Query 033355
Match_columns 121
No_of_seqs 139 out of 809
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 12:53:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033355.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033355hhsearch_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 4.6E-41 9.9E-46 241.2 10.0 108 1-111 3-111 (112)
2 PLN00138 large subunit ribosom 100.0 2.1E-40 4.6E-45 238.1 10.1 110 1-111 1-112 (113)
3 KOG3449 60S acidic ribosomal p 100.0 1.8E-39 3.9E-44 231.5 10.0 109 1-111 1-111 (112)
4 cd05833 Ribosomal_P2 Ribosomal 100.0 3.3E-39 7.2E-44 230.5 10.0 107 1-111 1-108 (109)
5 cd04411 Ribosomal_P1_P2_L12p R 100.0 4.9E-37 1.1E-41 218.1 9.8 104 1-111 1-105 (105)
6 COG2058 RPP1A Ribosomal protei 100.0 7.9E-30 1.7E-34 181.7 9.3 107 1-111 1-108 (109)
7 PRK06402 rpl12p 50S ribosomal 99.9 1.7E-27 3.7E-32 169.6 8.9 55 1-56 1-55 (106)
8 cd05831 Ribosomal_P1 Ribosomal 99.9 5E-27 1.1E-31 166.2 8.7 99 3-111 4-103 (103)
9 cd05832 Ribosomal_L12p Ribosom 99.9 1E-24 2.3E-29 155.3 8.2 55 1-56 1-55 (106)
10 TIGR03685 L21P_arch 50S riboso 99.9 2.1E-24 4.6E-29 153.4 8.2 55 1-56 1-55 (105)
11 KOG1762 60s acidic ribosomal p 99.9 3.3E-24 7.1E-29 153.9 6.4 102 4-112 8-114 (114)
12 PF00428 Ribosomal_60s: 60s Ac 99.8 1.3E-22 2.9E-27 139.0 -0.9 47 17-63 1-47 (88)
13 PTZ00135 60S acidic ribosomal 98.6 6E-08 1.3E-12 80.0 4.1 28 21-48 220-247 (310)
14 PTZ00240 60S ribosomal protein 97.4 0.0002 4.3E-09 59.7 4.2 15 97-111 307-322 (323)
15 PRK06402 rpl12p 50S ribosomal 96.4 0.01 2.2E-07 42.5 5.6 27 26-53 9-35 (106)
16 cd04411 Ribosomal_P1_P2_L12p R 96.3 0.0096 2.1E-07 42.4 5.2 38 9-48 25-63 (105)
17 PRK04019 rplP0 acidic ribosoma 96.3 0.011 2.4E-07 49.1 6.3 44 6-56 245-289 (330)
18 KOG3449 60S acidic ribosomal p 94.7 0.17 3.6E-06 36.7 6.6 22 12-34 29-50 (112)
19 PTZ00373 60S Acidic ribosomal 94.7 0.11 2.5E-06 37.4 5.7 26 10-36 29-55 (112)
20 COG2058 RPP1A Ribosomal protei 93.1 0.25 5.4E-06 35.6 5.0 27 26-53 9-35 (109)
21 cd05832 Ribosomal_L12p Ribosom 93.1 0.27 5.8E-06 35.2 5.2 27 26-53 9-35 (106)
22 TIGR03685 L21P_arch 50S riboso 92.1 0.42 9E-06 34.0 5.0 27 26-53 9-35 (105)
23 cd05833 Ribosomal_P2 Ribosomal 91.6 0.66 1.4E-05 33.2 5.7 37 10-47 27-63 (109)
24 cd05831 Ribosomal_P1 Ribosomal 91.2 0.52 1.1E-05 33.3 4.8 27 26-53 10-36 (103)
25 PLN00138 large subunit ribosom 87.2 0.46 1E-05 34.2 2.1 22 10-32 27-48 (113)
26 KOG1762 60s acidic ribosomal p 78.5 2.3 5E-05 30.9 2.8 26 26-52 15-40 (114)
27 PF00428 Ribosomal_60s: 60s Ac 75.1 0.21 4.5E-06 33.9 -3.3 11 101-111 77-88 (88)
28 PF15017 AF1Q: Drug resistance 71.6 1.5 3.3E-05 30.4 0.4 19 97-115 62-80 (87)
29 PF11116 DUF2624: Protein of u 67.4 10 0.00022 26.2 3.8 36 17-52 14-49 (85)
30 PTZ00135 60S acidic ribosomal 65.3 3.1 6.8E-05 34.5 1.1 15 97-111 294-309 (310)
31 cd04752 Commd4 COMM_Domain con 55.1 29 0.00063 26.1 4.7 35 1-36 6-40 (174)
32 PF07308 DUF1456: Protein of u 50.6 23 0.00049 23.2 3.1 33 17-49 13-45 (68)
33 PF12844 HTH_19: Helix-turn-he 50.1 23 0.00049 21.5 2.9 31 6-36 27-57 (64)
34 smart00576 BTP Bromodomain tra 49.4 35 0.00076 22.2 3.9 27 9-35 50-76 (77)
35 PF13833 EF-hand_8: EF-hand do 45.0 35 0.00075 19.9 3.1 31 17-47 4-35 (54)
36 PF03540 TFIID_30kDa: Transcri 43.5 35 0.00075 21.4 3.0 40 18-57 3-42 (51)
37 cd05027 S-100B S-100B: S-100B 42.4 87 0.0019 20.9 5.1 54 3-56 10-75 (88)
38 COG2036 HHT1 Histones H3 and H 42.0 37 0.00079 23.6 3.2 30 6-35 60-89 (91)
39 PF13405 EF-hand_6: EF-hand do 41.7 35 0.00077 18.0 2.5 26 6-31 5-31 (31)
40 PF07524 Bromo_TP: Bromodomain 41.3 64 0.0014 20.7 4.2 27 10-36 51-77 (77)
41 PF14788 EF-hand_10: EF hand; 37.3 63 0.0014 20.2 3.4 29 19-47 3-31 (51)
42 cd05031 S-100A10_like S-100A10 34.5 1.3E+02 0.0029 19.6 5.4 53 3-55 10-74 (94)
43 PHA01976 helix-turn-helix prot 32.9 50 0.0011 20.1 2.5 22 14-35 38-59 (67)
44 PRK04019 rplP0 acidic ribosoma 32.2 22 0.00047 29.6 0.9 19 47-65 256-274 (330)
45 cd00051 EFh EF-hand, calcium b 31.9 92 0.002 17.0 5.2 39 9-47 8-46 (63)
46 PTZ00184 calmodulin; Provision 29.4 1.7E+02 0.0036 19.6 4.9 34 13-46 96-129 (149)
47 cd00630 RNAP_largest_subunit_C 27.6 79 0.0017 23.8 3.2 30 20-49 67-96 (158)
48 PF01381 HTH_3: Helix-turn-hel 27.6 85 0.0018 18.1 2.8 24 12-35 30-53 (55)
49 smart00874 B5 tRNA synthetase 27.5 61 0.0013 20.1 2.3 19 17-35 18-36 (71)
50 PRK00034 gatC aspartyl/glutamy 27.2 87 0.0019 20.8 3.1 31 17-47 2-32 (95)
51 KOG0031 Myosin regulatory ligh 27.1 2.3E+02 0.0049 22.0 5.6 40 18-57 65-105 (171)
52 KOG0027 Calmodulin and related 26.9 2.3E+02 0.0051 20.0 6.1 54 3-56 10-68 (151)
53 TIGR02684 dnstrm_HI1420 probab 25.7 1.4E+02 0.003 20.2 3.9 24 11-34 63-86 (89)
54 PF10987 DUF2806: Protein of u 25.4 96 0.0021 24.3 3.5 22 29-50 34-55 (219)
55 COG5126 FRQ1 Ca2+-binding prot 25.3 2.7E+02 0.0058 21.1 5.7 52 6-57 25-80 (160)
56 PF03948 Ribosomal_L9_C: Ribos 25.2 55 0.0012 22.0 1.8 23 17-39 31-54 (87)
57 PF02084 Bindin: Bindin; Inte 25.2 68 0.0015 26.1 2.6 40 15-56 98-145 (238)
58 PF04220 YihI: Der GTPase acti 24.6 23 0.00049 27.3 -0.2 13 99-111 156-168 (169)
59 PF13443 HTH_26: Cro/C1-type H 23.9 66 0.0014 19.3 1.9 21 16-36 36-56 (63)
60 PRK09726 antitoxin HipB; Provi 23.6 1.7E+02 0.0037 19.1 4.0 18 17-34 51-68 (88)
61 TIGR02836 spore_IV_A stage IV 23.6 50 0.0011 29.5 1.7 49 14-66 416-465 (492)
62 TIGR00135 gatC glutamyl-tRNA(G 23.5 1.1E+02 0.0023 20.4 3.0 47 18-70 1-47 (93)
63 PF01323 DSBA: DSBA-like thior 23.2 1.9E+02 0.0041 20.6 4.5 46 15-65 117-163 (193)
64 PF02885 Glycos_trans_3N: Glyc 23.0 2E+02 0.0043 17.9 4.2 42 15-56 12-56 (66)
65 PF05037 DUF669: Protein of un 22.8 1E+02 0.0022 22.2 3.0 41 16-56 69-111 (141)
66 TIGR03070 couple_hipB transcri 22.5 1.6E+02 0.0035 16.6 4.0 21 13-33 37-57 (58)
67 cd03019 DsbA_DsbA DsbA family, 22.4 2.8E+02 0.0061 19.4 6.1 47 14-65 93-139 (178)
68 PF09547 Spore_IV_A: Stage IV 22.2 58 0.0013 29.1 1.8 47 16-66 418-465 (492)
69 PF15176 LRR19-TM: Leucine-ric 21.9 35 0.00076 24.4 0.3 8 101-108 80-87 (102)
70 smart00803 TAF TATA box bindin 21.8 1.6E+02 0.0034 18.8 3.4 39 18-57 3-42 (65)
71 PF14246 TetR_C_7: AefR-like t 21.3 1.6E+02 0.0034 17.2 3.1 27 10-44 27-53 (55)
72 cd05022 S-100A13 S-100A13: S-1 21.1 2.7E+02 0.0058 18.7 4.8 44 3-46 10-56 (89)
73 TIGR02607 antidote_HigA addict 20.7 1.2E+02 0.0025 18.8 2.6 24 12-35 39-62 (78)
74 PF12169 DNA_pol3_gamma3: DNA 20.4 1.7E+02 0.0038 20.3 3.7 34 18-55 1-34 (143)
75 PF13499 EF-hand_7: EF-hand do 20.3 1.8E+02 0.004 17.2 3.4 36 7-42 6-41 (66)
No 1
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=100.00 E-value=4.6e-41 Score=241.23 Aligned_cols=108 Identities=53% Similarity=0.799 Sum_probs=84.4
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCCcccccCCCCC
Q 033355 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAG 80 (121)
Q Consensus 1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~a~aaaaaa~a 80 (121)
||||+||||++|+||.+||++||++||+++||+||++|+++|++.|+||||++||++|++||+|+ ||+++++++++++
T Consensus 3 MkyvaAYlL~~lgG~~~pTaddI~kIL~AaGveVd~~~~~l~~~~L~GKdI~ELIa~G~~kl~sv--gg~~~aa~a~a~~ 80 (112)
T PTZ00373 3 MKYVAAYLMCVLGGNENPTKKEVKNVLSAVNADVEDDVLDNFFKSLEGKTPHELIAAGMKKLQNI--GGGVAAAAAPAAG 80 (112)
T ss_pred hHHHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHHHHhcc--cCccccccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999 3332211111111
Q ss_pred CCCCCcchhhhhhhhhhhccccccccc-cccc
Q 033355 81 GAGAAPAAAEAKKEEKVEEKEESDDVR-FTYL 111 (121)
Q Consensus 81 ~~~~~~a~~~~~~e~k~eeeEE~ddDm-f~l~ 111 (121)
++++++++ ++++++|+||+||||||| ||||
T Consensus 81 ~~~~~~~~-~~~~e~k~ee~ee~ddDmgf~LF 111 (112)
T PTZ00373 81 AATAGAKA-EAKKEEKKEEEEEEEDDLGFSLF 111 (112)
T ss_pred ccccccch-hhhhhhccccccccccccccccc
Confidence 11122222 234444556667888899 9998
No 2
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=100.00 E-value=2.1e-40 Score=238.08 Aligned_cols=110 Identities=82% Similarity=1.105 Sum_probs=87.0
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCCcccccCCCCC
Q 033355 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAG 80 (121)
Q Consensus 1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~a~aaaaaa~a 80 (121)
||||+||||++|+||.+||++||++||+++|++||++|+++|++.|+||||++||.+|++||+++|+||+++++++++++
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 99999999999999999999999999999999999999999999999999999999999999999987764432221111
Q ss_pred C-CCCCcchhhhhhhhhhhccccccccc-cccc
Q 033355 81 G-AGAAPAAAEAKKEEKVEEKEESDDVR-FTYL 111 (121)
Q Consensus 81 ~-~~~~~a~~~~~~e~k~eeeEE~ddDm-f~l~ 111 (121)
+ +++++++ ++++++|+|++||+|||| ||||
T Consensus 81 ~~~~~~~~~-~~~~e~k~e~eeE~ddDmGfgLF 112 (113)
T PLN00138 81 AGGAAAPAA-EAKKEEKVEEKEESDDDMGFSLF 112 (113)
T ss_pred ccccccccc-chhhhhhcccccccccccccccc
Confidence 1 1111111 223344456667788888 9998
No 3
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.8e-39 Score=231.51 Aligned_cols=109 Identities=74% Similarity=1.015 Sum_probs=89.6
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCCcccccCC-CC
Q 033355 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAP-SA 79 (121)
Q Consensus 1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~a~aaaaa-a~ 79 (121)
||||+||||++|+||.+|++.||++||+++|+++|++|+++|++.|+||||+|||++|.+||+|||+||++++++++ ++
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 99999999999999999999999999999999999999999999999999999999999999999999885432221 21
Q ss_pred CCCCCCcchhhhhhhhhhhccccccccc-cccc
Q 033355 80 GGAGAAPAAAEAKKEEKVEEKEESDDVR-FTYL 111 (121)
Q Consensus 80 a~~~~~~a~~~~~~e~k~eeeEE~ddDm-f~l~ 111 (121)
+++++++. ..++++|+||+||||||| |+||
T Consensus 81 gaa~aa~~--a~~~e~keEe~eesddDmgf~lF 111 (112)
T KOG3449|consen 81 GAAGAAPA--AAKEEEKEEEKEESDDDMGFGLF 111 (112)
T ss_pred CCccCCcc--chhhhhhhhhccccccccccccc
Confidence 11212221 224455666668999999 9987
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=100.00 E-value=3.3e-39 Score=230.53 Aligned_cols=107 Identities=61% Similarity=0.864 Sum_probs=84.0
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCCcccccCCCCC
Q 033355 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAG 80 (121)
Q Consensus 1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~a~aaaaaa~a 80 (121)
||||+||||++++||.+||++||++||+++||+||++|+++|++.|+||||++||++|++||+++|++++++++++++
T Consensus 1 MkyvaAylL~~l~g~~~pTa~dI~~IL~AaGveVe~~~~~lf~~~L~GKdi~eLIa~g~~kl~s~~~~~~~aa~a~~~-- 78 (109)
T cd05833 1 MKYVAAYLLAVLGGNASPSAADVKKILGSVGVEVDDEKLNKVISELEGKDVEELIAAGKEKLASVPAGAGGAAPAAAA-- 78 (109)
T ss_pred CHHHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHhhhcCCCcccccccccccc--
Confidence 999999999999999999999999999999999999999999999999999999999999999987543222111111
Q ss_pred CCCCCcchhhhhhhhhhhccccccccc-cccc
Q 033355 81 GAGAAPAAAEAKKEEKVEEKEESDDVR-FTYL 111 (121)
Q Consensus 81 ~~~~~~a~~~~~~e~k~eeeEE~ddDm-f~l~ 111 (121)
++++++. ++++++|+|++||+|||| ||||
T Consensus 79 -~a~aa~~-~~~e~kkee~eee~ddDmGf~LF 108 (109)
T cd05833 79 -AAAAAAA-AKKEEKKEESEEESDDDMGFGLF 108 (109)
T ss_pred -ccccccc-hhhhhhccCCccccccccCCCCC
Confidence 1111111 234444555666678899 9998
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=4.9e-37 Score=218.08 Aligned_cols=104 Identities=39% Similarity=0.587 Sum_probs=84.6
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCCcccccCCCCC
Q 033355 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAG 80 (121)
Q Consensus 1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~a~aaaaaa~a 80 (121)
|+|++|||||+++|+. ||++||++||+++|++|+++|+++|++.|+||||++||++|+.||+++|+||++++ + ++ +
T Consensus 1 m~~v~A~Lll~~~g~~-~ta~~I~~IL~aaGveVe~~~~~~~~~aLaGk~V~eli~~g~~kl~~~~~~~~a~~-~-a~-~ 76 (105)
T cd04411 1 MEYVAAYLLLHKGGKE-LTEDKIKELLSAAGAEIEPERVKLFLSALNGKNIDEVISKGKELMSSQAAAAAAPA-A-TA-A 76 (105)
T ss_pred CHHHHHHHHHHhcCCC-CCHHHHHHHHHHcCCCcCHHHHHHHHHHHcCCCHHHHHHHHHhhccCCCCcccccc-c-cc-c
Confidence 9999999999999987 99999999999999999999999999999999999999999999999998765321 1 11 1
Q ss_pred CCCCCcchhhhhhhhhhhccccccccc-cccc
Q 033355 81 GAGAAPAAAEAKKEEKVEEKEESDDVR-FTYL 111 (121)
Q Consensus 81 ~~~~~~a~~~~~~e~k~eeeEE~ddDm-f~l~ 111 (121)
++++ ++ ++++++|+||+||||||| ||||
T Consensus 77 -~~~~-~~-~~~~e~k~ee~eE~dddmgf~LF 105 (105)
T cd04411 77 -ATAE-PA-EKAEEAKEEEEEEEDEDFGFGLF 105 (105)
T ss_pred -cccc-ch-hhhhhhhcccccccccccCcccC
Confidence 1111 11 233444556667888899 9998
No 6
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=7.9e-30 Score=181.67 Aligned_cols=107 Identities=35% Similarity=0.522 Sum_probs=81.5
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCCcccccCCCCC
Q 033355 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAG 80 (121)
Q Consensus 1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~a~aaaaaa~a 80 (121)
|+||++||||+++|+ +||++||++||+++||+||+.|++.|++.|+||||+++|.++..++..++.+++++++++++
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-EITEDNLKSVLEAAGVEVEEARAKALVAALEGVDIDEVIKNAAEAPAAAAAAGAAAAAAAGA-- 77 (109)
T ss_pred ChHHHHHHHHHHccC-cCCHHHHHHHHHHcCCCccHHHHHHHHHHhcCCCHHHHHHHhcccccccCCccccccccccc--
Confidence 999999999999998 69999999999999999999999999999999999999999988777776554433211111
Q ss_pred CCCCCcchhhhhhhhhhhccccccccc-cccc
Q 033355 81 GAGAAPAAAEAKKEEKVEEKEESDDVR-FTYL 111 (121)
Q Consensus 81 ~~~~~~a~~~~~~e~k~eeeEE~ddDm-f~l~ 111 (121)
..+.++.++++++++++.+||+|+|| |+||
T Consensus 78 -~~a~~~~ea~eEe~eEe~~EE~~~~~lf~LF 108 (109)
T COG2058 78 -EAAAEADEAEEEEKEEEAEEESDDDMLFGLF 108 (109)
T ss_pred -ccccchhhHHHHHhhhchhhcccccchhhcc
Confidence 11111111223334455667888888 9998
No 7
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=99.95 E-value=1.7e-27 Score=169.57 Aligned_cols=55 Identities=25% Similarity=0.457 Sum_probs=54.1
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHH
Q 033355 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIA 56 (121)
Q Consensus 1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~ 56 (121)
|||++|||||+++|+ +||++||++||+++|++||++|+++|++.|+||||++||.
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 999999999999998 7999999999999999999999999999999999999997
No 8
>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=99.94 E-value=5e-27 Score=166.15 Aligned_cols=99 Identities=37% Similarity=0.484 Sum_probs=66.9
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCCcccccCCCCCCC
Q 033355 3 VVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAGGA 82 (121)
Q Consensus 3 yvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~a~aaaaaa~a~~ 82 (121)
|++|-|+|+.. +.+||++||++||+++|++|+++|+++|++.|+||||++||+ +++++|+++++++++++ +
T Consensus 4 c~yAaLiL~d~-~~~~Tae~I~~ilkAaGveve~~~~~~f~~~L~gk~i~elIa-------~~~~~~~~aap~a~~a~-~ 74 (103)
T cd05831 4 CTYAALILHDD-GIEITADNINALLKAAGVNVEPYWPGLFAKALEGKDIKDLLS-------NVGGGGGGAAPAAAAAA-A 74 (103)
T ss_pred HHHHHHHHccC-CCCCCHHHHHHHHHHcCCcccHHHHHHHHHHHcCCCHHHHhh-------ccccccccccccccccc-c
Confidence 45555555555 567999999999999999999999999999999999999998 44433332111111111 1
Q ss_pred CCCcchhhhhhhhhhhccccccccc-cccc
Q 033355 83 GAAPAAAEAKKEEKVEEKEESDDVR-FTYL 111 (121)
Q Consensus 83 ~~~~a~~~~~~e~k~eeeEE~ddDm-f~l~ 111 (121)
+++.++ ++++++|+|++||+|||| ||||
T Consensus 75 ~~~~~~-~~~~~kk~e~eee~d~dmgfglF 103 (103)
T cd05831 75 AAAAAE-AKKEEKKEEEEEESDDDMGFGLF 103 (103)
T ss_pred cccccc-chhhhcccccccccccccccccC
Confidence 111111 233445566667789999 9986
No 9
>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=99.91 E-value=1e-24 Score=155.30 Aligned_cols=55 Identities=24% Similarity=0.448 Sum_probs=54.1
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHH
Q 033355 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIA 56 (121)
Q Consensus 1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~ 56 (121)
|||++|||||+++|+ +||.++|++||+++||+||++|+++|++.|+|+||+++|.
T Consensus 1 M~yvyAaLLL~~~G~-eITae~I~~IL~AAGveVd~~~~~ala~aL~gkdIeElIa 55 (106)
T cd05832 1 MEYIYAALLLHYAGK-EINEENLKKVLEAAGIEVDEARVKALVAALEEVNIDEAIK 55 (106)
T ss_pred CHHHHHHHHHHhcCC-CCCHHHHHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHH
Confidence 999999999999998 7999999999999999999999999999999999999998
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=99.91 E-value=2.1e-24 Score=153.35 Aligned_cols=55 Identities=25% Similarity=0.494 Sum_probs=54.1
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHH
Q 033355 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIA 56 (121)
Q Consensus 1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~ 56 (121)
|||++|||||+++|+ +||.++|++||+++||+||++|+.+|++.|+||+|++||.
T Consensus 1 M~yvyA~Lll~~~g~-~iT~e~I~~IL~AAGv~ve~~~~~~la~~L~gk~i~eli~ 55 (105)
T TIGR03685 1 MEYIYAALLLHSAGK-EINEENLKAVLEAAGVEVDEARVKALVAALEGVNIEEAIK 55 (105)
T ss_pred CHHHHHHHHHHhcCC-CCCHHHHHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHH
Confidence 999999999999998 7999999999999999999999999999999999999997
No 11
>KOG1762 consensus 60s acidic ribosomal protein P1 [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=3.3e-24 Score=153.91 Aligned_cols=102 Identities=35% Similarity=0.484 Sum_probs=73.1
Q ss_pred HHHHHHHHhc-CCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCCcccccC--CCC-
Q 033355 4 VAAYLLAVLG-GNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAA--PSA- 79 (121)
Q Consensus 4 vaAYlLl~l~-G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~a~aaaa--aa~- 79 (121)
...|.-++|. ....+|.++|++|+|++|++|+++||.+|++.|.++||.+||+ ++++||+++++++ +++
T Consensus 8 ac~yaalIL~d~~i~it~dki~tl~kaa~v~ve~~Wp~lfakale~vni~~li~-------n~gag~~a~a~~~~~~~~a 80 (114)
T KOG1762|consen 8 ACSYAALILHDDEIEVTADKINTLTKAAGVNVEPYWPGLFAKALEGVNIKELIC-------NVGAGGGALAAGAAAAGGA 80 (114)
T ss_pred HHhhhhhhccccceeeehhhhhhHHHhccCcccccchhHHHHHhccCChHHHHH-------hcccCCccCCCcccccccc
Confidence 3445555554 2567999999999999999999999999999999999999999 6776555443221 111
Q ss_pred CCCCCCcchhhhhhhhhhhccccccccc-ccccc
Q 033355 80 GGAGAAPAAAEAKKEEKVEEKEESDDVR-FTYLM 112 (121)
Q Consensus 80 a~~~~~~a~~~~~~e~k~eeeEE~ddDm-f~l~~ 112 (121)
++++++++.++++++.|+||.||+|||| ||||.
T Consensus 81 a~~~~aA~~~Ekk~eak~EeseesddDmgfGLfd 114 (114)
T KOG1762|consen 81 AAAGGAAAAEEKKEEAKKEESEESDDDMGFGLFD 114 (114)
T ss_pred ccccccccchHHHHHhhhhhhcccccccccCCCC
Confidence 1111122222455566778889999999 99983
No 12
>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=1.3e-22 Score=139.00 Aligned_cols=47 Identities=43% Similarity=0.693 Sum_probs=44.2
Q ss_pred CCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhc
Q 033355 17 SPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLA 63 (121)
Q Consensus 17 ~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~ 63 (121)
+||.++|++||+++|++|+++|+.+|++.|+|++|++||++|..+|+
T Consensus 1 ~pT~~~i~~vl~aag~~v~~~~~~~~~~~l~~~~i~~li~~~~~~~~ 47 (88)
T PF00428_consen 1 EPTAENIKKVLKAAGVEVEAIWLELFAKALEGKDIKELIANGSAGMA 47 (88)
T ss_dssp S-SCCCHHHHHHHHTHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHhCCchhHHHHHHHHHHHcCCcHHHHHhccccccc
Confidence 48999999999999999999999999999999999999999988876
No 13
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=98.56 E-value=6e-08 Score=79.96 Aligned_cols=28 Identities=18% Similarity=0.230 Sum_probs=24.8
Q ss_pred HHHHHHHHhcCCCcchhHHHHHHHHhCC
Q 033355 21 DDIKGILGSVGADCEDNRLELLLSEVKG 48 (121)
Q Consensus 21 e~I~kIl~AaGveVd~~~~~~f~~~L~g 48 (121)
.+|.+|..++|+.++..|+.+|++++++
T Consensus 220 ~~i~als~aag~pt~~s~p~~ia~a~k~ 247 (310)
T PTZ00135 220 QNVAAISLAAGYPTEASAPHSILNAFKN 247 (310)
T ss_pred HHHHHHHHHhCCCcHHHHHHHHHHHHHH
Confidence 4678899999999999999999999853
No 14
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=97.38 E-value=0.0002 Score=59.73 Aligned_cols=15 Identities=33% Similarity=0.322 Sum_probs=9.8
Q ss_pred hhccccccccc-cccc
Q 033355 97 VEEKEESDDVR-FTYL 111 (121)
Q Consensus 97 ~eeeEE~ddDm-f~l~ 111 (121)
+||+||+|||| ||-+
T Consensus 307 ~~~~e~~~~d~~~~~~ 322 (323)
T PTZ00240 307 EEEEESDEDDFGMGAL 322 (323)
T ss_pred cCCccCcccccCcccc
Confidence 45566677777 8754
No 15
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=96.40 E-value=0.01 Score=42.47 Aligned_cols=27 Identities=26% Similarity=0.558 Sum_probs=17.4
Q ss_pred HHHhcCCCcchhHHHHHHHHhCCCChHH
Q 033355 26 ILGSVGADCEDNRLELLLSEVKGKDITE 53 (121)
Q Consensus 26 Il~AaGveVd~~~~~~f~~~L~gk~i~e 53 (121)
||.-.|.++...-++.++++. |.+|++
T Consensus 9 LL~~~g~~it~e~I~~IL~AA-GveVee 35 (106)
T PRK06402 9 LLHSAGKEINEDNLKKVLEAA-GVEVDE 35 (106)
T ss_pred HHHhcCCCCCHHHHHHHHHHc-CCCccH
Confidence 456666777777777777664 455554
No 16
>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=96.34 E-value=0.0096 Score=42.36 Aligned_cols=38 Identities=13% Similarity=0.127 Sum_probs=26.9
Q ss_pred HHHhcCCCCCCHHHHHHHHHh-cCCCcchhHHHHHHHHhCC
Q 033355 9 LAVLGGNTSPSADDIKGILGS-VGADCEDNRLELLLSEVKG 48 (121)
Q Consensus 9 Ll~l~G~~~~Tae~I~kIl~A-aGveVd~~~~~~f~~~L~g 48 (121)
+|...| .+++.+.++.++++ .|.+|+.-. ......|.+
T Consensus 25 IL~aaG-veVe~~~~~~~~~aLaGk~V~eli-~~g~~kl~~ 63 (105)
T cd04411 25 LLSAAG-AEIEPERVKLFLSALNGKNIDEVI-SKGKELMSS 63 (105)
T ss_pred HHHHcC-CCcCHHHHHHHHHHHcCCCHHHHH-HHHHhhccC
Confidence 445555 56999999999999 899987754 444444543
No 17
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=96.34 E-value=0.011 Score=49.07 Aligned_cols=44 Identities=20% Similarity=0.208 Sum_probs=35.0
Q ss_pred HHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCC-CChHHHHH
Q 033355 6 AYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKG-KDITELIA 56 (121)
Q Consensus 6 AYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~g-k~i~eLI~ 56 (121)
|..|.+-.| =||.+.|..||..+ ..+...++..|.+ .++++-|.
T Consensus 245 a~aLa~~~~--~~t~e~~~~il~kA-----~~~~~ala~~~~~~~~~~~~~~ 289 (330)
T PRK04019 245 AKALAVEAG--IVTPETADDILSKA-----VAQALALAAALADKDALDEELK 289 (330)
T ss_pred HHHHHHHcC--CCChhhHHHHHHHH-----HHHHHHHHHHhcCcccccHHHH
Confidence 344444443 38999999999999 5677789999999 99999997
No 18
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=94.69 E-value=0.17 Score=36.67 Aligned_cols=22 Identities=14% Similarity=0.132 Sum_probs=17.6
Q ss_pred hcCCCCCCHHHHHHHHHhcCCCc
Q 033355 12 LGGNTSPSADDIKGILGSVGADC 34 (121)
Q Consensus 12 l~G~~~~Tae~I~kIl~AaGveV 34 (121)
-.| .+++.+.|+++|+.+...-
T Consensus 29 sVG-~E~d~e~i~~visel~GK~ 50 (112)
T KOG3449|consen 29 SVG-AEIDDERINLVLSELKGKD 50 (112)
T ss_pred HhC-cccCHHHHHHHHHHhcCCC
Confidence 345 4699999999999998753
No 19
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=94.68 E-value=0.11 Score=37.45 Aligned_cols=26 Identities=8% Similarity=0.054 Sum_probs=18.3
Q ss_pred HHhcCCCCCCHHHHHHHHHhcCC-Ccch
Q 033355 10 AVLGGNTSPSADDIKGILGSVGA-DCED 36 (121)
Q Consensus 10 l~l~G~~~~Tae~I~kIl~AaGv-eVd~ 36 (121)
|.-.| .++..+.++.+++.... +|+.
T Consensus 29 L~AaG-veVd~~~~~l~~~~L~GKdI~E 55 (112)
T PTZ00373 29 LSAVN-ADVEDDVLDNFFKSLEGKTPHE 55 (112)
T ss_pred HHHcC-CCccHHHHHHHHHHHcCCCHHH
Confidence 44445 56899999999998854 4444
No 20
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=93.11 E-value=0.25 Score=35.64 Aligned_cols=27 Identities=22% Similarity=0.491 Sum_probs=22.5
Q ss_pred HHHhcCCCcchhHHHHHHHHhCCCChHH
Q 033355 26 ILGSVGADCEDNRLELLLSEVKGKDITE 53 (121)
Q Consensus 26 Il~AaGveVd~~~~~~f~~~L~gk~i~e 53 (121)
+|..+|-+++...++.+.+.. |.+|++
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 688899999999999888865 777765
No 21
>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=93.11 E-value=0.27 Score=35.22 Aligned_cols=27 Identities=22% Similarity=0.486 Sum_probs=20.6
Q ss_pred HHHhcCCCcchhHHHHHHHHhCCCChHH
Q 033355 26 ILGSVGADCEDNRLELLLSEVKGKDITE 53 (121)
Q Consensus 26 Il~AaGveVd~~~~~~f~~~L~gk~i~e 53 (121)
||.-.|.++....++.+++.- |.++++
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 677788899998888888864 566654
No 22
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=92.06 E-value=0.42 Score=33.99 Aligned_cols=27 Identities=26% Similarity=0.553 Sum_probs=19.3
Q ss_pred HHHhcCCCcchhHHHHHHHHhCCCChHH
Q 033355 26 ILGSVGADCEDNRLELLLSEVKGKDITE 53 (121)
Q Consensus 26 Il~AaGveVd~~~~~~f~~~L~gk~i~e 53 (121)
||.-.|.++....++.++++- |.++++
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 566677888888888887764 555554
No 23
>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=91.63 E-value=0.66 Score=33.18 Aligned_cols=37 Identities=3% Similarity=0.036 Sum_probs=20.8
Q ss_pred HHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhC
Q 033355 10 AVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVK 47 (121)
Q Consensus 10 l~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~ 47 (121)
|.-.| .++..+.+..++++....--.+.+..-.+.|.
T Consensus 27 L~AaG-veVe~~~~~lf~~~L~GKdi~eLIa~g~~kl~ 63 (109)
T cd05833 27 LGSVG-VEVDDEKLNKVISELEGKDVEELIAAGKEKLA 63 (109)
T ss_pred HHHcC-CCccHHHHHHHHHHHcCCCHHHHHHHhHhhhc
Confidence 34444 45888888888887755333334443333343
No 24
>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=91.25 E-value=0.52 Score=33.29 Aligned_cols=27 Identities=22% Similarity=0.421 Sum_probs=20.0
Q ss_pred HHHhcCCCcchhHHHHHHHHhCCCChHH
Q 033355 26 ILGSVGADCEDNRLELLLSEVKGKDITE 53 (121)
Q Consensus 26 Il~AaGveVd~~~~~~f~~~L~gk~i~e 53 (121)
||...|.++....++.++++. |.++++
T Consensus 10 iL~d~~~~~Tae~I~~ilkAa-Gveve~ 36 (103)
T cd05831 10 ILHDDGIEITADNINALLKAA-GVNVEP 36 (103)
T ss_pred HHccCCCCCCHHHHHHHHHHc-CCcccH
Confidence 677788888888888888765 466654
No 25
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=87.18 E-value=0.46 Score=34.24 Aligned_cols=22 Identities=23% Similarity=0.210 Sum_probs=16.0
Q ss_pred HHhcCCCCCCHHHHHHHHHhcCC
Q 033355 10 AVLGGNTSPSADDIKGILGSVGA 32 (121)
Q Consensus 10 l~l~G~~~~Tae~I~kIl~AaGv 32 (121)
|.-.| .++..+.++.+++....
T Consensus 27 L~AaG-vevd~~~~~~f~~~L~g 48 (113)
T PLN00138 27 LGSVG-ADADDDRIELLLSEVKG 48 (113)
T ss_pred HHHcC-CcccHHHHHHHHHHHcC
Confidence 33444 56899999999988754
No 26
>KOG1762 consensus 60s acidic ribosomal protein P1 [Translation, ribosomal structure and biogenesis]
Probab=78.46 E-value=2.3 Score=30.93 Aligned_cols=26 Identities=15% Similarity=0.325 Sum_probs=20.9
Q ss_pred HHHhcCCCcchhHHHHHHHHhCCCChH
Q 033355 26 ILGSVGADCEDNRLELLLSEVKGKDIT 52 (121)
Q Consensus 26 Il~AaGveVd~~~~~~f~~~L~gk~i~ 52 (121)
||.--+|+|..+.+..++++. |.|++
T Consensus 15 IL~d~~i~it~dki~tl~kaa-~v~ve 40 (114)
T KOG1762|consen 15 ILHDDEIEVTADKINTLTKAA-GVNVE 40 (114)
T ss_pred hccccceeeehhhhhhHHHhc-cCccc
Confidence 677788999999999998875 56665
No 27
>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=75.11 E-value=0.21 Score=33.91 Aligned_cols=11 Identities=45% Similarity=0.610 Sum_probs=8.3
Q ss_pred ccccccc-cccc
Q 033355 101 EESDDVR-FTYL 111 (121)
Q Consensus 101 EE~ddDm-f~l~ 111 (121)
||+|||| ||||
T Consensus 77 EEed~dmGf~LF 88 (88)
T PF00428_consen 77 EEEDDDMGFGLF 88 (88)
T ss_dssp SS-SSSSSTTTT
T ss_pred cccccccCcCCC
Confidence 5788888 9997
No 28
>PF15017 AF1Q: Drug resistance and apoptosis regulator
Probab=71.56 E-value=1.5 Score=30.42 Aligned_cols=19 Identities=42% Similarity=0.464 Sum_probs=14.1
Q ss_pred hhccccccccccccccccc
Q 033355 97 VEEKEESDDVRFTYLMPSI 115 (121)
Q Consensus 97 ~eeeEE~ddDmf~l~~~~~ 115 (121)
+++++++|||.-|.+-||-
T Consensus 62 e~eee~~ddD~gGWITPsN 80 (87)
T PF15017_consen 62 EEEEEEEDDDGGGWITPSN 80 (87)
T ss_pred ccccccccCCCCccccchh
Confidence 3455677888899999984
No 29
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=67.40 E-value=10 Score=26.18 Aligned_cols=36 Identities=14% Similarity=0.219 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChH
Q 033355 17 SPSADDIKGILGSVGADCEDNRLELLLSEVKGKDIT 52 (121)
Q Consensus 17 ~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~ 52 (121)
++|.+++.+.-+.-|+.+....++..++.|.|++++
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=65.29 E-value=3.1 Score=34.50 Aligned_cols=15 Identities=40% Similarity=0.592 Sum_probs=10.9
Q ss_pred hhccccccccc-cccc
Q 033355 97 VEEKEESDDVR-FTYL 111 (121)
Q Consensus 97 ~eeeEE~ddDm-f~l~ 111 (121)
+|||||||||| ||||
T Consensus 294 ~~~~ee~~~~~g~~lf 309 (310)
T PTZ00135 294 AEEEEEEEDDMGFGLF 309 (310)
T ss_pred cccccCcchhccccCC
Confidence 45566677777 9998
No 31
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=55.12 E-value=29 Score=26.13 Aligned_cols=35 Identities=20% Similarity=0.245 Sum_probs=29.7
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcch
Q 033355 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCED 36 (121)
Q Consensus 1 MkyvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~ 36 (121)
||.+..+.+-.+-|.. ++.++|.+++..+|++...
T Consensus 6 ~k~~~~~v~~~~~~~~-~~~~~~~kl~~~~~~~~~~ 40 (174)
T cd04752 6 MKLLCAQVLKDLLGEG-IDYEKVLKLTADAKFESGD 40 (174)
T ss_pred HHHHHHHHHHHHHhcc-CCHHHHHHHHHHhCCCHhh
Confidence 6888888888887765 9999999999999987754
No 32
>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=50.56 E-value=23 Score=23.17 Aligned_cols=33 Identities=21% Similarity=0.280 Sum_probs=24.4
Q ss_pred CCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCC
Q 033355 17 SPSADDIKGILGSVGADCEDNRLELLLSEVKGK 49 (121)
Q Consensus 17 ~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk 49 (121)
+++.+++..|++.+|.+|++..+..|.+.=..+
T Consensus 13 ~l~d~~m~~if~l~~~~vs~~el~a~lrke~~~ 45 (68)
T PF07308_consen 13 DLKDDDMIEIFALAGFEVSKAELSAWLRKEDEK 45 (68)
T ss_pred cCChHHHHHHHHHcCCccCHHHHHHHHCCCCCc
Confidence 367788888888888888888877777654333
No 33
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=50.14 E-value=23 Score=21.48 Aligned_cols=31 Identities=19% Similarity=0.418 Sum_probs=22.0
Q ss_pred HHHHHHhcCCCCCCHHHHHHHHHhcCCCcch
Q 033355 6 AYLLAVLGGNTSPSADDIKGILGSVGADCED 36 (121)
Q Consensus 6 AYlLl~l~G~~~~Tae~I~kIl~AaGveVd~ 36 (121)
+|+--...|+..|+.+.+.+|.+..||+++.
T Consensus 27 ~~i~~~e~g~~~~~~~~l~~i~~~~~v~~~~ 57 (64)
T PF12844_consen 27 STISKIENGKRKPSVSTLKKIAEALGVSLDE 57 (64)
T ss_dssp HHHHHHHTTSS--BHHHHHHHHHHHTS-HHH
T ss_pred HHHHHHHCCCcCCCHHHHHHHHHHhCCCHHH
Confidence 4455556677789999999999999998764
No 34
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=49.35 E-value=35 Score=22.24 Aligned_cols=27 Identities=30% Similarity=0.425 Sum_probs=23.0
Q ss_pred HHHhcCCCCCCHHHHHHHHHhcCCCcc
Q 033355 9 LAVLGGNTSPSADDIKGILGSVGADCE 35 (121)
Q Consensus 9 Ll~l~G~~~~Tae~I~kIl~AaGveVd 35 (121)
.+.+.|...|+..||...|+-.|+.+.
T Consensus 50 ~a~~agR~~~~~~Dv~~Al~~~gi~~~ 76 (77)
T smart00576 50 YAELAGRTEPNLGDVVLALENLGISVG 76 (77)
T ss_pred HHHHcCCCCCCHHHHHHHHHHhCcccC
Confidence 446778888999999999999999875
No 35
>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=45.04 E-value=35 Score=19.87 Aligned_cols=31 Identities=13% Similarity=0.359 Sum_probs=24.7
Q ss_pred CCCHHHHHHHHHhcCCC-cchhHHHHHHHHhC
Q 033355 17 SPSADDIKGILGSVGAD-CEDNRLELLLSEVK 47 (121)
Q Consensus 17 ~~Tae~I~kIl~AaGve-Vd~~~~~~f~~~L~ 47 (121)
.||.+++..+|...|++ ..+..+..+++.+.
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 47888888888777888 88888887777663
No 36
>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=43.54 E-value=35 Score=21.39 Aligned_cols=40 Identities=20% Similarity=0.183 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHh
Q 033355 18 PSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIAS 57 (121)
Q Consensus 18 ~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~ 57 (121)
|-.+=+...|+.+|.+..+.++..+++...-|=|.|++..
T Consensus 3 IPD~v~~~yL~~~G~~~~D~rv~RLvSLaaQKFisdI~~d 42 (51)
T PF03540_consen 3 IPDEVTDYYLERSGFQTSDPRVKRLVSLAAQKFISDIAND 42 (51)
T ss_pred CCHHHHHHHHHHCCCCCCCHhHHHHHHHHHHHHHHHHHHH
Confidence 3445678899999999999999999999999999998864
No 37
>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=42.40 E-value=87 Score=20.85 Aligned_cols=54 Identities=11% Similarity=0.266 Sum_probs=39.2
Q ss_pred HHHHHHHHH-hcCCC-CCCHHHHHHHHHh-----cCCCcchhHHHHHHHHhCC-----CChHHHHH
Q 033355 3 VVAAYLLAV-LGGNT-SPSADDIKGILGS-----VGADCEDNRLELLLSEVKG-----KDITELIA 56 (121)
Q Consensus 3 yvaAYlLl~-l~G~~-~~Tae~I~kIl~A-----aGveVd~~~~~~f~~~L~g-----k~i~eLI~ 56 (121)
++-+|-.+. ..|+. .++.++++.++++ .|-...+.-++.+++.+.. .++++.+.
T Consensus 10 l~~aF~~fD~~dgdG~~I~~~eL~~ll~~~~~~~lg~~~~~~~v~~~i~~~D~n~dG~v~f~eF~~ 75 (88)
T cd05027 10 LIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMA 75 (88)
T ss_pred HHHHHHHhcccCCCcCEECHHHHHHHHHHHhHHHhcCCCCHHHHHHHHHHhCCCCCCcCcHHHHHH
Confidence 345566664 34565 4999999999999 8988888888888888842 44555543
No 38
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=42.00 E-value=37 Score=23.60 Aligned_cols=30 Identities=30% Similarity=0.212 Sum_probs=25.4
Q ss_pred HHHHHHhcCCCCCCHHHHHHHHHhcCCCcc
Q 033355 6 AYLLAVLGGNTSPSADDIKGILGSVGADCE 35 (121)
Q Consensus 6 AYlLl~l~G~~~~Tae~I~kIl~AaGveVd 35 (121)
|+.++.+.|.+.|+.+||+..++..|....
T Consensus 60 A~~~A~ha~RKTV~~~DI~la~~~~~~~~~ 89 (91)
T COG2036 60 AVELAEHAKRKTVKAEDIKLALKRLGRRIY 89 (91)
T ss_pred HHHHHHHcCCCeecHHHHHHHHHHhccccc
Confidence 567788889999999999999998887543
No 39
>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=41.70 E-value=35 Score=17.98 Aligned_cols=26 Identities=23% Similarity=0.392 Sum_probs=18.4
Q ss_pred HHHHHHhcCCCCCCHHHHHHHHH-hcC
Q 033355 6 AYLLAVLGGNTSPSADDIKGILG-SVG 31 (121)
Q Consensus 6 AYlLl~l~G~~~~Tae~I~kIl~-AaG 31 (121)
++-+.--.++-.||.+++.++|+ +.|
T Consensus 5 ~F~~~D~d~dG~I~~~el~~~l~~~lG 31 (31)
T PF13405_consen 5 AFKMFDKDGDGFIDFEELRAILRKSLG 31 (31)
T ss_dssp HHHHH-TTSSSEEEHHHHHHHHHHHTT
T ss_pred HHHHHCCCCCCcCcHHHHHHHHHHhcC
Confidence 34444445666799999999999 766
No 40
>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=41.29 E-value=64 Score=20.73 Aligned_cols=27 Identities=26% Similarity=0.482 Sum_probs=23.3
Q ss_pred HHhcCCCCCCHHHHHHHHHhcCCCcch
Q 033355 10 AVLGGNTSPSADDIKGILGSVGADCED 36 (121)
Q Consensus 10 l~l~G~~~~Tae~I~kIl~AaGveVd~ 36 (121)
+.+.|...|+..||...|.-.|+.|.+
T Consensus 51 ae~~gRt~~~~~Dv~~al~~~gi~v~e 77 (77)
T PF07524_consen 51 AEHAGRTEPNLQDVEQALEEMGISVNE 77 (77)
T ss_pred HHHcCCCCCCHHHHHHHHHHhCCCCCC
Confidence 367788889999999999999998863
No 41
>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=37.28 E-value=63 Score=20.22 Aligned_cols=29 Identities=21% Similarity=0.346 Sum_probs=20.0
Q ss_pred CHHHHHHHHHhcCCCcchhHHHHHHHHhC
Q 033355 19 SADDIKGILGSVGADCEDNRLELLLSEVK 47 (121)
Q Consensus 19 Tae~I~kIl~AaGveVd~~~~~~f~~~L~ 47 (121)
+-..|+++|+-.+|+++...+..+.+...
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 45689999999999999999887777653
No 42
>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=34.53 E-value=1.3e+02 Score=19.65 Aligned_cols=53 Identities=8% Similarity=0.256 Sum_probs=35.6
Q ss_pred HHHHHHHHHh-cC-CCCCCHHHHHHHHHh-----cCCCcchhHHHHHHHHhCC-----CChHHHH
Q 033355 3 VVAAYLLAVL-GG-NTSPSADDIKGILGS-----VGADCEDNRLELLLSEVKG-----KDITELI 55 (121)
Q Consensus 3 yvaAYlLl~l-~G-~~~~Tae~I~kIl~A-----aGveVd~~~~~~f~~~L~g-----k~i~eLI 55 (121)
+.-+|-++.. .| +-.||.+++..++.+ .|..+....++.+++.+.. .+..+.+
T Consensus 10 l~~~F~~~D~~dg~dG~Is~~El~~~l~~~~g~~lg~~~s~~ei~~~~~~~D~~~dg~I~f~eF~ 74 (94)
T cd05031 10 LILTFHRYAGKDGDKNTLSRKELKKLMEKELSEFLKNQKDPMAVDKIMKDLDQNRDGKVNFEEFV 74 (94)
T ss_pred HHHHHHHHhccCCCCCeECHHHHHHHHHHHhHHHhhccccHHHHHHHHHHhCCCCCCcCcHHHHH
Confidence 3445656654 44 356999999999987 5677777777777777632 4455554
No 43
>PHA01976 helix-turn-helix protein
Probab=32.90 E-value=50 Score=20.09 Aligned_cols=22 Identities=9% Similarity=0.283 Sum_probs=12.1
Q ss_pred CCCCCCHHHHHHHHHhcCCCcc
Q 033355 14 GNTSPSADDIKGILGSVGADCE 35 (121)
Q Consensus 14 G~~~~Tae~I~kIl~AaGveVd 35 (121)
|...|+.+.+.+|.+..|++++
T Consensus 38 g~~~p~~~~l~~ia~~l~v~~~ 59 (67)
T PHA01976 38 DKRLPNLKTLLRLADALGVTLD 59 (67)
T ss_pred CCCCCCHHHHHHHHHHHCcCHH
Confidence 4444566666666665555443
No 44
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=32.25 E-value=22 Score=29.56 Aligned_cols=19 Identities=0% Similarity=0.158 Sum_probs=11.0
Q ss_pred CCCChHHHHHhhhhhhccc
Q 033355 47 KGKDITELIASGREKLASV 65 (121)
Q Consensus 47 ~gk~i~eLI~~G~~kl~sv 65 (121)
.-.++..+|...-.++.++
T Consensus 256 t~e~~~~il~kA~~~~~al 274 (330)
T PRK04019 256 TPETADDILSKAVAQALAL 274 (330)
T ss_pred ChhhHHHHHHHHHHHHHHH
Confidence 3456667776665555443
No 45
>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=31.95 E-value=92 Score=16.95 Aligned_cols=39 Identities=28% Similarity=0.454 Sum_probs=30.1
Q ss_pred HHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhC
Q 033355 9 LAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVK 47 (121)
Q Consensus 9 Ll~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~ 47 (121)
.+-..++..++.+++..+++..|.......+..+.+.+.
T Consensus 8 ~~d~~~~g~l~~~e~~~~l~~~~~~~~~~~~~~~~~~~~ 46 (63)
T cd00051 8 LFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREVD 46 (63)
T ss_pred HhCCCCCCcCcHHHHHHHHHHhCCCCCHHHHHHHHHHhC
Confidence 333344556999999999999999888888777777663
No 46
>PTZ00184 calmodulin; Provisional
Probab=29.40 E-value=1.7e+02 Score=19.63 Aligned_cols=34 Identities=21% Similarity=0.441 Sum_probs=27.6
Q ss_pred cCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHh
Q 033355 13 GGNTSPSADDIKGILGSVGADCEDNRLELLLSEV 46 (121)
Q Consensus 13 ~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L 46 (121)
.|+..+|.+++.+++...|..+....+..+++.+
T Consensus 96 ~~~g~i~~~e~~~~l~~~~~~~~~~~~~~~~~~~ 129 (149)
T PTZ00184 96 DGNGFISAAELRHVMTNLGEKLTDEEVDEMIREA 129 (149)
T ss_pred CCCCeEeHHHHHHHHHHHCCCCCHHHHHHHHHhc
Confidence 3555689999999999999888888777777666
No 47
>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe
Probab=27.64 E-value=79 Score=23.82 Aligned_cols=30 Identities=20% Similarity=0.370 Sum_probs=25.0
Q ss_pred HHHHHHHHHhcCCCcchhHHHHHHHHhCCC
Q 033355 20 ADDIKGILGSVGADCEDNRLELLLSEVKGK 49 (121)
Q Consensus 20 ae~I~kIl~AaGveVd~~~~~~f~~~L~gk 49 (121)
-+.|+++++.-|+.|+...+.+.++.|.-+
T Consensus 67 v~El~~v~~~~Gi~V~~rHl~LIAD~MT~~ 96 (158)
T cd00630 67 IREIQKVLASQGVSVDRRHIELIADVMTYS 96 (158)
T ss_pred HHHHHHHHHhcCceecHHHHHHHHHHHhcC
Confidence 367889999999999999999999888544
No 48
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=27.57 E-value=85 Score=18.15 Aligned_cols=24 Identities=33% Similarity=0.504 Sum_probs=17.3
Q ss_pred hcCCCCCCHHHHHHHHHhcCCCcc
Q 033355 12 LGGNTSPSADDIKGILGSVGADCE 35 (121)
Q Consensus 12 l~G~~~~Tae~I~kIl~AaGveVd 35 (121)
..|+..|+.+.+.+|.+..|++++
T Consensus 30 ~~g~~~~~~~~~~~ia~~l~~~~~ 53 (55)
T PF01381_consen 30 ENGKRNPSLDTLKKIAKALGVSPE 53 (55)
T ss_dssp HTTSSTSBHHHHHHHHHHHTSEHH
T ss_pred hcCCCCCCHHHHHHHHHHHCCCHH
Confidence 445666888888888888876554
No 49
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=27.50 E-value=61 Score=20.13 Aligned_cols=19 Identities=37% Similarity=0.557 Sum_probs=16.2
Q ss_pred CCCHHHHHHHHHhcCCCcc
Q 033355 17 SPSADDIKGILGSVGADCE 35 (121)
Q Consensus 17 ~~Tae~I~kIl~AaGveVd 35 (121)
+++.++|.++|+..|.+++
T Consensus 18 ~i~~~ei~~~L~~lg~~~~ 36 (71)
T smart00874 18 DLSAEEIEEILKRLGFEVE 36 (71)
T ss_pred CCCHHHHHHHHHHCCCeEE
Confidence 5899999999999998764
No 50
>PRK00034 gatC aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed
Probab=27.15 E-value=87 Score=20.84 Aligned_cols=31 Identities=10% Similarity=0.243 Sum_probs=27.9
Q ss_pred CCCHHHHHHHHHhcCCCcchhHHHHHHHHhC
Q 033355 17 SPSADDIKGILGSVGADCEDNRLELLLSEVK 47 (121)
Q Consensus 17 ~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~ 47 (121)
.+|.++|++|.+-+-+++++.-...|.+.|+
T Consensus 2 ~i~~e~i~~la~La~l~l~~ee~~~~~~~l~ 32 (95)
T PRK00034 2 AITREEVKHLAKLARLELSEEELEKFAGQLN 32 (95)
T ss_pred CCCHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 4899999999999999999999999988774
No 51
>KOG0031 consensus Myosin regulatory light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=27.10 E-value=2.3e+02 Score=22.00 Aligned_cols=40 Identities=15% Similarity=0.275 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHhcCCCcchh-HHHHHHHHhCCCChHHHHHh
Q 033355 18 PSADDIKGILGSVGADCEDN-RLELLLSEVKGKDITELIAS 57 (121)
Q Consensus 18 ~Tae~I~kIl~AaGveVd~~-~~~~f~~~L~gk~i~eLI~~ 57 (121)
++.+.|...++.++..+.=. .+++|-..|.|.+-++.|-+
T Consensus 65 ~~d~elDaM~~Ea~gPINft~FLTmfGekL~gtdpe~~I~~ 105 (171)
T KOG0031|consen 65 ASDEELDAMMKEAPGPINFTVFLTMFGEKLNGTDPEEVILN 105 (171)
T ss_pred CCHHHHHHHHHhCCCCeeHHHHHHHHHHHhcCCCHHHHHHH
Confidence 77888888888777766533 57789999999999999874
No 52
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=26.95 E-value=2.3e+02 Score=20.04 Aligned_cols=54 Identities=22% Similarity=0.366 Sum_probs=42.9
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCC-----CChHHHHH
Q 033355 3 VVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKG-----KDITELIA 56 (121)
Q Consensus 3 yvaAYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~g-----k~i~eLI~ 56 (121)
+--++.++-..|+-.|+...+.+++.+.|.......+..+++.+.. .++.+++.
T Consensus 10 l~~~F~~fD~d~~G~i~~~el~~~lr~lg~~~t~~el~~~~~~~D~dg~g~I~~~eF~~ 68 (151)
T KOG0027|consen 10 LKEAFQLFDKDGDGKISVEELGAVLRSLGQNPTEEELRDLIKEIDLDGDGTIDFEEFLD 68 (151)
T ss_pred HHHHHHHHCCCCCCcccHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCCCCeEcHHHHHH
Confidence 4456777767777779999999999999999888888888888873 46666664
No 53
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=25.72 E-value=1.4e+02 Score=20.23 Aligned_cols=24 Identities=25% Similarity=0.445 Sum_probs=19.8
Q ss_pred HhcCCCCCCHHHHHHHHHhcCCCc
Q 033355 11 VLGGNTSPSADDIKGILGSVGADC 34 (121)
Q Consensus 11 ~l~G~~~~Tae~I~kIl~AaGveV 34 (121)
+..|+..|+-+.|.+|+++.|+.+
T Consensus 63 iE~g~~~Ps~~tL~kI~~aLgi~l 86 (89)
T TIGR02684 63 ALSGKGNPTFDTILKVTKALGLKL 86 (89)
T ss_pred HHcCCCCCCHHHHHHHHHHcCCce
Confidence 446777899999999999999875
No 54
>PF10987 DUF2806: Protein of unknown function (DUF2806); InterPro: IPR021254 This bacterial family of proteins has no known function.
Probab=25.41 E-value=96 Score=24.28 Aligned_cols=22 Identities=9% Similarity=0.137 Sum_probs=16.6
Q ss_pred hcCCCcchhHHHHHHHHhCCCC
Q 033355 29 SVGADCEDNRLELLLSEVKGKD 50 (121)
Q Consensus 29 AaGveVd~~~~~~f~~~L~gk~ 50 (121)
..|-+||++|+..|.+.-+..+
T Consensus 34 ~~~~~vD~DWl~~f~~~A~~is 55 (219)
T PF10987_consen 34 VTGEPVDPDWLYRFFDMAEDIS 55 (219)
T ss_pred cCCCCCChHHHHHHHHHHHhcC
Confidence 4567889999999987664433
No 55
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=25.34 E-value=2.7e+02 Score=21.13 Aligned_cols=52 Identities=19% Similarity=0.310 Sum_probs=36.3
Q ss_pred HHHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhC----CCChHHHHHh
Q 033355 6 AYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVK----GKDITELIAS 57 (121)
Q Consensus 6 AYlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~----gk~i~eLI~~ 57 (121)
||.|+--.+.-.|+-+++.+|+++.|-......+..+++.+. ..+.+++|.-
T Consensus 25 aF~l~D~d~~G~I~~~el~~ilr~lg~~~s~~ei~~l~~~~d~~~~~idf~~Fl~~ 80 (160)
T COG5126 25 AFQLFDRDSDGLIDRNELGKILRSLGFNPSEAEINKLFEEIDAGNETVDFPEFLTV 80 (160)
T ss_pred HHHHhCcCCCCCCcHHHHHHHHHHcCCCCcHHHHHHHHHhccCCCCccCHHHHHHH
Confidence 455655544446899999999999998766665555556565 4677777763
No 56
>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=25.24 E-value=55 Score=22.00 Aligned_cols=23 Identities=22% Similarity=0.413 Sum_probs=20.5
Q ss_pred CCCHHHHHHHHHhc-CCCcchhHH
Q 033355 17 SPSADDIKGILGSV-GADCEDNRL 39 (121)
Q Consensus 17 ~~Tae~I~kIl~Aa-GveVd~~~~ 39 (121)
++|..||.+.|+.. |+++|..++
T Consensus 31 SVt~~dIa~~l~~~~g~~Idk~~I 54 (87)
T PF03948_consen 31 SVTSKDIAKALKEQTGIEIDKKKI 54 (87)
T ss_dssp EBSHHHHHHHHHHCCSSSSSSSSB
T ss_pred CcCHHHHHHHHHHhhCCeEeccEE
Confidence 68999999999999 999998664
No 57
>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=25.17 E-value=68 Score=26.08 Aligned_cols=40 Identities=38% Similarity=0.568 Sum_probs=30.2
Q ss_pred CCCCCH---HHHHHHHHhcCCCc-----chhHHHHHHHHhCCCChHHHHH
Q 033355 15 NTSPSA---DDIKGILGSVGADC-----EDNRLELLLSEVKGKDITELIA 56 (121)
Q Consensus 15 ~~~~Ta---e~I~kIl~AaGveV-----d~~~~~~f~~~L~gk~i~eLI~ 56 (121)
...||+ +|||.||-+..|+. |+|-+-++++-|...+ .||+
T Consensus 98 etTISAKvm~~ikavLgaTKiDLPVDINDPYDlGLLLRhLRHHS--NLLA 145 (238)
T PF02084_consen 98 ETTISAKVMEDIKAVLGATKIDLPVDINDPYDLGLLLRHLRHHS--NLLA 145 (238)
T ss_pred CccccHHHHHHHHHHhcccccccccccCChhhHHHHHHHHHHHH--HHHh
Confidence 344655 68999999998864 7899999999986432 5665
No 58
>PF04220 YihI: Der GTPase activator (YihI); InterPro: IPR007336 This entry contains Escherichia coli (strain K12) YihI. YihI activates the GTPase activity of Der, a 50S ribosomal subunit stability factor and can therefore be considered a GAP (GTPase activating)-like protein. The stimulation is specific to Der as YihI does not stimulate the GTPase activity of Era or ObgE. The interaction of YihI with Der requires only the C-terminal 78 amino acids of YihI []. A yihI deletion mutant is viable and shows a shorter lag period, but the same post-lag growth rate as a wild-type strain. yihI is expressed during the lag period. Overexpression of yihI inhibits cell growth and biogenesis of the 50S ribosomal subunit []. YihI is an unusual, highly hydrophilic protein with an uneven distribution of charged residues, resulting in an N-terminal region with high pI and a C-terminal region with low pI [].
Probab=24.58 E-value=23 Score=27.34 Aligned_cols=13 Identities=46% Similarity=0.529 Sum_probs=10.1
Q ss_pred ccccccccccccc
Q 033355 99 EKEESDDVRFTYL 111 (121)
Q Consensus 99 eeEE~ddDmf~l~ 111 (121)
+++++|||||.+|
T Consensus 156 ~~~~~~dDll~~f 168 (169)
T PF04220_consen 156 EEEESDDDLLRQF 168 (169)
T ss_pred ccccchhHHhhcc
Confidence 3667889998877
No 59
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=23.90 E-value=66 Score=19.26 Aligned_cols=21 Identities=24% Similarity=0.442 Sum_probs=10.5
Q ss_pred CCCCHHHHHHHHHhcCCCcch
Q 033355 16 TSPSADDIKGILGSVGADCED 36 (121)
Q Consensus 16 ~~~Tae~I~kIl~AaGveVd~ 36 (121)
..++.+.|.+|.++.|++++.
T Consensus 36 ~~~~~~~l~~ia~~l~~~~~e 56 (63)
T PF13443_consen 36 SNPSLDTLEKIAKALNCSPEE 56 (63)
T ss_dssp ----HHHHHHHHHHHT--HHH
T ss_pred ccccHHHHHHHHHHcCCCHHH
Confidence 457777777777777776544
No 60
>PRK09726 antitoxin HipB; Provisional
Probab=23.62 E-value=1.7e+02 Score=19.11 Aligned_cols=18 Identities=17% Similarity=0.122 Sum_probs=9.5
Q ss_pred CCCHHHHHHHHHhcCCCc
Q 033355 17 SPSADDIKGILGSVGADC 34 (121)
Q Consensus 17 ~~Tae~I~kIl~AaGveV 34 (121)
.|+.++|.+|++..|+.+
T Consensus 51 ~ps~~~l~~ia~~lgv~~ 68 (88)
T PRK09726 51 NTTLTTFFKILQSLELSM 68 (88)
T ss_pred CCCHHHHHHHHHHcCCCc
Confidence 455555555555555543
No 61
>TIGR02836 spore_IV_A stage IV sporulation protein A. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis.
Probab=23.62 E-value=50 Score=29.50 Aligned_cols=49 Identities=27% Similarity=0.402 Sum_probs=35.3
Q ss_pred CCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhh-hhhhcccC
Q 033355 14 GNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASG-REKLASVP 66 (121)
Q Consensus 14 G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G-~~kl~sv~ 66 (121)
|.+.=+++=|+.|++...-+.+..| -+.+=||++++|+.+| ..||..+|
T Consensus 416 GtEkQseeLv~yl~~~fe~~p~~iW----~sniFGKsl~~LV~eGi~nKl~~mp 465 (492)
T TIGR02836 416 GTEKQSEELVKYLLEQFEDDPLKIW----ESNIFGKSLSDLVKEGIQNKLSLMP 465 (492)
T ss_pred cCHHHHHHHHHHHHHHhhcChhhee----cccccCccHHHHHHHHHHHHHHhCC
Confidence 3333456667777777777777777 5667799999999999 46776664
No 62
>TIGR00135 gatC glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, C subunit. This model has been revised to remove the candidate sequence from Methanococcus jannaschii, now part of a related model.
Probab=23.55 E-value=1.1e+02 Score=20.44 Aligned_cols=47 Identities=13% Similarity=0.196 Sum_probs=34.4
Q ss_pred CCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhcccCCCCC
Q 033355 18 PSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGG 70 (121)
Q Consensus 18 ~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv~agg~ 70 (121)
+|.++|++|.+-+-+++++.-...|...|+ .++ .--++|..+...|.
T Consensus 1 i~~~~v~~lA~La~L~l~eee~~~~~~~l~-----~il-~~~~~L~~vdt~~v 47 (93)
T TIGR00135 1 ISDEEVKHLAKLARLELSEEEAESFAGDLD-----KIL-GFVEQLNEVDTENV 47 (93)
T ss_pred CCHHHHHHHHHHhCCCCCHHHHHHHHHHHH-----HHH-HHHHHHhcCccCCC
Confidence 578899999999999999999999988874 222 23345666665543
No 63
>PF01323 DSBA: DSBA-like thioredoxin domain; InterPro: IPR001853 DSBA is a sub-family of the Thioredoxin family []. The efficient and correct folding of bacterial disulphide bonded proteins in vivo is dependent upon a class of periplasmic oxidoreductase proteins called DsbA, after the Escherichia coli enzyme. The bacterial protein-folding factor DsbA is the most oxidizing of the thioredoxin family. DsbA catalyses disulphide-bond formation during the folding of secreted proteins. The extremely oxidizing nature of DsbA has been proposed to result from either domain motion or stabilising active-site interactions in the reduced form. DsbA's highly oxidizing nature is a result of hydrogen bond, electrostatic and helix-dipole interactions that favour the thiolate over the disulphide at the active site []. In the pathogenic bacterium Vibrio cholerae, the DsbA homologue (TcpG) is responsible for the folding, maturation and secretion of virulence factors. While the overall architecture of TcpG and DsbA is similar and the surface features are retained in TcpG, there are significant differences. For example, the kinked active site helix results from a three-residue loop in DsbA, but is caused by a proline in TcpG (making TcpG more similar to thioredoxin in this respect). Furthermore, the proposed peptide binding groove of TcpG is substantially shortened compared with that of DsbA due to a six-residue deletion. Also, the hydrophobic pocket of TcpG is more shallow and the acidic patch is much less extensive than that of E. coli DsbA [].; GO: 0015035 protein disulfide oxidoreductase activity; PDB: 3GL5_A 3DKS_D 3RPP_C 3RPN_B 1YZX_A 3L9V_C 2IMD_A 2IME_A 2IMF_A 2B3S_B ....
Probab=23.17 E-value=1.9e+02 Score=20.59 Aligned_cols=46 Identities=11% Similarity=0.223 Sum_probs=28.5
Q ss_pred CCCCCHHH-HHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhccc
Q 033355 15 NTSPSADD-IKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASV 65 (121)
Q Consensus 15 ~~~~Tae~-I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv 65 (121)
+.+|+..+ |..+++.+|++.+. |.+.+++-.+.+.+.+........
T Consensus 117 ~~~i~~~~vl~~~~~~~Gld~~~-----~~~~~~~~~~~~~~~~~~~~a~~~ 163 (193)
T PF01323_consen 117 GRDISDPDVLAEIAEEAGLDPDE-----FDAALDSPEVKAALEEDTAEARQL 163 (193)
T ss_dssp ST-TSSHHHHHHHHHHTT--HHH-----HHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCCCCHHHHHHHHHHcCCcHHH-----HHHHhcchHHHHHHHHHHHHHHHc
Confidence 34566655 99999999995443 566677767777776654444343
No 64
>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=23.03 E-value=2e+02 Score=17.89 Aligned_cols=42 Identities=17% Similarity=0.329 Sum_probs=28.2
Q ss_pred CCCCCHHHHHHHHHhcC-CCcchhHHHHHHHHh--CCCChHHHHH
Q 033355 15 NTSPSADDIKGILGSVG-ADCEDNRLELLLSEV--KGKDITELIA 56 (121)
Q Consensus 15 ~~~~Tae~I~kIl~AaG-veVd~~~~~~f~~~L--~gk~i~eLI~ 56 (121)
+...|.+++..++...= .++++..+..|.-.| +|-+.+|+..
T Consensus 12 g~~Ls~~e~~~~~~~i~~g~~s~~qiaAfL~al~~kget~~Eiag 56 (66)
T PF02885_consen 12 GEDLSREEAKAAFDAILDGEVSDAQIAAFLMALRMKGETPEEIAG 56 (66)
T ss_dssp T----HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHH
T ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCcCHHHHHH
Confidence 35699999999999875 489999999988877 6788888875
No 65
>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=22.77 E-value=1e+02 Score=22.21 Aligned_cols=41 Identities=20% Similarity=0.275 Sum_probs=31.6
Q ss_pred CCCCHHHHHHHHHhcCCC--cchhHHHHHHHHhCCCChHHHHH
Q 033355 16 TSPSADDIKGILGSVGAD--CEDNRLELLLSEVKGKDITELIA 56 (121)
Q Consensus 16 ~~~Tae~I~kIl~AaGve--Vd~~~~~~f~~~L~gk~i~eLI~ 56 (121)
...+...+..|++++|+. .+-..+..|+..|.||.+.=.+.
T Consensus 69 ~~~~~~~l~~i~~a~G~~~~~~~~sl~~~~~~l~gk~l~V~v~ 111 (141)
T PF05037_consen 69 GEYSIKRLNAIAKAAGIPEGTDFESLEQFLNQLLGKPLRVTVK 111 (141)
T ss_pred hhhhHHHHHHHHHHhCCCCCCCcccHHHHHHHHcCCeeEEEec
Confidence 346788899999999984 44556889999999988865443
No 66
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=22.52 E-value=1.6e+02 Score=16.64 Aligned_cols=21 Identities=19% Similarity=0.471 Sum_probs=14.8
Q ss_pred cCCCCCCHHHHHHHHHhcCCC
Q 033355 13 GGNTSPSADDIKGILGSVGAD 33 (121)
Q Consensus 13 ~G~~~~Tae~I~kIl~AaGve 33 (121)
.|...|+.+.+.+|.+..|++
T Consensus 37 ~g~~~~~~~~~~~i~~~lgv~ 57 (58)
T TIGR03070 37 NGKPTVRLDKVLRVLDALGLE 57 (58)
T ss_pred CCCCCCCHHHHHHHHHHcCCC
Confidence 455567788888887777765
No 67
>cd03019 DsbA_DsbA DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol oxidant known, due to the unusual stability of the thiolate anion form of the first cysteine in the CXXC motif. The highly unstable oxidized form of DsbA directly donates disulfide bonds to reduced proteins secreted into the bacterial periplasm. This rapid and unidirectional process helps to catalyze the folding of newly-synthesized polypeptides. To regain catalytic activity, reduced DsbA is then reoxidized by the membrane protein DsbB, which generates its disulfides from oxidized quinones, which in turn are reoxidized by the electron transport chain.
Probab=22.42 E-value=2.8e+02 Score=19.40 Aligned_cols=47 Identities=19% Similarity=0.198 Sum_probs=33.2
Q ss_pred CCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhhhhhhccc
Q 033355 14 GNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASV 65 (121)
Q Consensus 14 G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G~~kl~sv 65 (121)
+....+.+.|.++.+..|++.+ .|.+.++...+...|.+........
T Consensus 93 ~~~~~~~~~l~~~a~~~Gl~~~-----~~~~~~~s~~~~~~i~~~~~~~~~~ 139 (178)
T cd03019 93 RKRLLDPDDIRKIFLSQGVDKK-----KFDAAYNSFSVKALVAKAEKLAKKY 139 (178)
T ss_pred CCCCCCHHHHHHHHHHhCCCHH-----HHHHHHhCHHHHHHHHHHHHHHHHc
Confidence 3333458899999999999653 4667788888888887665544333
No 68
>PF09547 Spore_IV_A: Stage IV sporulation protein A (spore_IV_A); InterPro: IPR014201 This entry is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=22.23 E-value=58 Score=29.08 Aligned_cols=47 Identities=30% Similarity=0.398 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHHHhh-hhhhcccC
Q 033355 16 TSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASG-REKLASVP 66 (121)
Q Consensus 16 ~~~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI~~G-~~kl~sv~ 66 (121)
+.=+++=|+.|++...-+.+..| -+.+=||++++|+.+| ..||..+|
T Consensus 418 E~QseeLv~yl~~~~e~dp~~iW----esnIFGKsl~~LV~eGi~~Kl~~mp 465 (492)
T PF09547_consen 418 EKQSEELVKYLLEEFEEDPEKIW----ESNIFGKSLHELVREGIQNKLYRMP 465 (492)
T ss_pred HHHHHHHHHHHHHhhccChhhhc----ccccccccHHHHHHHHHHHHHHhCC
Confidence 33355566667776666666666 5667799999999999 46777764
No 69
>PF15176 LRR19-TM: Leucine-rich repeat family 19 TM domain
Probab=21.93 E-value=35 Score=24.39 Aligned_cols=8 Identities=38% Similarity=0.563 Sum_probs=5.2
Q ss_pred cccccccc
Q 033355 101 EESDDVRF 108 (121)
Q Consensus 101 EE~ddDmf 108 (121)
+++|||+|
T Consensus 80 ~~eDDDGF 87 (102)
T PF15176_consen 80 TNEDDDGF 87 (102)
T ss_pred CCCCCCcc
Confidence 34588876
No 70
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=21.79 E-value=1.6e+02 Score=18.83 Aligned_cols=39 Identities=26% Similarity=0.411 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHhcCCC-cchhHHHHHHHHhCCCChHHHHHh
Q 033355 18 PSADDIKGILGSVGAD-CEDNRLELLLSEVKGKDITELIAS 57 (121)
Q Consensus 18 ~Tae~I~kIl~AaGve-Vd~~~~~~f~~~L~gk~i~eLI~~ 57 (121)
++.+.|+.|.++.|++ +.......+...++ .-+.+++..
T Consensus 3 ~p~~~i~ria~~~Gi~ris~~a~~~l~~~~e-~rl~~i~~~ 42 (65)
T smart00803 3 LPKETIKDVAESLGIGNLSDEAAKLLAEDVE-YRIKEIVQE 42 (65)
T ss_pred CCHHHHHHHHHHCCCccccHHHHHHHHHHHH-HHHHHHHHH
Confidence 5778999999999997 88888777777765 344555554
No 71
>PF14246 TetR_C_7: AefR-like transcriptional repressor, C-terminal region; PDB: 3BHQ_B 3CDL_A.
Probab=21.33 E-value=1.6e+02 Score=17.18 Aligned_cols=27 Identities=37% Similarity=0.652 Sum_probs=16.9
Q ss_pred HHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHHHH
Q 033355 10 AVLGGNTSPSADDIKGILGSVGADCEDNRLELLLS 44 (121)
Q Consensus 10 l~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f~~ 44 (121)
..+++...+|.+++..+++.+ .+.|++
T Consensus 27 ~llg~~~~~s~~e~~~~v~~a--------V~~FL~ 53 (55)
T PF14246_consen 27 ALLGLAPPPSAEEIERIVESA--------VDMFLR 53 (55)
T ss_dssp HHHHTS----HHHHHHHHHHH--------HHHHHH
T ss_pred HHhCCCCCcCHHHHHHHHHHH--------HHHHHh
Confidence 445566678999999999876 666654
No 72
>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=21.12 E-value=2.7e+02 Score=18.66 Aligned_cols=44 Identities=23% Similarity=0.356 Sum_probs=29.7
Q ss_pred HHHHHHHHHh-cCCCCCCHHHHHHHHHh-cCCCcch-hHHHHHHHHh
Q 033355 3 VVAAYLLAVL-GGNTSPSADDIKGILGS-VGADCED-NRLELLLSEV 46 (121)
Q Consensus 3 yvaAYlLl~l-~G~~~~Tae~I~kIl~A-aGveVd~-~~~~~f~~~L 46 (121)
++.+|-...- +|+..++.++++.+++. .|-.+.. .-++.+++.+
T Consensus 10 l~~~F~~fd~~~~~g~i~~~ELk~ll~~elg~~ls~~~~v~~mi~~~ 56 (89)
T cd05022 10 LVSNFHKASVKGGKESLTASEFQELLTQQLPHLLKDVEGLEEKMKNL 56 (89)
T ss_pred HHHHHHHHhCCCCCCeECHHHHHHHHHHHhhhhccCHHHHHHHHHHh
Confidence 3455555655 66778999999999998 7754444 4455555555
No 73
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=20.70 E-value=1.2e+02 Score=18.84 Aligned_cols=24 Identities=21% Similarity=0.279 Sum_probs=17.3
Q ss_pred hcCCCCCCHHHHHHHHHhcCCCcc
Q 033355 12 LGGNTSPSADDIKGILGSVGADCE 35 (121)
Q Consensus 12 l~G~~~~Tae~I~kIl~AaGveVd 35 (121)
+.|+..|+.+.+.+|.+..|++++
T Consensus 39 ~~g~~~~~~~~~~~l~~~l~v~~~ 62 (78)
T TIGR02607 39 VNGRRGITADMALRLAKALGTSPE 62 (78)
T ss_pred HcCCCCCCHHHHHHHHHHcCCCHH
Confidence 345566788888888888887653
No 74
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=20.39 E-value=1.7e+02 Score=20.27 Aligned_cols=34 Identities=29% Similarity=0.474 Sum_probs=15.3
Q ss_pred CCHHHHHHHHHhcCCCcchhHHHHHHHHhCCCChHHHH
Q 033355 18 PSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELI 55 (121)
Q Consensus 18 ~Tae~I~kIl~AaGveVd~~~~~~f~~~L~gk~i~eLI 55 (121)
||.++|..++-.++ ..+.-.+++++-.+|..+++
T Consensus 1 It~e~V~~~lG~v~----~~~i~~l~~ai~~~d~~~~l 34 (143)
T PF12169_consen 1 ITAEDVREILGLVD----EEQIFELLDAILEGDAAEAL 34 (143)
T ss_dssp B-HHHHHHHHTHTS----THHHHHHHHHHHTT-HHHHH
T ss_pred CCHHHHHHHHCCCC----HHHHHHHHHHHHcCCHHHHH
Confidence 45566666665443 33344444444444444433
No 75
>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=20.27 E-value=1.8e+02 Score=17.15 Aligned_cols=36 Identities=17% Similarity=0.269 Sum_probs=25.2
Q ss_pred HHHHHhcCCCCCCHHHHHHHHHhcCCCcchhHHHHH
Q 033355 7 YLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELL 42 (121)
Q Consensus 7 YlLl~l~G~~~~Tae~I~kIl~AaGveVd~~~~~~f 42 (121)
+-.+-..++-.+|.+++..+++..+...........
T Consensus 6 F~~~D~d~~G~i~~~el~~~~~~~~~~~~~~~~~~~ 41 (66)
T PF13499_consen 6 FKKFDKDGDGYISKEELRRALKHLGRDMSDEESDEM 41 (66)
T ss_dssp HHHHSTTSSSEEEHHHHHHHHHHTTSHSTHHHHHHH
T ss_pred HHHHcCCccCCCCHHHHHHHHHHhcccccHHHHHHH
Confidence 334444555679999999999999987754444433
Done!