHCCC
Confidence 57778888888888888888777776653
No 36
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=39.33 E-value=65 Score=22.07 Aligned_cols=44 Identities=18% Similarity=0.251 Sum_probs=29.6
Q ss_pred CCCCCCHHHHHHHHHHcC-CCcCHHHHHHHHHHh--CCCCHHHHHHh
Q psy2830 52 GKENPAQGDVEKILSSVG-IESDAEKLKIVLKEL--NGKNLEEIIAA 95 (183)
Q Consensus 52 Gn~spTaedI~kVLkAaG-veVe~~~~~lFakaL--~GKdI~ELIa~ 95 (183)
.+...|.+++..++...= .++.+..+..|.-+| +|-+.+|+...
T Consensus 11 ~g~~Ls~~e~~~~~~~i~~g~~s~~qiaAfL~al~~kget~~Eiag~ 57 (66)
T PF02885_consen 11 DGEDLSREEAKAAFDAILDGEVSDAQIAAFLMALRMKGETPEEIAGF 57 (66)
T ss_dssp TT----HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHH
T ss_pred cCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCcCHHHHHHH
Confidence 346799999999998764 589999999998887 78888888853
No 37
>cd00051 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
Probab=36.97 E-value=91 Score=18.43 Aligned_cols=40 Identities=18% Similarity=0.331 Sum_probs=29.2
Q ss_pred HHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHh
Q psy2830 45 YLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIVLKEL 84 (183)
Q Consensus 45 ylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lFakaL 84 (183)
+-.++..++-.++.+++..+++..|.......+..+.+.+
T Consensus 6 f~~~d~~~~g~l~~~e~~~~l~~~~~~~~~~~~~~~~~~~ 45 (63)
T cd00051 6 FRLFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREV 45 (63)
T ss_pred HHHhCCCCCCcCcHHHHHHHHHHhCCCCCHHHHHHHHHHh
Confidence 3344555555689999999999988888777777666665
No 38
>PTZ00184 calmodulin; Provisional
Probab=35.10 E-value=1.2e+02 Score=22.14 Aligned_cols=42 Identities=12% Similarity=0.295 Sum_probs=32.8
Q ss_pred HHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHh
Q psy2830 43 AAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIVLKEL 84 (183)
Q Consensus 43 AAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lFakaL 84 (183)
.++-+++..++-.+|.+++.+++..+|..+....+..+++.+
T Consensus 88 ~~F~~~D~~~~g~i~~~e~~~~l~~~~~~~~~~~~~~~~~~~ 129 (149)
T PTZ00184 88 EAFKVFDRDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREA 129 (149)
T ss_pred HHHHhhCCCCCCeEeHHHHHHHHHHHCCCCCHHHHHHHHHhc
Confidence 345555655666799999999999999988888887777766
No 39
>KOG1668|consensus
Probab=34.50 E-value=15 Score=32.38 Aligned_cols=19 Identities=21% Similarity=0.466 Sum_probs=11.3
Q ss_pred ccccCCcCcccccCCCCCccc
Q psy2830 140 DASDDDMGFGVWEARTNGKKE 160 (183)
Q Consensus 140 EEsDdDMGFgLFD~~~~~~~~ 160 (183)
.++|||+ +||+.+++..++
T Consensus 101 ~dddDDi--DLFGsd~EEEd~ 119 (231)
T KOG1668|consen 101 ADDDDDV--DLFGSDDEEEDE 119 (231)
T ss_pred ccccccc--cccCCccccchh
Confidence 3455665 699866554444
No 40
>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=32.08 E-value=77 Score=19.98 Aligned_cols=30 Identities=20% Similarity=0.442 Sum_probs=21.3
Q ss_pred CCCHHHHHHHHHHcCCC-cCHHHHHHHHHHh
Q psy2830 55 NPAQGDVEKILSSVGIE-SDAEKLKIVLKEL 84 (183)
Q Consensus 55 spTaedI~kVLkAaGve-Ve~~~~~lFakaL 84 (183)
.||.+++..+|...|+. ..+..+..+++.+
T Consensus 4 ~i~~~~~~~~l~~~g~~~~s~~e~~~l~~~~ 34 (54)
T PF13833_consen 4 KITREEFRRALSKLGIKDLSEEEVDRLFREF 34 (54)
T ss_dssp EEEHHHHHHHHHHTTSSSSCHHHHHHHHHHH
T ss_pred EECHHHHHHHHHHhCCCCCCHHHHHHHHHhc
Confidence 36777777777666777 7777777766665
No 41
>KOG0027|consensus
Probab=30.87 E-value=2.5e+02 Score=21.65 Aligned_cols=55 Identities=22% Similarity=0.365 Sum_probs=44.6
Q ss_pred HHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHhCC-----CCHHHHHH
Q psy2830 40 RYVAAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIVLKELNG-----KNLEEIIA 94 (183)
Q Consensus 40 ~ylAAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lFakaL~G-----KdI~ELIa 94 (183)
.+-.|+-+.+..++-.|+...+.+++.+.|.......+..+++.+.. .++.+++.
T Consensus 9 el~~~F~~fD~d~~G~i~~~el~~~lr~lg~~~t~~el~~~~~~~D~dg~g~I~~~eF~~ 68 (151)
T KOG0027|consen 9 ELKEAFQLFDKDGDGKISVEELGAVLRSLGQNPTEEELRDLIKEIDLDGDGTIDFEEFLD 68 (151)
T ss_pred HHHHHHHHHCCCCCCcccHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCCCCeEcHHHHHH
Confidence 55678888888777789999999999999999888888888888863 56666664
No 42
>KOG0031|consensus
Probab=26.59 E-value=3.1e+02 Score=23.26 Aligned_cols=48 Identities=25% Similarity=0.369 Sum_probs=37.7
Q ss_pred HHHhCCCCCCCHHHHHHHHHHcCCCcCHH-HHHHHHHHhCCCCHHHHHHhh
Q psy2830 47 LAALGGKENPAQGDVEKILSSVGIESDAE-KLKIVLKELNGKNLEEIIAAG 96 (183)
Q Consensus 47 L~~lgGn~spTaedI~kVLkAaGveVe~~-~~~lFakaL~GKdI~ELIa~G 96 (183)
|+.+| + .++.+.|...++.++..+.=. .+++|-..|.|.+-++.|-++
T Consensus 58 ~aSlG-k-~~~d~elDaM~~Ea~gPINft~FLTmfGekL~gtdpe~~I~~A 106 (171)
T KOG0031|consen 58 LASLG-K-IASDEELDAMMKEAPGPINFTVFLTMFGEKLNGTDPEEVILNA 106 (171)
T ss_pred HHHcC-C-CCCHHHHHHHHHhCCCCeeHHHHHHHHHHHhcCCCHHHHHHHH
Confidence 34455 4 389999999999988776543 578999999999999999754
No 43
>cd05022 S-100A13 S-100A13: S-100A13 domain found in proteins similar to S100A13. S100A13 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A13 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100A13 is involved in the cellular export of interleukin-1 (IL-1) and of fibroblast growth factor-1 (FGF-1), which plays an important role in angiogenesis and tissue regeneration. Export is based on the CuII-dependent formation of multiprotein complexes containing the S100A13 protein. Assembly of these complexes occurs near the inner surface of the plasma membrane. Binding of two Ca(II) ions per monomer triggers key conformational changes leading to the creation of two identical and symmetrical Cu(II)-binding sites on the surface of the protein, close to the interface between the two monomers. These Cu
Probab=26.48 E-value=1.9e+02 Score=21.18 Aligned_cols=45 Identities=24% Similarity=0.383 Sum_probs=33.3
Q ss_pred HHHHHHHHHHh-CCCCCCCHHHHHHHHHH-cCCCcCH-HHHHHHHHHh
Q psy2830 40 RYVAAYLLAAL-GGKENPAQGDVEKILSS-VGIESDA-EKLKIVLKEL 84 (183)
Q Consensus 40 ~ylAAylL~~l-gGn~spTaedI~kVLkA-aGveVe~-~~~~lFakaL 84 (183)
.++.++-.++- +|+-.++.++++.|++. .|-.+.. .-++.+++.+
T Consensus 9 ~l~~~F~~fd~~~~~g~i~~~ELk~ll~~elg~~ls~~~~v~~mi~~~ 56 (89)
T cd05022 9 TLVSNFHKASVKGGKESLTASEFQELLTQQLPHLLKDVEGLEEKMKNL 56 (89)
T ss_pred HHHHHHHHHhCCCCCCeECHHHHHHHHHHHhhhhccCHHHHHHHHHHh
Confidence 56677777787 67778999999999998 7755554 5566666555
No 44
>PF07462 MSP1_C: Merozoite surface protein 1 (MSP1) C-terminus; InterPro: IPR010901 This entry represents the C-terminal region of merozoite surface protein 1 (MSP1), which is found in a number of Plasmodium species. MSP-1 is a 200 kDa protein expressed on the surface of the Plasmodium vivax merozoite. MSP-1 of Plasmodium species is synthesised as a high-molecular-weight precursor and then processed into several fragments. At the time of red cell invasion by the merozoite, only the 19 kDa C-terminal fragment (MSP-119), which contains two epidermal growth factor-like domains, remains on the surface. Antibodies against MSP-119 inhibit merozoite entry into red cells, and immunisation with MSP-119 protects monkeys from challenging infections. Hence, MSP-119 is considered a promising vaccine candidate [].; GO: 0009405 pathogenesis, 0016020 membrane
Probab=25.38 E-value=65 Score=31.88 Aligned_cols=12 Identities=0% Similarity=0.288 Sum_probs=7.7
Q ss_pred cCcccccCCCCC
Q psy2830 146 MGFGVWEARTNG 157 (183)
Q Consensus 146 MGFgLFD~~~~~ 157 (183)
+.+.||+.+|..
T Consensus 334 i~~p~fg~~ddd 345 (574)
T PF07462_consen 334 IALPLFGNNDDD 345 (574)
T ss_pred eeccCCCCCcCc
Confidence 456799865544
No 45
>cd05031 S-100A10_like S-100A10_like: S-100A10 domain found in proteins similar to S100A10. S100A10 is a member of the S100 family of EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A1_like group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. A unique feature of S100A10 is that it contains mutation in both of the calcium binding sites, making it calcium insensitive. S100A10 has been detected in brain, heart, gastrointestinal tract, kidney, liver, lung, spleen, testes, epidermis, aorta, and thymus. Structural data supports the homo- and hetero-dimeric as well as hetero-tetrameric nature of the protein. S100A10 has multiple binding partners in its calcium free state and is therefore involved in many diverse biological functions.
Probab=25.13 E-value=2.6e+02 Score=19.92 Aligned_cols=54 Identities=19% Similarity=0.367 Sum_probs=34.8
Q ss_pred HHHHHHHHHHh-CC-CCCCCHHHHHHHHHH-----cCCCcCHHHHHHHHHHhC-----CCCHHHHH
Q psy2830 40 RYVAAYLLAAL-GG-KENPAQGDVEKILSS-----VGIESDAEKLKIVLKELN-----GKNLEEII 93 (183)
Q Consensus 40 ~ylAAylL~~l-gG-n~spTaedI~kVLkA-----aGveVe~~~~~lFakaL~-----GKdI~ELI 93 (183)
.+.-+|-+.+- .| +-.||.+++..++.+ .|..+....+..+++.+. ..+..+.+
T Consensus 9 ~l~~~F~~~D~~dg~dG~Is~~El~~~l~~~~g~~lg~~~s~~ei~~~~~~~D~~~dg~I~f~eF~ 74 (94)
T cd05031 9 SLILTFHRYAGKDGDKNTLSRKELKKLMEKELSEFLKNQKDPMAVDKIMKDLDQNRDGKVNFEEFV 74 (94)
T ss_pred HHHHHHHHHhccCCCCCeECHHHHHHHHHHHhHHHhhccccHHHHHHHHHHhCCCCCCcCcHHHHH
Confidence 45566666664 43 346888999988887 466666666776666663 24555555
No 46
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=23.77 E-value=1.8e+02 Score=18.80 Aligned_cols=38 Identities=13% Similarity=0.205 Sum_probs=27.5
Q ss_pred HHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHH
Q psy2830 43 AAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIV 80 (183)
Q Consensus 43 AAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lF 80 (183)
-++-+++..++-.+|.+++..+++..+...........
T Consensus 4 ~~F~~~D~d~~G~i~~~el~~~~~~~~~~~~~~~~~~~ 41 (66)
T PF13499_consen 4 EAFKKFDKDGDGYISKEELRRALKHLGRDMSDEESDEM 41 (66)
T ss_dssp HHHHHHSTTSSSEEEHHHHHHHHHHTTSHSTHHHHHHH
T ss_pred HHHHHHcCCccCCCCHHHHHHHHHHhcccccHHHHHHH
Confidence 34556677667779999999999999987654444443
No 47
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=23.09 E-value=3e+02 Score=22.77 Aligned_cols=55 Identities=16% Similarity=0.324 Sum_probs=40.6
Q ss_pred HHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCcCHHHHHHHHHHhC----CCCHHHHHH
Q psy2830 40 RYVAAYLLAALGGKENPAQGDVEKILSSVGIESDAEKLKIVLKELN----GKNLEEIIA 94 (183)
Q Consensus 40 ~ylAAylL~~lgGn~spTaedI~kVLkAaGveVe~~~~~lFakaL~----GKdI~ELIa 94 (183)
++.=||.|.+.-+.-.|+-.++.+|+++.|-..-...+...+..+. ..+..++|.
T Consensus 21 ~lkeaF~l~D~d~~G~I~~~el~~ilr~lg~~~s~~ei~~l~~~~d~~~~~idf~~Fl~ 79 (160)
T COG5126 21 ELKEAFQLFDRDSDGLIDRNELGKILRSLGFNPSEAEINKLFEEIDAGNETVDFPEFLT 79 (160)
T ss_pred HHHHHHHHhCcCCCCCCcHHHHHHHHHHcCCCCcHHHHHHHHHhccCCCCccCHHHHHH
Confidence 5567889999855557999999999999997665555554445454 477788886
No 48
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=22.78 E-value=1.7e+02 Score=20.44 Aligned_cols=25 Identities=32% Similarity=0.585 Sum_probs=22.3
Q ss_pred HhCCCCCCCHHHHHHHHHHcCCCcC
Q psy2830 49 ALGGKENPAQGDVEKILSSVGIESD 73 (183)
Q Consensus 49 ~lgGn~spTaedI~kVLkAaGveVe 73 (183)
...|...|+..||...|...|+.|.
T Consensus 52 e~~gRt~~~~~Dv~~al~~~gi~v~ 76 (77)
T PF07524_consen 52 EHAGRTEPNLQDVEQALEEMGISVN 76 (77)
T ss_pred HHcCCCCCCHHHHHHHHHHhCCCCC
Confidence 5668899999999999999999875
No 49
>PF01581 FARP: FMRFamide related peptide family; InterPro: IPR002544 The neuropeptide Phe-Met-Arg-Phe-NH2 (FMRFamide) is a potent cardioactive neuropeptide in Lymnaea stagnalis []. FMRFamide (Phe-Met-Arg-Phe-NH2) was first demonstrated to be cardioactive in several molluscan species. FMRFamide is now known to be cardioexcitatory in mammals, to inhibit morphine-induced antinociception, and to block morphine-, defeat-, and deprivation-induced feeding []. Thirteen neuropeptides varying in length from 7 to 11 residues and ending C-terminally in -Phe-Met-Arg-Phe-NH2 (calliFMRFamides 1-13) and one dodecapeptide ending in -Met-Ile-Arg-Phe-NH2 (calliMIRFamide 1) have been isolated from thoracic ganglia of the blowfly Calliphora vomitoria. Results indicate that the N terminus (in addition to the C terminus as previously found for FMRFamides of other organisms) is crucial for at least some biological activities [].; GO: 0007218 neuropeptide signaling pathway
Probab=22.33 E-value=48 Score=15.94 Aligned_cols=10 Identities=40% Similarity=0.790 Sum_probs=7.2
Q ss_pred cCCCccccCC
Q psy2830 163 EDTNPIRMGK 172 (183)
Q Consensus 163 ~~~~~~~~~~ 172 (183)
.+.+.+|.||
T Consensus 2 ~~~~~~RFGr 11 (11)
T PF01581_consen 2 RDNNFMRFGR 11 (11)
T ss_pred CcccccccCC
Confidence 4677888875
No 50
>PF14658 EF-hand_9: EF-hand domain
Probab=22.24 E-value=1.8e+02 Score=20.89 Aligned_cols=39 Identities=15% Similarity=0.394 Sum_probs=27.8
Q ss_pred cccccchhhhhhHHHHHHHHHHhCCCCCCCHHHHHHHHHHcC
Q psy2830 28 LQSQAGGYLRIMRYVAAYLLAALGGKENPAQGDVEKILSSVG 69 (183)
Q Consensus 28 ~~~q~~~~~~~M~ylAAylL~~lgGn~spTaedI~kVLkAaG 69 (183)
+|+|+-+.. .++-+.+||-+. + ...|++.+|+.+.+...
T Consensus 7 fD~~~tG~V-~v~~l~~~Lra~-~-~~~p~e~~Lq~l~~elD 45 (66)
T PF14658_consen 7 FDTQKTGRV-PVSDLITYLRAV-T-GRSPEESELQDLINELD 45 (66)
T ss_pred cCCcCCceE-eHHHHHHHHHHH-c-CCCCcHHHHHHHHHHhC
Confidence 577777763 467888886666 3 34688888888887763
No 51
>PF13897 GOLD_2: Golgi-dynamics membrane-trafficking
Probab=21.71 E-value=66 Score=26.32 Aligned_cols=10 Identities=50% Similarity=1.102 Sum_probs=7.0
Q ss_pred ccCCcCcccc
Q psy2830 142 SDDDMGFGVW 151 (183)
Q Consensus 142 sDdDMGFgLF 151 (183)
++-|+|||||
T Consensus 27 d~yDIgFG~~ 36 (136)
T PF13897_consen 27 DSYDIGFGVY 36 (136)
T ss_pred CCCCceEEEE
Confidence 3558888866
No 52
>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=20.96 E-value=1.8e+02 Score=19.92 Aligned_cols=29 Identities=28% Similarity=0.423 Sum_probs=20.1
Q ss_pred CHHHHHHHHHHcCCCcCHHHHHHHHHHhC
Q psy2830 57 AQGDVEKILSSVGIESDAEKLKIVLKELN 85 (183)
Q Consensus 57 TaedI~kVLkAaGveVe~~~~~lFakaL~ 85 (183)
|-..|+++|+-.+|+++...+..+++...
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 44689999999999999999987777663
No 53
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=20.50 E-value=34 Score=35.01 Aligned_cols=13 Identities=8% Similarity=0.130 Sum_probs=0.0
Q ss_pred cCcccccCCCCCc
Q psy2830 146 MGFGVWEARTNGK 158 (183)
Q Consensus 146 MGFgLFD~~~~~~ 158 (183)
..|+|++.+++..
T Consensus 690 D~fDL~~~seSe~ 702 (787)
T PF03115_consen 690 DRFDLHPSSESED 702 (787)
T ss_dssp -------------
T ss_pred cccccCccccccc
Confidence 3577776555433
No 54
>PF11112 PyocinActivator: Pyocin activator protein PrtN
Probab=20.28 E-value=58 Score=23.77 Aligned_cols=29 Identities=24% Similarity=0.316 Sum_probs=24.9
Q ss_pred hhhhccCCCCCcccccchhhhhhHHHHHHH
Q psy2830 17 GLILIPTSNPGLQSQAGGYLRIMRYVAAYL 46 (183)
Q Consensus 17 ~~~~~~~~~~~~~~q~~~~~~~M~ylAAyl 46 (183)
|+|=+|.++.. ++|..-++....-+|+||
T Consensus 40 g~lplPv~rl~-~SqKs~~~V~v~dLA~yi 68 (76)
T PF11112_consen 40 GELPLPVFRLD-DSQKSPKFVHVQDLAAYI 68 (76)
T ss_pred CCCCCceeecC-CcccCCceeeHHHHHHHH
Confidence 77888888888 899999887788999996
Done!