Query 033702
Match_columns 113
No_of_seqs 140 out of 823
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 05:18:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033702.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033702hhsearch_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 9.6E-45 2.1E-49 254.7 10.4 110 1-113 3-112 (112)
2 PLN00138 large subunit ribosom 100.0 3.3E-44 7.2E-49 252.4 10.5 112 1-113 1-113 (113)
3 cd05833 Ribosomal_P2 Ribosomal 100.0 7.2E-43 1.6E-47 244.3 10.5 109 1-113 1-109 (109)
4 KOG3449 60S acidic ribosomal p 100.0 2.2E-42 4.8E-47 240.8 10.4 111 1-113 1-112 (112)
5 cd04411 Ribosomal_P1_P2_L12p R 100.0 2.5E-39 5.3E-44 225.1 10.2 105 1-112 1-105 (105)
6 COG2058 RPP1A Ribosomal protei 100.0 3.2E-32 7E-37 189.5 9.2 108 1-113 1-109 (109)
7 cd05831 Ribosomal_P1 Ribosomal 100.0 3E-29 6.5E-34 173.9 9.4 99 5-112 4-103 (103)
8 PRK06402 rpl12p 50S ribosomal 100.0 9.7E-29 2.1E-33 172.2 8.5 55 1-56 1-55 (106)
9 KOG1762 60s acidic ribosomal p 99.9 1.9E-27 4.1E-32 166.7 7.5 102 5-113 9-114 (114)
10 TIGR03685 L21P_arch 50S riboso 99.9 5.9E-25 1.3E-29 152.9 8.0 55 1-56 1-55 (105)
11 cd05832 Ribosomal_L12p Ribosom 99.9 8.2E-25 1.8E-29 152.5 7.9 55 1-56 1-55 (106)
12 PF00428 Ribosomal_60s: 60s Ac 99.9 4.3E-25 9.3E-30 148.5 -0.0 87 17-112 1-88 (88)
13 PTZ00135 60S acidic ribosomal 99.0 3.6E-10 7.9E-15 91.1 3.8 28 21-48 220-247 (310)
14 PTZ00240 60S ribosomal protein 98.0 9.6E-06 2.1E-10 66.1 5.2 16 97-112 307-323 (323)
15 PRK04019 rplP0 acidic ribosoma 97.0 0.0023 5E-08 52.0 6.2 46 5-57 244-290 (330)
16 COG2058 RPP1A Ribosomal protei 96.4 0.0062 1.3E-07 42.9 4.4 27 26-53 9-35 (109)
17 KOG3449 60S acidic ribosomal p 95.2 0.11 2.3E-06 36.8 6.5 19 15-33 31-49 (112)
18 cd04411 Ribosomal_P1_P2_L12p R 94.9 0.082 1.8E-06 36.8 5.2 29 9-38 25-54 (105)
19 cd05832 Ribosomal_L12p Ribosom 92.1 0.33 7.1E-06 34.0 4.5 27 26-53 9-35 (106)
20 PRK06402 rpl12p 50S ribosomal 90.8 0.63 1.4E-05 32.6 4.7 27 26-53 9-35 (106)
21 TIGR03685 L21P_arch 50S riboso 87.3 0.78 1.7E-05 31.9 3.2 27 26-53 9-35 (105)
22 cd05831 Ribosomal_P1 Ribosomal 86.3 1.8 4E-05 29.8 4.6 27 26-53 10-36 (103)
23 PTZ00373 60S Acidic ribosomal 84.7 0.55 1.2E-05 33.1 1.4 27 9-36 28-55 (112)
24 PLN00138 large subunit ribosom 83.8 0.92 2E-05 32.0 2.3 22 10-32 27-48 (113)
25 cd05833 Ribosomal_P2 Ribosomal 83.7 4.3 9.4E-05 28.3 5.6 22 10-32 27-48 (109)
26 PF11116 DUF2624: Protein of u 73.8 6.4 0.00014 26.5 3.8 36 17-52 14-49 (85)
27 KOG1762 60s acidic ribosomal p 69.2 4.5 9.7E-05 28.7 2.3 26 26-52 15-40 (114)
28 PF07308 DUF1456: Protein of u 59.7 15 0.00033 23.4 3.3 33 17-49 13-45 (68)
29 PF12844 HTH_19: Helix-turn-he 57.6 16 0.00034 21.8 3.0 32 6-37 27-58 (64)
30 PF13405 EF-hand_6: EF-hand do 52.3 20 0.00043 18.6 2.5 29 3-31 2-31 (31)
31 PF13833 EF-hand_8: EF-hand do 49.8 27 0.00058 19.9 3.1 30 17-46 4-34 (54)
32 cd05027 S-100B S-100B: S-100B 49.3 61 0.0013 21.1 5.0 45 3-47 10-61 (88)
33 smart00576 BTP Bromodomain tra 47.4 39 0.00085 21.5 3.8 27 9-35 50-76 (77)
34 KOG0027 Calmodulin and related 43.1 1.1E+02 0.0025 21.3 6.1 55 2-56 9-68 (151)
35 COG2036 HHT1 Histones H3 and H 40.2 39 0.00085 22.9 3.0 29 6-34 60-88 (91)
36 PF14788 EF-hand_10: EF hand; 39.2 62 0.0013 19.7 3.5 29 19-47 3-31 (51)
37 PF03540 TFIID_30kDa: Transcri 38.9 51 0.0011 20.1 3.1 40 18-57 3-42 (51)
38 cd05031 S-100A10_like S-100A10 38.3 1.1E+02 0.0024 19.7 5.4 53 3-55 10-74 (94)
39 cd04752 Commd4 COMM_Domain con 37.9 45 0.00098 24.5 3.3 36 1-37 6-41 (174)
40 PF07524 Bromo_TP: Bromodomain 37.7 78 0.0017 19.9 4.1 26 10-35 51-76 (77)
41 COG5126 FRQ1 Ca2+-binding prot 36.5 1.4E+02 0.003 22.2 5.8 51 6-56 25-79 (160)
42 PF02885 Glycos_trans_3N: Glyc 35.7 1.1E+02 0.0023 18.8 4.3 44 13-56 10-56 (66)
43 PTZ00184 calmodulin; Provision 34.8 1.1E+02 0.0024 20.2 4.7 35 12-46 95-129 (149)
44 smart00803 TAF TATA box bindin 33.0 91 0.002 19.5 3.7 42 18-60 3-45 (65)
45 PF08461 HTH_12: Ribonuclease 32.3 1E+02 0.0022 19.1 3.9 43 8-50 3-46 (66)
46 PF01381 HTH_3: Helix-turn-hel 31.6 68 0.0015 18.2 2.8 24 12-35 30-53 (55)
47 PRK00034 gatC aspartyl/glutamy 31.4 77 0.0017 20.7 3.3 47 17-69 2-48 (95)
48 PHA01976 helix-turn-helix prot 31.2 87 0.0019 18.6 3.4 22 14-35 38-59 (67)
49 smart00874 B5 tRNA synthetase 30.9 51 0.0011 20.1 2.3 20 16-35 17-36 (71)
50 PF01323 DSBA: DSBA-like thior 30.7 1.2E+02 0.0025 21.3 4.5 48 13-65 115-163 (193)
51 cd00051 EFh EF-hand, calcium b 30.3 94 0.002 16.6 5.2 40 7-46 6-45 (63)
52 TIGR00135 gatC glutamyl-tRNA(G 29.5 83 0.0018 20.5 3.3 47 18-70 1-47 (93)
53 COG1058 CinA Predicted nucleot 29.4 28 0.00061 27.7 1.1 58 10-69 64-125 (255)
54 PF02969 TAF: TATA box binding 28.4 90 0.002 19.8 3.1 45 18-63 4-49 (66)
55 PF13443 HTH_26: Cro/C1-type H 28.4 51 0.0011 19.3 1.9 21 16-36 36-56 (63)
56 PF03948 Ribosomal_L9_C: Ribos 27.9 45 0.00097 21.9 1.7 23 17-39 31-54 (87)
57 smart00414 H2A Histone 2A. 27.8 75 0.0016 22.0 2.9 13 1-14 40-52 (106)
58 cd00630 RNAP_largest_subunit_C 27.3 85 0.0018 23.1 3.3 29 21-49 68-96 (158)
59 PF10987 DUF2806: Protein of u 26.7 95 0.0021 23.8 3.6 22 29-50 34-55 (219)
60 TIGR02684 dnstrm_HI1420 probab 26.7 1.3E+02 0.0029 19.8 3.9 24 11-34 63-86 (89)
61 PF13499 EF-hand_7: EF-hand do 26.3 1.2E+02 0.0027 17.6 3.4 37 6-42 5-41 (66)
62 PRK09726 antitoxin HipB; Provi 25.6 1.5E+02 0.0033 18.9 4.0 18 17-34 51-68 (88)
63 cd05022 S-100A13 S-100A13: S-1 24.7 2.1E+02 0.0046 18.7 4.7 44 3-46 10-56 (89)
64 COG1393 ArsC Arsenate reductas 24.5 89 0.0019 21.7 2.8 33 15-47 35-69 (117)
65 smart00222 Sec7 Sec7 domain. D 23.7 2.8E+02 0.006 20.5 5.5 46 3-48 130-184 (187)
66 TIGR02607 antidote_HigA addict 23.6 97 0.0021 18.8 2.6 24 12-35 39-62 (78)
67 TIGR03070 couple_hipB transcri 23.6 1.5E+02 0.0031 16.5 4.0 21 13-33 37-57 (58)
68 cd00052 EH Eps15 homology doma 22.6 1.6E+02 0.0036 16.7 4.7 38 7-46 5-42 (67)
69 PF13069 DUF3933: Protein of u 22.5 46 0.001 20.2 0.9 7 2-8 14-20 (53)
70 PF02084 Bindin: Bindin; Inte 22.5 79 0.0017 25.1 2.4 40 15-56 98-145 (238)
71 PF05037 DUF669: Protein of un 22.3 99 0.0021 21.8 2.8 41 15-55 68-110 (141)
72 PLN00035 histone H4; Provision 22.3 1.6E+02 0.0035 20.4 3.7 26 8-33 72-97 (103)
73 PF10281 Ish1: Putative stress 22.0 1.4E+02 0.0029 16.4 2.8 21 18-38 4-24 (38)
74 smart00027 EH Eps15 homology d 21.8 2.3E+02 0.005 18.1 4.9 51 3-55 12-67 (96)
75 cd03019 DsbA_DsbA DsbA family, 21.6 2.8E+02 0.0061 19.0 5.9 42 18-64 97-138 (178)
76 PF14658 EF-hand_9: EF-hand do 21.5 1.5E+02 0.0031 19.0 3.1 38 9-46 6-44 (66)
77 PRK13890 conjugal transfer pro 21.3 1.5E+02 0.0032 20.5 3.4 30 7-36 34-63 (120)
78 PF12169 DNA_pol3_gamma3: DNA 21.3 1.8E+02 0.0039 19.8 3.9 13 18-30 1-13 (143)
79 PF14246 TetR_C_7: AefR-like t 21.3 1.4E+02 0.003 17.0 2.8 21 10-30 27-47 (55)
80 PF09494 Slx4: Slx4 endonuclea 21.2 2.1E+02 0.0045 17.5 3.8 30 16-45 23-56 (64)
81 PF03484 B5: tRNA synthetase B 21.0 68 0.0015 19.9 1.5 22 16-37 17-38 (70)
82 PRK14958 DNA polymerase III su 20.9 3.4E+02 0.0074 23.4 6.2 38 14-55 228-265 (509)
83 TIGR01859 fruc_bis_ald_ fructo 20.2 69 0.0015 25.5 1.7 38 10-47 203-242 (282)
84 PTZ00015 histone H4; Provision 20.1 1.9E+02 0.0041 20.0 3.7 26 8-33 73-98 (102)
No 1
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=100.00 E-value=9.6e-45 Score=254.71 Aligned_cols=110 Identities=56% Similarity=0.872 Sum_probs=86.5
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHHhhhhhhccCCCCCccccccCCCCC
Q 033702 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAG 80 (113)
Q Consensus 1 m~y~aAYlll~l~g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~~G~~kl~~~~~gg~a~a~~aa~~a 80 (113)
||||||||||+|+||.+||++||++||+++|++||++|+++|++.|+||||++||++|++||+|| ||+++++++++++
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 CCCCCcchhhhhhhhhhhcccccccccCCCCCC
Q 033702 81 GAGAAPAAAEAKKEEKVEEKEESDDDMGFSLFD 113 (113)
Q Consensus 81 ~~~~a~a~~~~~~e~k~eeeeE~ddDmGfgLFd 113 (113)
++++++++ ++++++|+|++|||||||||||||
T Consensus 81 ~~~~~~~~-~~~~e~k~ee~ee~ddDmgf~LFd 112 (112)
T PTZ00373 81 AATAGAKA-EAKKEEKKEEEEEEEDDLGFSLFG 112 (112)
T ss_pred ccccccch-hhhhhhcccccccccccccccccC
Confidence 11121112 233344556667889999999998
No 2
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=100.00 E-value=3.3e-44 Score=252.38 Aligned_cols=112 Identities=87% Similarity=1.188 Sum_probs=89.5
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHHhhhhhhccCCCCCccccccCCCCC
Q 033702 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAG 80 (113)
Q Consensus 1 m~y~aAYlll~l~g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~~G~~kl~~~~~gg~a~a~~aa~~a 80 (113)
||||+|||||+|+||.+||++||++||+++|++||++|+++|++.|+||||++||.+|++||+++|+||+++++++++++
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 99999999999999999999999999999999999999999999999999999999999999999998764332211111
Q ss_pred C-CCCCcchhhhhhhhhhhcccccccccCCCCCC
Q 033702 81 G-AGAAPAAAEAKKEEKVEEKEESDDDMGFSLFD 113 (113)
Q Consensus 81 ~-~~~a~a~~~~~~e~k~eeeeE~ddDmGfgLFd 113 (113)
+ +++++++ ++++++++|++||+||||||||||
T Consensus 81 ~~~~~~~~~-~~~~e~k~e~eeE~ddDmGfgLFd 113 (113)
T PLN00138 81 AGGAAAPAA-EAKKEEKVEEKEESDDDMGFSLFD 113 (113)
T ss_pred ccccccccc-chhhhhhccccccccccccccccC
Confidence 1 1111122 222334456667889999999998
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=7.2e-43 Score=244.27 Aligned_cols=109 Identities=65% Similarity=0.957 Sum_probs=86.4
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHHhhhhhhccCCCCCccccccCCCCC
Q 033702 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAG 80 (113)
Q Consensus 1 m~y~aAYlll~l~g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~~G~~kl~~~~~gg~a~a~~aa~~a 80 (113)
||||||||||+++||.+||++||++||+++|++|+++|+++|++.|+||||++||++|++||+++|+++++++ ++++
T Consensus 1 MkyvaAylL~~l~g~~~pTa~dI~~IL~AaGveVe~~~~~lf~~~L~GKdi~eLIa~g~~kl~s~~~~~~~aa-~a~~-- 77 (109)
T cd05833 1 MKYVAAYLLAVLGGNASPSAADVKKILGSVGVEVDDEKLNKVISELEGKDVEELIAAGKEKLASVPAGAGGAA-PAAA-- 77 (109)
T ss_pred CHHHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHhhhcCCCccccccc-cccc--
Confidence 9999999999999999999999999999999999999999999999999999999999999999985433221 1111
Q ss_pred CCCCCcchhhhhhhhhhhcccccccccCCCCCC
Q 033702 81 GAGAAPAAAEAKKEEKVEEKEESDDDMGFSLFD 113 (113)
Q Consensus 81 ~~~~a~a~~~~~~e~k~eeeeE~ddDmGfgLFd 113 (113)
+++++ +++++++++|+|++||+||||||||||
T Consensus 78 ~~a~a-a~~~~~e~kkee~eee~ddDmGf~LFd 109 (109)
T cd05833 78 AAAAA-AAAAKKEEKKEESEEESDDDMGFGLFD 109 (109)
T ss_pred ccccc-ccchhhhhhccCCccccccccCCCCCC
Confidence 11111 111233444555566679999999998
No 4
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.2e-42 Score=240.83 Aligned_cols=111 Identities=78% Similarity=1.103 Sum_probs=91.0
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHHhhhhhhccCCCCCccccccCC-CC
Q 033702 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAP-SA 79 (113)
Q Consensus 1 m~y~aAYlll~l~g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~~G~~kl~~~~~gg~a~a~~aa-~~ 79 (113)
||||+||||+.|+||.+|++.||++||.++|+++|+.|+++|++.|+||||+|||++|++||++||+||++++++++ ++
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 99999999999999999999999999999999999999999999999999999999999999999999885322211 11
Q ss_pred CCCCCCcchhhhhhhhhhhcccccccccCCCCCC
Q 033702 80 GGAGAAPAAAEAKKEEKVEEKEESDDDMGFSLFD 113 (113)
Q Consensus 80 a~~~~a~a~~~~~~e~k~eeeeE~ddDmGfgLFd 113 (113)
+++++++. ..++++|+|++|||||||||+|||
T Consensus 81 gaa~aa~~--a~~~e~keEe~eesddDmgf~lFd 112 (112)
T KOG3449|consen 81 GAAGAAPA--AAKEEEKEEEKEESDDDMGFGLFD 112 (112)
T ss_pred CCccCCcc--chhhhhhhhhcccccccccccccC
Confidence 11112211 223445556668999999999998
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=2.5e-39 Score=225.12 Aligned_cols=105 Identities=42% Similarity=0.674 Sum_probs=86.1
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHHhhhhhhccCCCCCccccccCCCCC
Q 033702 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAG 80 (113)
Q Consensus 1 m~y~aAYlll~l~g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~~G~~kl~~~~~gg~a~a~~aa~~a 80 (113)
|+|++|||||+++|+. ||++||++||+++|++|+++|+++|++.|+||||++||.+|+.||+++|+||++++ ++ + +
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-AT-A-A 76 (105)
T ss_pred CHHHHHHHHHHhcCCC-CCHHHHHHHHHHcCCCcCHHHHHHHHHHHcCCCHHHHHHHHHhhccCCCCcccccc-cc-c-c
Confidence 9999999999999987 99999999999999999999999999999999999999999999999998765321 11 1 1
Q ss_pred CCCCCcchhhhhhhhhhhcccccccccCCCCC
Q 033702 81 GAGAAPAAAEAKKEEKVEEKEESDDDMGFSLF 112 (113)
Q Consensus 81 ~~~~a~a~~~~~~e~k~eeeeE~ddDmGfgLF 112 (113)
++++++ ++++++|+|++||||||||||||
T Consensus 77 --~~~~~~-~~~~e~k~ee~eE~dddmgf~LF 105 (105)
T cd04411 77 --ATAEPA-EKAEEAKEEEEEEEDEDFGFGLF 105 (105)
T ss_pred --ccccch-hhhhhhhcccccccccccCcccC
Confidence 111111 23334455667888999999999
No 6
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=3.2e-32 Score=189.51 Aligned_cols=108 Identities=40% Similarity=0.607 Sum_probs=84.3
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHHhhhhhhccCCCCCccccccCCCCC
Q 033702 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAG 80 (113)
Q Consensus 1 m~y~aAYlll~l~g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~~G~~kl~~~~~gg~a~a~~aa~~a 80 (113)
|+||++||||+++|+ +||++||++||+++|++||+.|++.|++.|+||||+++|.++..++..++.+++++++++
T Consensus 1 MeYi~a~llL~~agk-ei~e~~l~~vl~aaGveve~~r~k~lvaaLeg~~idE~i~~~~~~~~a~a~a~aaaa~~A---- 75 (109)
T COG2058 1 MEYIYAYLLLHLAGK-EITEDNLKSVLEAAGVEVEEARAKALVAALEGVDIDEVIKNAAEAPAAAAAAGAAAAAAA---- 75 (109)
T ss_pred ChHHHHHHHHHHccC-cCCHHHHHHHHHHcCCCccHHHHHHHHHHhcCCCHHHHHHHhcccccccCCccccccccc----
Confidence 999999999999998 799999999999999999999999999999999999999999887777765544332111
Q ss_pred CCCCCcch-hhhhhhhhhhcccccccccCCCCCC
Q 033702 81 GAGAAPAA-AEAKKEEKVEEKEESDDDMGFSLFD 113 (113)
Q Consensus 81 ~~~~a~a~-~~~~~e~k~eeeeE~ddDmGfgLFd 113 (113)
++.+++.. +.++++++++.+||+|+||||+|||
T Consensus 76 ~~~~a~~~~ea~eEe~eEe~~EE~~~~~lf~LF~ 109 (109)
T COG2058 76 GAEAAAEADEAEEEEKEEEAEEESDDDMLFGLFG 109 (109)
T ss_pred ccccccchhhHHHHHhhhchhhcccccchhhccC
Confidence 11111111 1223334555668889999999998
No 7
>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=99.96 E-value=3e-29 Score=173.89 Aligned_cols=99 Identities=42% Similarity=0.632 Sum_probs=69.0
Q ss_pred HHHHHHHhcC-CCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHHhhhhhhccCCCCCccccccCCCCCCCC
Q 033702 5 AAYLLAVLGG-NTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAGGAG 83 (113)
Q Consensus 5 aAYlll~l~g-~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~~G~~kl~~~~~gg~a~a~~aa~~a~~~ 83 (113)
..|+.|+|++ +++||++||++||+++|++|+++|+++|++.|+||||++||. +++++|+++++++++ ++++
T Consensus 4 c~yAaLiL~d~~~~~Tae~I~~ilkAaGveve~~~~~~f~~~L~gk~i~elIa-------~~~~~~~~aap~a~~-a~~~ 75 (103)
T cd05831 4 CTYAALILHDDGIEITADNINALLKAAGVNVEPYWPGLFAKALEGKDIKDLLS-------NVGGGGGGAAPAAAA-AAAA 75 (103)
T ss_pred HHHHHHHHccCCCCCCHHHHHHHHHHcCCcccHHHHHHHHHHHcCCCHHHHhh-------ccccccccccccccc-cccc
Confidence 3455555555 678999999999999999999999999999999999999998 454443321111111 1111
Q ss_pred CCcchhhhhhhhhhhcccccccccCCCCC
Q 033702 84 AAPAAAEAKKEEKVEEKEESDDDMGFSLF 112 (113)
Q Consensus 84 ~a~a~~~~~~e~k~eeeeE~ddDmGfgLF 112 (113)
++ .++++++++|+|++||+|||||||||
T Consensus 76 ~~-~~~~~~~~kk~e~eee~d~dmgfglF 103 (103)
T cd05831 76 AA-AAEAKKEEKKEEEEEESDDDMGFGLF 103 (103)
T ss_pred cc-cccchhhhcccccccccccccccccC
Confidence 11 12123344556667778999999999
No 8
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=99.96 E-value=9.7e-29 Score=172.19 Aligned_cols=55 Identities=25% Similarity=0.457 Sum_probs=54.1
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHH
Q 033702 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIA 56 (113)
Q Consensus 1 m~y~aAYlll~l~g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~ 56 (113)
|||++|||||+++|+ +||++||++||+++|++|+++|+++|++.|+||||++||.
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 9
>KOG1762 consensus 60s acidic ribosomal protein P1 [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=1.9e-27 Score=166.73 Aligned_cols=102 Identities=42% Similarity=0.615 Sum_probs=76.0
Q ss_pred HHHHHHHhcC-CCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHHhhhhhhccCCCCCccccccC--C-CCC
Q 033702 5 AAYLLAVLGG-NTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAA--P-SAG 80 (113)
Q Consensus 5 aAYlll~l~g-~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~~G~~kl~~~~~gg~a~a~~a--a-~~a 80 (113)
..|.-|+|.. ...||.++|..|+|++|++|+++||.+|+++|.++||.+||+ |+++||+++++++ + .++
T Consensus 9 c~yaalIL~d~~i~it~dki~tl~kaa~v~ve~~Wp~lfakale~vni~~li~-------n~gag~~a~a~~~~~~~~aa 81 (114)
T KOG1762|consen 9 CSYAALILHDDEIEVTADKINTLTKAAGVNVEPYWPGLFAKALEGVNIKELIC-------NVGAGGGALAAGAAAAGGAA 81 (114)
T ss_pred HhhhhhhccccceeeehhhhhhHHHhccCcccccchhHHHHHhccCChHHHHH-------hcccCCccCCCccccccccc
Confidence 3456666655 578999999999999999999999999999999999999999 7877665543222 1 111
Q ss_pred CCCCCcchhhhhhhhhhhcccccccccCCCCCC
Q 033702 81 GAGAAPAAAEAKKEEKVEEKEESDDDMGFSLFD 113 (113)
Q Consensus 81 ~~~~a~a~~~~~~e~k~eeeeE~ddDmGfgLFd 113 (113)
+++++++.++++++.|+|+.||+||||||||||
T Consensus 82 ~~~~aA~~~Ekk~eak~EeseesddDmgfGLfd 114 (114)
T KOG1762|consen 82 AAGGAAAAEEKKEEAKKEESEESDDDMGFGLFD 114 (114)
T ss_pred cccccccchHHHHHhhhhhhcccccccccCCCC
Confidence 111222332445556677789999999999998
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=99.92 E-value=5.9e-25 Score=152.94 Aligned_cols=55 Identities=25% Similarity=0.494 Sum_probs=54.1
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHH
Q 033702 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIA 56 (113)
Q Consensus 1 m~y~aAYlll~l~g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~ 56 (113)
|||++|||||+++|+ +||.++|++||+++||+|+++|+.+|++.|+||+|++||.
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
>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=8.2e-25 Score=152.49 Aligned_cols=55 Identities=24% Similarity=0.448 Sum_probs=54.1
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHH
Q 033702 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIA 56 (113)
Q Consensus 1 m~y~aAYlll~l~g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~ 56 (113)
|||++|||||+++|+ +||+++|++||+++|++|+++|+.+|++.|+|+||+++|.
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 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=99.89 E-value=4.3e-25 Score=148.46 Aligned_cols=87 Identities=52% Similarity=0.748 Sum_probs=58.9
Q ss_pred CCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHHhhhhhhccCCCCCccccccCCCCCCCCCCcchhhhhhhhh
Q 033702 17 SPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAPSAGGAGAAPAAAEAKKEEK 96 (113)
Q Consensus 17 ~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~~G~~kl~~~~~gg~a~a~~aa~~a~~~~a~a~~~~~~e~k 96 (113)
+||.++|++||+++|++|+++|+.+|++.|++++|++||+++..+|... +++++++ +++.++++++++++|
T Consensus 1 ~pT~~~i~~vl~aag~~v~~~~~~~~~~~l~~~~i~~li~~~~~~~~~~------aaa~aaa---~aa~~~a~a~~e~kk 71 (88)
T PF00428_consen 1 EPTAENIKKVLKAAGVEVEAIWLELFAKALEGKDIKELIANGSAGMAAA------AAAAAAA---AAAAAAAAAAEEEKK 71 (88)
T ss_dssp S-SCCCHHHHHHHHTHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHH------HHHTTSS---HHHHHHHHHHSTTHH
T ss_pred CCCHHHHHHHHHHhCCchhHHHHHHHHHHHcCCcHHHHHhccccccccc------ccccccc---cccccccccchhccc
Confidence 4899999999999999999999999999999999999999998877611 1111111 011111112222222
Q ss_pred hhcc-cccccccCCCCC
Q 033702 97 VEEK-EESDDDMGFSLF 112 (113)
Q Consensus 97 ~eee-eE~ddDmGfgLF 112 (113)
++++ ||+|+|||||||
T Consensus 72 EeeeeEEed~dmGf~LF 88 (88)
T PF00428_consen 72 EEEEEEEEDDDMGFGLF 88 (88)
T ss_dssp HHT--SS-SSSSSTTTT
T ss_pred ccccccccccccCcCCC
Confidence 2322 688999999999
No 13
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=98.98 E-value=3.6e-10 Score=91.14 Aligned_cols=28 Identities=18% Similarity=0.230 Sum_probs=24.3
Q ss_pred HHHHHHHHhcCCCcchHHHHHHHHhhcC
Q 033702 21 DDIKGILGSVGADCEDNRLELLLSEVKG 48 (113)
Q Consensus 21 e~I~kvl~aaGveve~~~~~~f~~~L~g 48 (113)
-+|.+|..++|+.++++|+.+|++++++
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 3677889999999999999999998743
No 14
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=98.00 E-value=9.6e-06 Score=66.12 Aligned_cols=16 Identities=50% Similarity=0.918 Sum_probs=12.2
Q ss_pred hhcccccccccCCC-CC
Q 033702 97 VEEKEESDDDMGFS-LF 112 (113)
Q Consensus 97 ~eeeeE~ddDmGfg-LF 112 (113)
+|+|||+||||||| ||
T Consensus 307 ~~~~e~~~~d~~~~~~~ 323 (323)
T PTZ00240 307 EEEEESDEDDFGMGALF 323 (323)
T ss_pred cCCccCcccccCccccC
Confidence 46667788999997 55
No 15
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=96.96 E-value=0.0023 Score=52.02 Aligned_cols=46 Identities=20% Similarity=0.201 Sum_probs=35.8
Q ss_pred HHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhcC-CChHHHHHh
Q 033702 5 AAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKG-KDITELIAS 57 (113)
Q Consensus 5 aAYlll~l~g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~g-k~v~eLI~~ 57 (113)
-|..|.+-.+ =||.+.|..||..+ ......++..+.+ .++.+-|.+
T Consensus 244 ~a~aLa~~~~--~~t~e~~~~il~kA-----~~~~~ala~~~~~~~~~~~~~~~ 290 (330)
T PRK04019 244 EAKALAVEAG--IVTPETADDILSKA-----VAQALALAAALADKDALDEELKE 290 (330)
T ss_pred HHHHHHHHcC--CCChhhHHHHHHHH-----HHHHHHHHHHhcCcccccHHHHh
Confidence 3445555553 38999999999999 5667788999999 999988873
No 16
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=96.42 E-value=0.0062 Score=42.86 Aligned_cols=27 Identities=22% Similarity=0.485 Sum_probs=22.5
Q ss_pred HHHhcCCCcchHHHHHHHHhhcCCChHH
Q 033702 26 ILGSVGADCEDNRLELLLSEVKGKDITE 53 (113)
Q Consensus 26 vl~aaGveve~~~~~~f~~~L~gk~v~e 53 (113)
+|..+|-+++...++.+.+. -|.+|++
T Consensus 9 lL~~agkei~e~~l~~vl~a-aGveve~ 35 (109)
T COG2058 9 LLHLAGKEITEDNLKSVLEA-AGVEVEE 35 (109)
T ss_pred HHHHccCcCCHHHHHHHHHH-cCCCccH
Confidence 68889999999999988886 4888765
No 17
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=95.16 E-value=0.11 Score=36.77 Aligned_cols=19 Identities=11% Similarity=0.195 Sum_probs=16.6
Q ss_pred CCCCCHHHHHHHHHhcCCC
Q 033702 15 NTSPSADDIKGILGSVGAD 33 (113)
Q Consensus 15 ~~~~t~e~I~kvl~aaGve 33 (113)
..+++.+.|++||+.....
T Consensus 31 G~E~d~e~i~~visel~GK 49 (112)
T KOG3449|consen 31 GAEIDDERINLVLSELKGK 49 (112)
T ss_pred CcccCHHHHHHHHHHhcCC
Confidence 4679999999999999875
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=94.87 E-value=0.082 Score=36.76 Aligned_cols=29 Identities=17% Similarity=0.267 Sum_probs=23.3
Q ss_pred HHHhcCCCCCCHHHHHHHHHh-cCCCcchHH
Q 033702 9 LAVLGGNTSPSADDIKGILGS-VGADCEDNR 38 (113)
Q Consensus 9 ll~l~g~~~~t~e~I~kvl~a-aGveve~~~ 38 (113)
+|...| .+++.+.++.++++ .|.+|+.-.
T Consensus 25 IL~aaG-veVe~~~~~~~~~aLaGk~V~eli 54 (105)
T cd04411 25 LLSAAG-AEIEPERVKLFLSALNGKNIDEVI 54 (105)
T ss_pred HHHHcC-CCcCHHHHHHHHHHHcCCCHHHHH
Confidence 455555 57999999999999 889987755
No 19
>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=92.12 E-value=0.33 Score=33.98 Aligned_cols=27 Identities=22% Similarity=0.480 Sum_probs=20.5
Q ss_pred HHHhcCCCcchHHHHHHHHhhcCCChHH
Q 033702 26 ILGSVGADCEDNRLELLLSEVKGKDITE 53 (113)
Q Consensus 26 vl~aaGveve~~~~~~f~~~L~gk~v~e 53 (113)
||.-.|.++....++.+++. .|.+|++
T Consensus 9 LL~~~G~eITae~I~~IL~A-AGveVd~ 35 (106)
T cd05832 9 LLHYAGKEINEENLKKVLEA-AGIEVDE 35 (106)
T ss_pred HHHhcCCCCCHHHHHHHHHH-hCCcccH
Confidence 57778888888888888876 4666654
No 20
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=90.76 E-value=0.63 Score=32.56 Aligned_cols=27 Identities=26% Similarity=0.551 Sum_probs=15.7
Q ss_pred HHHhcCCCcchHHHHHHHHhhcCCChHH
Q 033702 26 ILGSVGADCEDNRLELLLSEVKGKDITE 53 (113)
Q Consensus 26 vl~aaGveve~~~~~~f~~~L~gk~v~e 53 (113)
||.-.|.++...-++.++++ .|.+|++
T Consensus 9 LL~~~g~~it~e~I~~IL~A-AGveVee 35 (106)
T PRK06402 9 LLHSAGKEINEDNLKKVLEA-AGVEVDE 35 (106)
T ss_pred HHHhcCCCCCHHHHHHHHHH-cCCCccH
Confidence 45555666666666666665 3455554
No 21
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=87.33 E-value=0.78 Score=31.88 Aligned_cols=27 Identities=26% Similarity=0.546 Sum_probs=18.8
Q ss_pred HHHhcCCCcchHHHHHHHHhhcCCChHH
Q 033702 26 ILGSVGADCEDNRLELLLSEVKGKDITE 53 (113)
Q Consensus 26 vl~aaGveve~~~~~~f~~~L~gk~v~e 53 (113)
||.-.|.++....++.++++ .|.+|++
T Consensus 9 ll~~~g~~iT~e~I~~IL~A-AGv~ve~ 35 (105)
T TIGR03685 9 LLHSAGKEINEENLKAVLEA-AGVEVDE 35 (105)
T ss_pred HHHhcCCCCCHHHHHHHHHH-hCCcccH
Confidence 56667778888888877776 4555554
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=86.26 E-value=1.8 Score=29.82 Aligned_cols=27 Identities=22% Similarity=0.421 Sum_probs=19.9
Q ss_pred HHHhcCCCcchHHHHHHHHhhcCCChHH
Q 033702 26 ILGSVGADCEDNRLELLLSEVKGKDITE 53 (113)
Q Consensus 26 vl~aaGveve~~~~~~f~~~L~gk~v~e 53 (113)
||...|.++....++..+++. |.++++
T Consensus 10 iL~d~~~~~Tae~I~~ilkAa-Gveve~ 36 (103)
T cd05831 10 ILHDDGIEITADNINALLKAA-GVNVEP 36 (103)
T ss_pred HHccCCCCCCHHHHHHHHHHc-CCcccH
Confidence 677778888888888887764 566664
No 23
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=84.75 E-value=0.55 Score=33.13 Aligned_cols=27 Identities=7% Similarity=0.074 Sum_probs=18.8
Q ss_pred HHHhcCCCCCCHHHHHHHHHhcCC-Ccch
Q 033702 9 LAVLGGNTSPSADDIKGILGSVGA-DCED 36 (113)
Q Consensus 9 ll~l~g~~~~t~e~I~kvl~aaGv-eve~ 36 (113)
+|...| .++..+.++.+++...- +|+.
T Consensus 28 IL~AaG-veVd~~~~~l~~~~L~GKdI~E 55 (112)
T PTZ00373 28 VLSAVN-ADVEDDVLDNFFKSLEGKTPHE 55 (112)
T ss_pred HHHHcC-CCccHHHHHHHHHHHcCCCHHH
Confidence 344454 56899999999998764 4444
No 24
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=83.84 E-value=0.92 Score=31.95 Aligned_cols=22 Identities=23% Similarity=0.210 Sum_probs=15.2
Q ss_pred HHhcCCCCCCHHHHHHHHHhcCC
Q 033702 10 AVLGGNTSPSADDIKGILGSVGA 32 (113)
Q Consensus 10 l~l~g~~~~t~e~I~kvl~aaGv 32 (113)
|...| .++..+.++.+++...-
T Consensus 27 L~AaG-vevd~~~~~~f~~~L~g 48 (113)
T PLN00138 27 LGSVG-ADADDDRIELLLSEVKG 48 (113)
T ss_pred HHHcC-CcccHHHHHHHHHHHcC
Confidence 34444 56788888888887754
No 25
>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=83.69 E-value=4.3 Score=28.31 Aligned_cols=22 Identities=5% Similarity=0.139 Sum_probs=14.5
Q ss_pred HHhcCCCCCCHHHHHHHHHhcCC
Q 033702 10 AVLGGNTSPSADDIKGILGSVGA 32 (113)
Q Consensus 10 l~l~g~~~~t~e~I~kvl~aaGv 32 (113)
|.-.| .++..+.+..++++...
T Consensus 27 L~AaG-veVe~~~~~lf~~~L~G 48 (109)
T cd05833 27 LGSVG-VEVDDEKLNKVISELEG 48 (109)
T ss_pred HHHcC-CCccHHHHHHHHHHHcC
Confidence 44444 56777788888877654
No 26
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=73.75 E-value=6.4 Score=26.54 Aligned_cols=36 Identities=14% Similarity=0.219 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChH
Q 033702 17 SPSADDIKGILGSVGADCEDNRLELLLSEVKGKDIT 52 (113)
Q Consensus 17 ~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~ 52 (113)
++|.+++.+.-+.-|+.+.+..++..++.|.|++++
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 589999999999999999999999999999999985
No 27
>KOG1762 consensus 60s acidic ribosomal protein P1 [Translation, ribosomal structure and biogenesis]
Probab=69.18 E-value=4.5 Score=28.74 Aligned_cols=26 Identities=15% Similarity=0.325 Sum_probs=20.4
Q ss_pred HHHhcCCCcchHHHHHHHHhhcCCChH
Q 033702 26 ILGSVGADCEDNRLELLLSEVKGKDIT 52 (113)
Q Consensus 26 vl~aaGveve~~~~~~f~~~L~gk~v~ 52 (113)
||.--+++|..+....+.++. |.|++
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 677778999999999888864 66665
No 28
>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=59.73 E-value=15 Score=23.45 Aligned_cols=33 Identities=21% Similarity=0.280 Sum_probs=26.2
Q ss_pred CCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCC
Q 033702 17 SPSADDIKGILGSVGADCEDNRLELLLSEVKGK 49 (113)
Q Consensus 17 ~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk 49 (113)
.++.++|..|++.+|.+|.+..+..|.+.=..+
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 467889999999999999998888887754333
No 29
>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=57.58 E-value=16 Score=21.76 Aligned_cols=32 Identities=19% Similarity=0.374 Sum_probs=22.1
Q ss_pred HHHHHHhcCCCCCCHHHHHHHHHhcCCCcchH
Q 033702 6 AYLLAVLGGNTSPSADDIKGILGSVGADCEDN 37 (113)
Q Consensus 6 AYlll~l~g~~~~t~e~I~kvl~aaGveve~~ 37 (113)
.|+--+..|+..|+.+.+.+|.+..|++++..
T Consensus 27 ~~i~~~e~g~~~~~~~~l~~i~~~~~v~~~~l 58 (64)
T PF12844_consen 27 STISKIENGKRKPSVSTLKKIAEALGVSLDEL 58 (64)
T ss_dssp HHHHHHHTTSS--BHHHHHHHHHHHTS-HHHH
T ss_pred HHHHHHHCCCcCCCHHHHHHHHHHhCCCHHHH
Confidence 34455567777899999999999999987653
No 30
>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=52.34 E-value=20 Score=18.56 Aligned_cols=29 Identities=21% Similarity=0.350 Sum_probs=20.8
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHH-hcC
Q 033702 3 VVAAYLLAVLGGNTSPSADDIKGILG-SVG 31 (113)
Q Consensus 3 y~aAYlll~l~g~~~~t~e~I~kvl~-aaG 31 (113)
+-.+|-.+--.++-.||.+++..+|+ +.|
T Consensus 2 l~~~F~~~D~d~dG~I~~~el~~~l~~~lG 31 (31)
T PF13405_consen 2 LREAFKMFDKDGDGFIDFEELRAILRKSLG 31 (31)
T ss_dssp HHHHHHHH-TTSSSEEEHHHHHHHHHHHTT
T ss_pred HHHHHHHHCCCCCCcCcHHHHHHHHHHhcC
Confidence 33455566666677899999999999 665
No 31
>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=49.79 E-value=27 Score=19.94 Aligned_cols=30 Identities=13% Similarity=0.366 Sum_probs=23.8
Q ss_pred CCCHHHHHHHHHhcCCC-cchHHHHHHHHhh
Q 033702 17 SPSADDIKGILGSVGAD-CEDNRLELLLSEV 46 (113)
Q Consensus 17 ~~t~e~I~kvl~aaGve-ve~~~~~~f~~~L 46 (113)
.||.+++..+|...|+. ..+..+..+.+.+
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 47888888888777888 8888877777765
No 32
>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=49.31 E-value=61 Score=21.15 Aligned_cols=45 Identities=7% Similarity=0.217 Sum_probs=35.0
Q ss_pred HHHHHHHHH-hcCCC-CCCHHHHHHHHHh-----cCCCcchHHHHHHHHhhc
Q 033702 3 VVAAYLLAV-LGGNT-SPSADDIKGILGS-----VGADCEDNRLELLLSEVK 47 (113)
Q Consensus 3 y~aAYlll~-l~g~~-~~t~e~I~kvl~a-----aGveve~~~~~~f~~~L~ 47 (113)
++.+|-.+- ..|+- .|+.++++.+|++ .|-...+..++.+++.+.
T Consensus 10 l~~aF~~fD~~dgdG~~I~~~eL~~ll~~~~~~~lg~~~~~~~v~~~i~~~D 61 (88)
T cd05027 10 LIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLD 61 (88)
T ss_pred HHHHHHHhcccCCCcCEECHHHHHHHHHHHhHHHhcCCCCHHHHHHHHHHhC
Confidence 455666675 45665 4999999999999 888888887888888773
No 33
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=47.35 E-value=39 Score=21.51 Aligned_cols=27 Identities=30% Similarity=0.425 Sum_probs=22.9
Q ss_pred HHHhcCCCCCCHHHHHHHHHhcCCCcc
Q 033702 9 LAVLGGNTSPSADDIKGILGSVGADCE 35 (113)
Q Consensus 9 ll~l~g~~~~t~e~I~kvl~aaGveve 35 (113)
.+.+.|...|+..||...|+-.|+.+.
T Consensus 50 ~a~~agR~~~~~~Dv~~Al~~~gi~~~ 76 (77)
T smart00576 50 YAELAGRTEPNLGDVVLALENLGISVG 76 (77)
T ss_pred HHHHcCCCCCCHHHHHHHHHHhCcccC
Confidence 456788778999999999999998775
No 34
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=43.08 E-value=1.1e+02 Score=21.27 Aligned_cols=55 Identities=22% Similarity=0.367 Sum_probs=44.4
Q ss_pred hHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhcC-----CChHHHHH
Q 033702 2 KVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVKG-----KDITELIA 56 (113)
Q Consensus 2 ~y~aAYlll~l~g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~g-----k~v~eLI~ 56 (113)
++-.+|.++-..++-.|+...+.+++.+.|..+....+..+.+.+.. .++.+++.
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 35567888888887789999999999999999888888888888873 46666654
No 35
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=40.25 E-value=39 Score=22.90 Aligned_cols=29 Identities=31% Similarity=0.250 Sum_probs=24.8
Q ss_pred HHHHHHhcCCCCCCHHHHHHHHHhcCCCc
Q 033702 6 AYLLAVLGGNTSPSADDIKGILGSVGADC 34 (113)
Q Consensus 6 AYlll~l~g~~~~t~e~I~kvl~aaGvev 34 (113)
|+.++.+.|...|+.+||+-.++..|...
T Consensus 60 A~~~A~ha~RKTV~~~DI~la~~~~~~~~ 88 (91)
T COG2036 60 AVELAEHAKRKTVKAEDIKLALKRLGRRI 88 (91)
T ss_pred HHHHHHHcCCCeecHHHHHHHHHHhcccc
Confidence 56788899988999999999999887654
No 36
>PF14788 EF-hand_10: EF hand; PDB: 1DJW_B 1DJI_B 1DJG_B 1QAS_B 2ISD_B 1DJZ_B 1DJY_B 1DJX_B 1QAT_A 1DJH_A ....
Probab=39.19 E-value=62 Score=19.73 Aligned_cols=29 Identities=21% Similarity=0.346 Sum_probs=19.8
Q ss_pred CHHHHHHHHHhcCCCcchHHHHHHHHhhc
Q 033702 19 SADDIKGILGSVGADCEDNRLELLLSEVK 47 (113)
Q Consensus 19 t~e~I~kvl~aaGveve~~~~~~f~~~L~ 47 (113)
|-..|+++|+-.+|+++...+..+.+...
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 45689999999999999999887776553
No 37
>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=38.95 E-value=51 Score=20.12 Aligned_cols=40 Identities=20% Similarity=0.183 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHHh
Q 033702 18 PSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIAS 57 (113)
Q Consensus 18 ~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~~ 57 (113)
|..+=+...|+.+|.+..+.++..+++...-|=|.+++..
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 4456678899999999999999999998888888888864
No 38
>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=38.27 E-value=1.1e+02 Score=19.68 Aligned_cols=53 Identities=8% Similarity=0.256 Sum_probs=35.3
Q ss_pred HHHHHHHHHh-cC-CCCCCHHHHHHHHHh-----cCCCcchHHHHHHHHhhc-----CCChHHHH
Q 033702 3 VVAAYLLAVL-GG-NTSPSADDIKGILGS-----VGADCEDNRLELLLSEVK-----GKDITELI 55 (113)
Q Consensus 3 y~aAYlll~l-~g-~~~~t~e~I~kvl~a-----aGveve~~~~~~f~~~L~-----gk~v~eLI 55 (113)
+.-+|-++.- .| +-.||.+++..++.+ .|..+....+..+++.+. ..+..+.+
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 4456666654 44 457999999999987 566767777777766663 24455554
No 39
>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=37.87 E-value=45 Score=24.55 Aligned_cols=36 Identities=19% Similarity=0.218 Sum_probs=28.2
Q ss_pred ChHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchH
Q 033702 1 MKVVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDN 37 (113)
Q Consensus 1 m~y~aAYlll~l~g~~~~t~e~I~kvl~aaGveve~~ 37 (113)
||.+-.+.+-.+-|.. ++.++|.+++..+|++..+-
T Consensus 6 ~k~~~~~v~~~~~~~~-~~~~~~~kl~~~~~~~~~~l 41 (174)
T cd04752 6 MKLLCAQVLKDLLGEG-IDYEKVLKLTADAKFESGDV 41 (174)
T ss_pred HHHHHHHHHHHHHhcc-CCHHHHHHHHHHhCCCHhhH
Confidence 5677778877777654 89999999999998877543
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=37.68 E-value=78 Score=19.85 Aligned_cols=26 Identities=27% Similarity=0.466 Sum_probs=23.0
Q ss_pred HHhcCCCCCCHHHHHHHHHhcCCCcc
Q 033702 10 AVLGGNTSPSADDIKGILGSVGADCE 35 (113)
Q Consensus 10 l~l~g~~~~t~e~I~kvl~aaGveve 35 (113)
+.+.|...|+..||...|.-.|+.|.
T Consensus 51 ae~~gRt~~~~~Dv~~al~~~gi~v~ 76 (77)
T PF07524_consen 51 AEHAGRTEPNLQDVEQALEEMGISVN 76 (77)
T ss_pred HHHcCCCCCCHHHHHHHHHHhCCCCC
Confidence 46888888999999999999999875
No 41
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=36.49 E-value=1.4e+02 Score=22.15 Aligned_cols=51 Identities=20% Similarity=0.323 Sum_probs=36.2
Q ss_pred HHHHHHhcCCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhc----CCChHHHHH
Q 033702 6 AYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVK----GKDITELIA 56 (113)
Q Consensus 6 AYlll~l~g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~----gk~v~eLI~ 56 (113)
||.|+.-.+.-.|+-+++.+|+++.|-.+....+..+++.+. ..+..++|.
T Consensus 25 aF~l~D~d~~G~I~~~el~~ilr~lg~~~s~~ei~~l~~~~d~~~~~idf~~Fl~ 79 (160)
T COG5126 25 AFQLFDRDSDGLIDRNELGKILRSLGFNPSEAEINKLFEEIDAGNETVDFPEFLT 79 (160)
T ss_pred HHHHhCcCCCCCCcHHHHHHHHHHcCCCCcHHHHHHHHHhccCCCCccCHHHHHH
Confidence 567777655557999999999999997655555454444554 467777775
No 42
>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=35.70 E-value=1.1e+02 Score=18.77 Aligned_cols=44 Identities=16% Similarity=0.307 Sum_probs=28.9
Q ss_pred cCCCCCCHHHHHHHHHhcC-CCcchHHHHHHHHhh--cCCChHHHHH
Q 033702 13 GGNTSPSADDIKGILGSVG-ADCEDNRLELLLSEV--KGKDITELIA 56 (113)
Q Consensus 13 ~g~~~~t~e~I~kvl~aaG-veve~~~~~~f~~~L--~gk~v~eLI~ 56 (113)
..+.+.|.+++..++...= .++++.....|.-.| +|-+.+|+..
T Consensus 10 ~~g~~Ls~~e~~~~~~~i~~g~~s~~qiaAfL~al~~kget~~Eiag 56 (66)
T PF02885_consen 10 RDGEDLSREEAKAAFDAILDGEVSDAQIAAFLMALRMKGETPEEIAG 56 (66)
T ss_dssp HTT----HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHH
T ss_pred HcCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCcCHHHHHH
Confidence 3346799999999999875 489999999998877 6777888764
No 43
>PTZ00184 calmodulin; Provisional
Probab=34.80 E-value=1.1e+02 Score=20.17 Aligned_cols=35 Identities=20% Similarity=0.408 Sum_probs=27.3
Q ss_pred hcCCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhh
Q 033702 12 LGGNTSPSADDIKGILGSVGADCEDNRLELLLSEV 46 (113)
Q Consensus 12 l~g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L 46 (113)
..++..+|.+++.+++...|..+....+..+.+.+
T Consensus 95 ~~~~g~i~~~e~~~~l~~~~~~~~~~~~~~~~~~~ 129 (149)
T PTZ00184 95 RDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREA 129 (149)
T ss_pred CCCCCeEeHHHHHHHHHHHCCCCCHHHHHHHHHhc
Confidence 34556689999999999999888877777666655
No 44
>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=33.04 E-value=91 Score=19.47 Aligned_cols=42 Identities=24% Similarity=0.378 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHhcCCC-cchHHHHHHHHhhcCCChHHHHHhhhh
Q 033702 18 PSADDIKGILGSVGAD-CEDNRLELLLSEVKGKDITELIASGRE 60 (113)
Q Consensus 18 ~t~e~I~kvl~aaGve-ve~~~~~~f~~~L~gk~v~eLI~~G~~ 60 (113)
++.+.|+.|.+..|++ +.+.....+...++ .-+.+++....+
T Consensus 3 ~p~~~i~ria~~~Gi~ris~~a~~~l~~~~e-~rl~~i~~~A~k 45 (65)
T smart00803 3 LPKETIKDVAESLGIGNLSDEAAKLLAEDVE-YRIKEIVQEALK 45 (65)
T ss_pred CCHHHHHHHHHHCCCccccHHHHHHHHHHHH-HHHHHHHHHHHH
Confidence 5778999999999997 88888788887765 445566654433
No 45
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=32.26 E-value=1e+02 Score=19.14 Aligned_cols=43 Identities=12% Similarity=0.214 Sum_probs=34.3
Q ss_pred HHHHhcC-CCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCC
Q 033702 8 LLAVLGG-NTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKD 50 (113)
Q Consensus 8 lll~l~g-~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~ 50 (113)
.|-+|.. +.+++...|.+-|+-.|.++....+....++|+-.-
T Consensus 3 IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~G 46 (66)
T PF08461_consen 3 ILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDG 46 (66)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCC
Confidence 3444443 567899999999999999998888998888886555
No 46
>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=31.63 E-value=68 Score=18.19 Aligned_cols=24 Identities=33% Similarity=0.504 Sum_probs=17.4
Q ss_pred hcCCCCCCHHHHHHHHHhcCCCcc
Q 033702 12 LGGNTSPSADDIKGILGSVGADCE 35 (113)
Q Consensus 12 l~g~~~~t~e~I~kvl~aaGveve 35 (113)
..|+..||.+.+.+|.+..|++++
T Consensus 30 ~~g~~~~~~~~~~~ia~~l~~~~~ 53 (55)
T PF01381_consen 30 ENGKRNPSLDTLKKIAKALGVSPE 53 (55)
T ss_dssp HTTSSTSBHHHHHHHHHHHTSEHH
T ss_pred hcCCCCCCHHHHHHHHHHHCCCHH
Confidence 455667888888888888876554
No 47
>PRK00034 gatC aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed
Probab=31.37 E-value=77 Score=20.66 Aligned_cols=47 Identities=15% Similarity=0.296 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHHhhhhhhccCCCCC
Q 033702 17 SPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGG 69 (113)
Q Consensus 17 ~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~~G~~kl~~~~~gg 69 (113)
.+|.++|++|.+-+-+++.+.-...|.+.|+ ++| .-.++|..+..-+
T Consensus 2 ~i~~e~i~~la~La~l~l~~ee~~~~~~~l~-----~il-~~~~~l~~vd~~~ 48 (95)
T PRK00034 2 AITREEVKHLAKLARLELSEEELEKFAGQLN-----KIL-DFVEQLNEVDTEG 48 (95)
T ss_pred CCCHHHHHHHHHHhCCCCCHHHHHHHHHHHH-----HHH-HHHHHHhhcccCC
Confidence 4799999999999999999999999888763 222 2344566665544
No 48
>PHA01976 helix-turn-helix protein
Probab=31.17 E-value=87 Score=18.56 Aligned_cols=22 Identities=9% Similarity=0.283 Sum_probs=12.2
Q ss_pred CCCCCCHHHHHHHHHhcCCCcc
Q 033702 14 GNTSPSADDIKGILGSVGADCE 35 (113)
Q Consensus 14 g~~~~t~e~I~kvl~aaGveve 35 (113)
|...|+.+.|.+|.+..|+.++
T Consensus 38 g~~~p~~~~l~~ia~~l~v~~~ 59 (67)
T PHA01976 38 DKRLPNLKTLLRLADALGVTLD 59 (67)
T ss_pred CCCCCCHHHHHHHHHHHCcCHH
Confidence 3344566666666666555443
No 49
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=30.93 E-value=51 Score=20.08 Aligned_cols=20 Identities=35% Similarity=0.508 Sum_probs=16.7
Q ss_pred CCCCHHHHHHHHHhcCCCcc
Q 033702 16 TSPSADDIKGILGSVGADCE 35 (113)
Q Consensus 16 ~~~t~e~I~kvl~aaGveve 35 (113)
.++|.++|.++|+..|.+++
T Consensus 17 ~~i~~~ei~~~L~~lg~~~~ 36 (71)
T smart00874 17 LDLSAEEIEEILKRLGFEVE 36 (71)
T ss_pred CCCCHHHHHHHHHHCCCeEE
Confidence 46889999999999998764
No 50
>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=30.73 E-value=1.2e+02 Score=21.32 Aligned_cols=48 Identities=10% Similarity=0.185 Sum_probs=28.8
Q ss_pred cCCCCCCHHH-HHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHHhhhhhhccC
Q 033702 13 GGNTSPSADD-IKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASV 65 (113)
Q Consensus 13 ~g~~~~t~e~-I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~~G~~kl~~~ 65 (113)
..+.+|+..+ |..+++.+|++.+. |...+..-.+.+.+.+-.......
T Consensus 115 ~~~~~i~~~~vl~~~~~~~Gld~~~-----~~~~~~~~~~~~~~~~~~~~a~~~ 163 (193)
T PF01323_consen 115 VEGRDISDPDVLAEIAEEAGLDPDE-----FDAALDSPEVKAALEEDTAEARQL 163 (193)
T ss_dssp TSST-TSSHHHHHHHHHHTT--HHH-----HHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred hcccCCCCHHHHHHHHHHcCCcHHH-----HHHHhcchHHHHHHHHHHHHHHHc
Confidence 3344566554 99999999995443 555666667777776554444444
No 51
>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=30.28 E-value=94 Score=16.57 Aligned_cols=40 Identities=28% Similarity=0.463 Sum_probs=30.0
Q ss_pred HHHHHhcCCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhh
Q 033702 7 YLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEV 46 (113)
Q Consensus 7 Ylll~l~g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L 46 (113)
|-.+...++..++.+++..+++..|.......+..+.+.+
T Consensus 6 f~~~d~~~~g~l~~~e~~~~l~~~~~~~~~~~~~~~~~~~ 45 (63)
T cd00051 6 FRLFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREV 45 (63)
T ss_pred HHHhCCCCCCcCcHHHHHHHHHHhCCCCCHHHHHHHHHHh
Confidence 3344444555689999999999999888887777666655
No 52
>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=29.47 E-value=83 Score=20.53 Aligned_cols=47 Identities=13% Similarity=0.196 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHHhhhhhhccCCCCCc
Q 033702 18 PSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLASVPSGGG 70 (113)
Q Consensus 18 ~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~~G~~kl~~~~~gg~ 70 (113)
+|.++|++|.+-+-+++.+.-...|...|+ .+| .-.++|..+..-|.
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 578899999999999999999999888763 222 23445667765543
No 53
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=29.35 E-value=28 Score=27.71 Aligned_cols=58 Identities=17% Similarity=0.397 Sum_probs=42.2
Q ss_pred HHhcCCCCCCHHHHHH--HHHhcCC--CcchHHHHHHHHhhcCCChHHHHHhhhhhhccCCCCC
Q 033702 10 AVLGGNTSPSADDIKG--ILGSVGA--DCEDNRLELLLSEVKGKDITELIASGREKLASVPSGG 69 (113)
Q Consensus 10 l~l~g~~~~t~e~I~k--vl~aaGv--eve~~~~~~f~~~L~gk~v~eLI~~G~~kl~~~~~gg 69 (113)
+++.|+.-||.|||.+ +-++.|. ..++.|+..+.+...... .-+.+-+.||+.+|-|.
T Consensus 64 vI~tGGLGPT~DDiT~e~vAka~g~~lv~~~~al~~i~~~~~~r~--~~~~~~~~K~A~~P~Ga 125 (255)
T COG1058 64 VITTGGLGPTHDDLTAEAVAKALGRPLVLDEEALAMIEEKYAKRG--REMTEANRKQAMLPEGA 125 (255)
T ss_pred EEECCCcCCCccHhHHHHHHHHhCCCcccCHHHHHHHHHHHHhcC--CCCChhhhhhccCCCCC
Confidence 4566778899999975 6677775 578888887777655443 34456778999998775
No 54
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=28.40 E-value=90 Score=19.80 Aligned_cols=45 Identities=22% Similarity=0.324 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHhcCC-CcchHHHHHHHHhhcCCChHHHHHhhhhhhc
Q 033702 18 PSADDIKGILGSVGA-DCEDNRLELLLSEVKGKDITELIASGREKLA 63 (113)
Q Consensus 18 ~t~e~I~kvl~aaGv-eve~~~~~~f~~~L~gk~v~eLI~~G~~kl~ 63 (113)
.+.|.|+.+-++.|+ +..+.....++..++ .-|.++|.+..+.|.
T Consensus 4 ~~~esvk~iAes~Gi~~l~de~a~~La~dve-yrlreiiq~a~kfm~ 49 (66)
T PF02969_consen 4 FSQESVKDIAESLGISNLSDEAAKALAEDVE-YRLREIIQEALKFMR 49 (66)
T ss_dssp --HHHHHHHHHHTT---B-HHHHHHHHHHHH-HHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHcCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Confidence 578999999999999 788888888887653 456788877666553
No 55
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=28.37 E-value=51 Score=19.34 Aligned_cols=21 Identities=24% Similarity=0.442 Sum_probs=10.6
Q ss_pred CCCCHHHHHHHHHhcCCCcch
Q 033702 16 TSPSADDIKGILGSVGADCED 36 (113)
Q Consensus 16 ~~~t~e~I~kvl~aaGveve~ 36 (113)
..|+.+.|.+|.++.|++++.
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 467777777777777776554
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=27.92 E-value=45 Score=21.93 Aligned_cols=23 Identities=22% Similarity=0.413 Sum_probs=20.3
Q ss_pred CCCHHHHHHHHHhc-CCCcchHHH
Q 033702 17 SPSADDIKGILGSV-GADCEDNRL 39 (113)
Q Consensus 17 ~~t~e~I~kvl~aa-Gveve~~~~ 39 (113)
+||..+|.+.|+.. |+++|..+.
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 999998654
No 57
>smart00414 H2A Histone 2A.
Probab=27.79 E-value=75 Score=21.97 Aligned_cols=13 Identities=31% Similarity=0.514 Sum_probs=7.7
Q ss_pred ChHHHHHHHHHhcC
Q 033702 1 MKVVAAYLLAVLGG 14 (113)
Q Consensus 1 m~y~aAYlll~l~g 14 (113)
|+|+.+..| .|.|
T Consensus 40 LEYLtaEIL-eLag 52 (106)
T smart00414 40 LEYLTAEVL-ELAG 52 (106)
T ss_pred HHHHHHHHH-HHHH
Confidence 478888744 3444
No 58
>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=27.29 E-value=85 Score=23.13 Aligned_cols=29 Identities=21% Similarity=0.392 Sum_probs=24.2
Q ss_pred HHHHHHHHhcCCCcchHHHHHHHHhhcCC
Q 033702 21 DDIKGILGSVGADCEDNRLELLLSEVKGK 49 (113)
Q Consensus 21 e~I~kvl~aaGveve~~~~~~f~~~L~gk 49 (113)
++|++|++.-|+.|+..-+.+.++.|.-+
T Consensus 68 ~El~~v~~~~Gi~V~~rHl~LIAD~MT~~ 96 (158)
T cd00630 68 REIQKVLASQGVSVDRRHIELIADVMTYS 96 (158)
T ss_pred HHHHHHHHhcCceecHHHHHHHHHHHhcC
Confidence 57888999999999999999999877544
No 59
>PF10987 DUF2806: Protein of unknown function (DUF2806); InterPro: IPR021254 This bacterial family of proteins has no known function.
Probab=26.67 E-value=95 Score=23.80 Aligned_cols=22 Identities=9% Similarity=0.137 Sum_probs=16.1
Q ss_pred hcCCCcchHHHHHHHHhhcCCC
Q 033702 29 SVGADCEDNRLELLLSEVKGKD 50 (113)
Q Consensus 29 aaGveve~~~~~~f~~~L~gk~ 50 (113)
..+-+||+.|+..|.+.-+..+
T Consensus 34 ~~~~~vD~DWl~~f~~~A~~is 55 (219)
T PF10987_consen 34 VTGEPVDPDWLYRFFDMAEDIS 55 (219)
T ss_pred cCCCCCChHHHHHHHHHHHhcC
Confidence 4567889999999987654333
No 60
>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=26.65 E-value=1.3e+02 Score=19.84 Aligned_cols=24 Identities=25% Similarity=0.445 Sum_probs=19.7
Q ss_pred HhcCCCCCCHHHHHHHHHhcCCCc
Q 033702 11 VLGGNTSPSADDIKGILGSVGADC 34 (113)
Q Consensus 11 ~l~g~~~~t~e~I~kvl~aaGvev 34 (113)
+..|+..|+-+.|.+|+++.|+.+
T Consensus 63 iE~g~~~Ps~~tL~kI~~aLgi~l 86 (89)
T TIGR02684 63 ALSGKGNPTFDTILKVTKALGLKL 86 (89)
T ss_pred HHcCCCCCCHHHHHHHHHHcCCce
Confidence 456777899999999999998865
No 61
>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=26.34 E-value=1.2e+02 Score=17.56 Aligned_cols=37 Identities=19% Similarity=0.284 Sum_probs=26.6
Q ss_pred HHHHHHhcCCCCCCHHHHHHHHHhcCCCcchHHHHHH
Q 033702 6 AYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELL 42 (113)
Q Consensus 6 AYlll~l~g~~~~t~e~I~kvl~aaGveve~~~~~~f 42 (113)
++-.+-..++-.||.+++..+++..+....+......
T Consensus 5 ~F~~~D~d~~G~i~~~el~~~~~~~~~~~~~~~~~~~ 41 (66)
T PF13499_consen 5 AFKKFDKDGDGYISKEELRRALKHLGRDMSDEESDEM 41 (66)
T ss_dssp HHHHHSTTSSSEEEHHHHHHHHHHTTSHSTHHHHHHH
T ss_pred HHHHHcCCccCCCCHHHHHHHHHHhcccccHHHHHHH
Confidence 4445555666679999999999999987754444433
No 62
>PRK09726 antitoxin HipB; Provisional
Probab=25.64 E-value=1.5e+02 Score=18.94 Aligned_cols=18 Identities=17% Similarity=0.122 Sum_probs=9.7
Q ss_pred CCCHHHHHHHHHhcCCCc
Q 033702 17 SPSADDIKGILGSVGADC 34 (113)
Q Consensus 17 ~~t~e~I~kvl~aaGvev 34 (113)
.|+-++|.+|++..|+.+
T Consensus 51 ~ps~~~l~~ia~~lgv~~ 68 (88)
T PRK09726 51 NTTLTTFFKILQSLELSM 68 (88)
T ss_pred CCCHHHHHHHHHHcCCCc
Confidence 455555555555555543
No 63
>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=24.69 E-value=2.1e+02 Score=18.75 Aligned_cols=44 Identities=23% Similarity=0.356 Sum_probs=29.0
Q ss_pred HHHHHHHHHh-cCCCCCCHHHHHHHHHh-cCCCcch-HHHHHHHHhh
Q 033702 3 VVAAYLLAVL-GGNTSPSADDIKGILGS-VGADCED-NRLELLLSEV 46 (113)
Q Consensus 3 y~aAYlll~l-~g~~~~t~e~I~kvl~a-aGveve~-~~~~~f~~~L 46 (113)
++.+|-.+.- +|+-.|+.++++.|++. .|-.+.. .-++.+++.+
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 4556666666 67778999999999998 7644443 3444444444
No 64
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=24.49 E-value=89 Score=21.70 Aligned_cols=33 Identities=27% Similarity=0.416 Sum_probs=24.2
Q ss_pred CCCCCHHHHHHHHHhcCCCcchHHHH--HHHHhhc
Q 033702 15 NTSPSADDIKGILGSVGADCEDNRLE--LLLSEVK 47 (113)
Q Consensus 15 ~~~~t~e~I~kvl~aaGveve~~~~~--~f~~~L~ 47 (113)
...||.+.|+++++..|..++....+ .+.+.|.
T Consensus 35 ~~~~s~~eL~~~l~~~g~~~~~li~t~~~~~r~L~ 69 (117)
T COG1393 35 KTPPSREELKKILSKLGDGVEELINTRGTTYRELN 69 (117)
T ss_pred cCCCCHHHHHHHHHHcCccHHHHHHhccchHHHcC
Confidence 45789999999999999876665544 4555565
No 65
>smart00222 Sec7 Sec7 domain. Domain named after the S. cerevisiae SEC7 gene product, which is required for proper protein transport through the Golgi. The domain facilitates guanine nucleotide exchange on the small GTPases, ARFs (ADP ribosylation factors).
Probab=23.69 E-value=2.8e+02 Score=20.47 Aligned_cols=46 Identities=22% Similarity=0.234 Sum_probs=32.5
Q ss_pred HHHHHHHHHhcC-------CCCCCHHHHHHHHHhcC--CCcchHHHHHHHHhhcC
Q 033702 3 VVAAYLLAVLGG-------NTSPSADDIKGILGSVG--ADCEDNRLELLLSEVKG 48 (113)
Q Consensus 3 y~aAYlll~l~g-------~~~~t~e~I~kvl~aaG--veve~~~~~~f~~~L~g 48 (113)
|+.+|+++.|.- +...|.++..+.+...+ .++...|+..+-+.+..
T Consensus 130 y~l~~s~lmLnTdlhn~~~k~kmt~~~Fi~~~~~~~~~~~~~~~~L~~iY~~I~~ 184 (187)
T smart00222 130 YTLAYSLIMLNTDLHNPNVKKKMTLEDFIKNVRGSNDGEDLPREFLEELYDSIKN 184 (187)
T ss_pred HHHHHHHHHHhHHhcCCccCCCCCHHHHHHHHhccCCCCCCCHHHHHHHHHHHHh
Confidence 788888887762 23458888888888764 67888887766655443
No 66
>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=23.64 E-value=97 Score=18.84 Aligned_cols=24 Identities=21% Similarity=0.279 Sum_probs=17.7
Q ss_pred hcCCCCCCHHHHHHHHHhcCCCcc
Q 033702 12 LGGNTSPSADDIKGILGSVGADCE 35 (113)
Q Consensus 12 l~g~~~~t~e~I~kvl~aaGveve 35 (113)
+.|+..|+.+.+.+|.+..|++++
T Consensus 39 ~~g~~~~~~~~~~~l~~~l~v~~~ 62 (78)
T TIGR02607 39 VNGRRGITADMALRLAKALGTSPE 62 (78)
T ss_pred HcCCCCCCHHHHHHHHHHcCCCHH
Confidence 445566888888888888887653
No 67
>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=23.57 E-value=1.5e+02 Score=16.49 Aligned_cols=21 Identities=19% Similarity=0.471 Sum_probs=14.3
Q ss_pred cCCCCCCHHHHHHHHHhcCCC
Q 033702 13 GGNTSPSADDIKGILGSVGAD 33 (113)
Q Consensus 13 ~g~~~~t~e~I~kvl~aaGve 33 (113)
.|...|+.+.+.+|.+..|++
T Consensus 37 ~g~~~~~~~~~~~i~~~lgv~ 57 (58)
T TIGR03070 37 NGKPTVRLDKVLRVLDALGLE 57 (58)
T ss_pred CCCCCCCHHHHHHHHHHcCCC
Confidence 444567777777777777765
No 68
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=22.61 E-value=1.6e+02 Score=16.75 Aligned_cols=38 Identities=18% Similarity=0.216 Sum_probs=24.5
Q ss_pred HHHHHhcCCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhh
Q 033702 7 YLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEV 46 (113)
Q Consensus 7 Ylll~l~g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L 46 (113)
|-.+-..++..+|.+++..++...|. ....+..+.+.+
T Consensus 5 F~~~D~~~~G~i~~~el~~~l~~~g~--~~~~~~~i~~~~ 42 (67)
T cd00052 5 FRSLDPDGDGLISGDEARPFLGKSGL--PRSVLAQIWDLA 42 (67)
T ss_pred HHHhCCCCCCcCcHHHHHHHHHHcCC--CHHHHHHHHHHh
Confidence 44444445556999999999999886 333444444444
No 69
>PF13069 DUF3933: Protein of unknown function (DUF3933)
Probab=22.49 E-value=46 Score=20.17 Aligned_cols=7 Identities=57% Similarity=0.728 Sum_probs=5.8
Q ss_pred hHHHHHH
Q 033702 2 KVVAAYL 8 (113)
Q Consensus 2 ~y~aAYl 8 (113)
||+|||+
T Consensus 14 kylaaya 20 (53)
T PF13069_consen 14 KYLAAYA 20 (53)
T ss_pred cHHHHHH
Confidence 7889885
No 70
>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=22.46 E-value=79 Score=25.13 Aligned_cols=40 Identities=38% Similarity=0.576 Sum_probs=29.7
Q ss_pred CCCCCH---HHHHHHHHhcCCCc-----chHHHHHHHHhhcCCChHHHHH
Q 033702 15 NTSPSA---DDIKGILGSVGADC-----EDNRLELLLSEVKGKDITELIA 56 (113)
Q Consensus 15 ~~~~t~---e~I~kvl~aaGvev-----e~~~~~~f~~~L~gk~v~eLI~ 56 (113)
...||+ +|||.||-+..|+. |+|-+-++++-|... ..||+
T Consensus 98 etTISAKvm~~ikavLgaTKiDLPVDINDPYDlGLLLRhLRHH--SNLLA 145 (238)
T PF02084_consen 98 ETTISAKVMEDIKAVLGATKIDLPVDINDPYDLGLLLRHLRHH--SNLLA 145 (238)
T ss_pred CccccHHHHHHHHHHhcccccccccccCChhhHHHHHHHHHHH--HHHHh
Confidence 344655 69999999998863 689999999988643 25665
No 71
>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=22.30 E-value=99 Score=21.80 Aligned_cols=41 Identities=20% Similarity=0.282 Sum_probs=31.7
Q ss_pred CCCCCHHHHHHHHHhcCCC--cchHHHHHHHHhhcCCChHHHH
Q 033702 15 NTSPSADDIKGILGSVGAD--CEDNRLELLLSEVKGKDITELI 55 (113)
Q Consensus 15 ~~~~t~e~I~kvl~aaGve--ve~~~~~~f~~~L~gk~v~eLI 55 (113)
+..++...+..|++++|+. .+-..+..|+..|.||.+.=.+
T Consensus 68 ~~~~~~~~l~~i~~a~G~~~~~~~~sl~~~~~~l~gk~l~V~v 110 (141)
T PF05037_consen 68 TGEYSIKRLNAIAKAAGIPEGTDFESLEQFLNQLLGKPLRVTV 110 (141)
T ss_pred hhhhhHHHHHHHHHHhCCCCCCCcccHHHHHHHHcCCeeEEEe
Confidence 3456788899999999983 4455688999999998887544
No 72
>PLN00035 histone H4; Provisional
Probab=22.29 E-value=1.6e+02 Score=20.41 Aligned_cols=26 Identities=15% Similarity=0.060 Sum_probs=21.3
Q ss_pred HHHHhcCCCCCCHHHHHHHHHhcCCC
Q 033702 8 LLAVLGGNTSPSADDIKGILGSVGAD 33 (113)
Q Consensus 8 lll~l~g~~~~t~e~I~kvl~aaGve 33 (113)
.++.+++...||++||.-.|+..|-.
T Consensus 72 ~ya~HA~RKTV~~~DV~~Alkr~g~~ 97 (103)
T PLN00035 72 TYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred HHHHhcCCCcCcHHHHHHHHHHcCCc
Confidence 45677888889999999999988764
No 73
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=22.01 E-value=1.4e+02 Score=16.43 Aligned_cols=21 Identities=29% Similarity=0.243 Sum_probs=17.4
Q ss_pred CCHHHHHHHHHhcCCCcchHH
Q 033702 18 PSADDIKGILGSVGADCEDNR 38 (113)
Q Consensus 18 ~t~e~I~kvl~aaGveve~~~ 38 (113)
=|.++|+.-|+.-||.+.+..
T Consensus 4 Ws~~~L~~wL~~~gi~~~~~~ 24 (38)
T PF10281_consen 4 WSDSDLKSWLKSHGIPVPKSA 24 (38)
T ss_pred CCHHHHHHHHHHcCCCCCCCC
Confidence 367899999999999988743
No 74
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=21.80 E-value=2.3e+02 Score=18.13 Aligned_cols=51 Identities=14% Similarity=0.056 Sum_probs=33.5
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhc-----CCChHHHH
Q 033702 3 VVAAYLLAVLGGNTSPSADDIKGILGSVGADCEDNRLELLLSEVK-----GKDITELI 55 (113)
Q Consensus 3 y~aAYlll~l~g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~-----gk~v~eLI 55 (113)
|-.+|-.+...++..||.+++..++...|+ ....+..+.+.+. ..++++.+
T Consensus 12 l~~~F~~~D~d~~G~Is~~el~~~l~~~~~--~~~ev~~i~~~~d~~~~g~I~~~eF~ 67 (96)
T smart00027 12 YEQIFRSLDKNQDGTVTGAQAKPILLKSGL--PQTLLAKIWNLADIDNDGELDKDEFA 67 (96)
T ss_pred HHHHHHHhCCCCCCeEeHHHHHHHHHHcCC--CHHHHHHHHHHhcCCCCCCcCHHHHH
Confidence 445666666666667999999999999774 4445555555552 24555555
No 75
>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=21.57 E-value=2.8e+02 Score=19.04 Aligned_cols=42 Identities=21% Similarity=0.249 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHHHhhhhhhcc
Q 033702 18 PSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELIASGREKLAS 64 (113)
Q Consensus 18 ~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI~~G~~kl~~ 64 (113)
.+.+.|.++++..|++.+ .|...++...+...|.........
T Consensus 97 ~~~~~l~~~a~~~Gl~~~-----~~~~~~~s~~~~~~i~~~~~~~~~ 138 (178)
T cd03019 97 LDPDDIRKIFLSQGVDKK-----KFDAAYNSFSVKALVAKAEKLAKK 138 (178)
T ss_pred CCHHHHHHHHHHhCCCHH-----HHHHHHhCHHHHHHHHHHHHHHHH
Confidence 458899999999999664 466677787887777655544433
No 76
>PF14658 EF-hand_9: EF-hand domain
Probab=21.49 E-value=1.5e+02 Score=18.97 Aligned_cols=38 Identities=18% Similarity=0.168 Sum_probs=26.8
Q ss_pred HHHhcCCCCCCHHHHHHHHHhcCC-CcchHHHHHHHHhh
Q 033702 9 LAVLGGNTSPSADDIKGILGSVGA-DCEDNRLELLLSEV 46 (113)
Q Consensus 9 ll~l~g~~~~t~e~I~kvl~aaGv-eve~~~~~~f~~~L 46 (113)
+|---....|...+|..+|++.|. ......+..+.+.|
T Consensus 6 ~fD~~~tG~V~v~~l~~~Lra~~~~~p~e~~Lq~l~~el 44 (66)
T PF14658_consen 6 AFDTQKTGRVPVSDLITYLRAVTGRSPEESELQDLINEL 44 (66)
T ss_pred hcCCcCCceEeHHHHHHHHHHHcCCCCcHHHHHHHHHHh
Confidence 333333334677888888888888 78777777777766
No 77
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=21.32 E-value=1.5e+02 Score=20.51 Aligned_cols=30 Identities=17% Similarity=0.272 Sum_probs=21.5
Q ss_pred HHHHHhcCCCCCCHHHHHHHHHhcCCCcch
Q 033702 7 YLLAVLGGNTSPSADDIKGILGSVGADCED 36 (113)
Q Consensus 7 Ylll~l~g~~~~t~e~I~kvl~aaGveve~ 36 (113)
|+--...|+..|+.+.|.+|.++.|+.++.
T Consensus 34 ~is~iE~g~~~ps~~~l~kIa~aL~v~~~~ 63 (120)
T PRK13890 34 FLSDLTTGKANPSLKVMEAIADALETPLPL 63 (120)
T ss_pred HHHHHHcCCCCCCHHHHHHHHHHHCCCHHH
Confidence 333445666678999999999888887664
No 78
>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=21.30 E-value=1.8e+02 Score=19.78 Aligned_cols=13 Identities=46% Similarity=0.759 Sum_probs=6.4
Q ss_pred CCHHHHHHHHHhc
Q 033702 18 PSADDIKGILGSV 30 (113)
Q Consensus 18 ~t~e~I~kvl~aa 30 (113)
||.++|..++-.+
T Consensus 1 It~e~V~~~lG~v 13 (143)
T PF12169_consen 1 ITAEDVREILGLV 13 (143)
T ss_dssp B-HHHHHHHHTHT
T ss_pred CCHHHHHHHHCCC
Confidence 3555555555443
No 79
>PF14246 TetR_C_7: AefR-like transcriptional repressor, C-terminal region; PDB: 3BHQ_B 3CDL_A.
Probab=21.30 E-value=1.4e+02 Score=17.03 Aligned_cols=21 Identities=43% Similarity=0.631 Sum_probs=13.3
Q ss_pred HHhcCCCCCCHHHHHHHHHhc
Q 033702 10 AVLGGNTSPSADDIKGILGSV 30 (113)
Q Consensus 10 l~l~g~~~~t~e~I~kvl~aa 30 (113)
+.++....+|.+++..+++.+
T Consensus 27 ~llg~~~~~s~~e~~~~v~~a 47 (55)
T PF14246_consen 27 ALLGLAPPPSAEEIERIVESA 47 (55)
T ss_dssp HHHHTS----HHHHHHHHHHH
T ss_pred HHhCCCCCcCHHHHHHHHHHH
Confidence 445666678999999999876
No 80
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=21.16 E-value=2.1e+02 Score=17.55 Aligned_cols=30 Identities=13% Similarity=0.293 Sum_probs=24.8
Q ss_pred CCCCHHHHHHHHHhcCC----CcchHHHHHHHHh
Q 033702 16 TSPSADDIKGILGSVGA----DCEDNRLELLLSE 45 (113)
Q Consensus 16 ~~~t~e~I~kvl~aaGv----eve~~~~~~f~~~ 45 (113)
++|.=+++..-|+..|+ .|+...+..|.+.
T Consensus 23 ePI~L~el~~~L~~~g~~~~~~~~~~~l~~~lD~ 56 (64)
T PF09494_consen 23 EPINLEELHAWLKASGIGFDRKVDPSKLKEWLDS 56 (64)
T ss_pred CCccHHHHHHHHHHcCCCccceeCHHHHHHHHHH
Confidence 46888899999999999 8888888887763
No 81
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=20.99 E-value=68 Score=19.90 Aligned_cols=22 Identities=27% Similarity=0.314 Sum_probs=15.0
Q ss_pred CCCCHHHHHHHHHhcCCCcchH
Q 033702 16 TSPSADDIKGILGSVGADCEDN 37 (113)
Q Consensus 16 ~~~t~e~I~kvl~aaGveve~~ 37 (113)
.+++.++|.++|+..|.+++..
T Consensus 17 ~~i~~~~i~~~L~~lg~~~~~~ 38 (70)
T PF03484_consen 17 IDISPEEIIKILKRLGFKVEKI 38 (70)
T ss_dssp S---HHHHHHHHHHTT-EEEE-
T ss_pred CCCCHHHHHHHHHHCCCEEEEC
Confidence 4689999999999999888764
No 82
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.87 E-value=3.4e+02 Score=23.42 Aligned_cols=38 Identities=29% Similarity=0.305 Sum_probs=27.4
Q ss_pred CCCCCCHHHHHHHHHhcCCCcchHHHHHHHHhhcCCChHHHH
Q 033702 14 GNTSPSADDIKGILGSVGADCEDNRLELLLSEVKGKDITELI 55 (113)
Q Consensus 14 g~~~~t~e~I~kvl~aaGveve~~~~~~f~~~L~gk~v~eLI 55 (113)
|+..||.++|..++. .+++..+-.++++|..+|...++
T Consensus 228 ~~~~It~~~V~~~lg----~~~~~~i~~ll~al~~~d~~~~l 265 (509)
T PRK14958 228 GNGKVLIADVKTMLG----TIEPLLLFDILEALAAKAGDRLL 265 (509)
T ss_pred CCCCcCHHHHHHHHC----CCCHHHHHHHHHHHHcCCHHHHH
Confidence 455799999999884 35666666677777777777554
No 83
>TIGR01859 fruc_bis_ald_ fructose-1,6-bisphosphate aldolase, class II, various bacterial and amitochondriate protist. This model represents of one of several subtypes of the class II fructose-1,6-bisphosphate aldolase, an enzyme of glycolysis. The subtypes are split into several models to allow separation of a family of tagatose bisphosphate aldolases. This form is found in Gram-positive bacteria, a variety of Gram-negative, and in amitochondriate protists. The class II enzymes share homology with tagatose bisphosphate aldolase but not with class I aldolase.
Probab=20.16 E-value=69 Score=25.48 Aligned_cols=38 Identities=13% Similarity=0.202 Sum_probs=28.2
Q ss_pred HHhcCCCCCCHHHHHHHHHh--cCCCcchHHHHHHHHhhc
Q 033702 10 AVLGGNTSPSADDIKGILGS--VGADCEDNRLELLLSEVK 47 (113)
Q Consensus 10 l~l~g~~~~t~e~I~kvl~a--aGveve~~~~~~f~~~L~ 47 (113)
+++.|..-++.++|.++++. .+++|...+...|.+.+.
T Consensus 203 lv~hGgSGi~~e~i~~~i~~Gi~kiNv~T~l~~a~~~~~~ 242 (282)
T TIGR01859 203 LVLHGASGIPEEQIKKAIKLGIAKINIDTDCRIAFTAAIR 242 (282)
T ss_pred EEEECCCCCCHHHHHHHHHcCCCEEEECcHHHHHHHHHHH
Confidence 34555456899999999886 446788888888877663
No 84
>PTZ00015 histone H4; Provisional
Probab=20.12 E-value=1.9e+02 Score=20.00 Aligned_cols=26 Identities=15% Similarity=0.086 Sum_probs=21.2
Q ss_pred HHHHhcCCCCCCHHHHHHHHHhcCCC
Q 033702 8 LLAVLGGNTSPSADDIKGILGSVGAD 33 (113)
Q Consensus 8 lll~l~g~~~~t~e~I~kvl~aaGve 33 (113)
.++.+++...||.+||.-.|+..|-.
T Consensus 73 ~~aeHA~RKTVt~~DV~~AlKr~g~~ 98 (102)
T PTZ00015 73 AYTEYARRKTVTAMDVVYALKRQGRT 98 (102)
T ss_pred HHHHhcCCCcccHHHHHHHHHhcCCC
Confidence 45677888889999999999888753
Done!