Query 034868
Match_columns 80
No_of_seqs 125 out of 863
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 07:12:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034868.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034868hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd05833 Ribosomal_P2 Ribosomal 99.9 7.6E-27 1.6E-31 152.1 5.9 78 3-80 23-109 (109)
2 PTZ00373 60S Acidic ribosomal 99.9 8.4E-27 1.8E-31 152.6 5.8 78 3-80 25-112 (112)
3 KOG3449 60S acidic ribosomal p 99.9 1.5E-26 3.2E-31 150.7 5.8 78 3-80 23-112 (112)
4 cd04411 Ribosomal_P1_P2_L12p R 99.9 4.4E-26 9.6E-31 147.6 6.2 77 3-79 22-105 (105)
5 PLN00138 large subunit ribosom 99.9 8.1E-26 1.8E-30 148.1 6.4 78 3-80 23-113 (113)
6 cd05831 Ribosomal_P1 Ribosomal 99.9 5.4E-22 1.2E-26 128.1 5.9 77 3-79 23-103 (103)
7 PF00428 Ribosomal_60s: 60s Ac 99.8 1.6E-21 3.5E-26 122.0 1.2 77 3-79 7-88 (88)
8 COG2058 RPP1A Ribosomal protei 99.8 2.3E-20 4.9E-25 121.4 6.1 78 3-80 22-109 (109)
9 KOG1762 60s acidic ribosomal p 99.8 3.6E-20 7.7E-25 121.3 5.4 77 4-80 29-114 (114)
10 PRK06402 rpl12p 50S ribosomal 99.6 4.4E-16 9.6E-21 101.2 5.1 38 3-40 22-59 (106)
11 TIGR03685 L21P_arch 50S riboso 99.4 4.2E-13 9.2E-18 87.0 4.8 37 3-39 22-58 (105)
12 cd05832 Ribosomal_L12p Ribosom 99.3 2.5E-12 5.5E-17 83.6 4.8 37 3-39 22-58 (106)
13 PTZ00135 60S acidic ribosomal 98.9 2.4E-09 5.2E-14 80.0 4.3 74 3-80 222-310 (310)
14 PTZ00240 60S ribosomal protein 97.9 1.3E-05 2.9E-10 60.5 3.5 18 62-79 305-323 (323)
15 PRK06402 rpl12p 50S ribosomal 96.9 0.0019 4.2E-08 42.1 4.1 31 2-33 5-35 (106)
16 TIGR03685 L21P_arch 50S riboso 96.0 0.009 1.9E-07 38.7 3.4 31 2-33 5-35 (105)
17 COG2058 RPP1A Ribosomal protei 96.0 0.014 3E-07 38.3 4.1 29 3-32 6-34 (109)
18 cd05831 Ribosomal_P1 Ribosomal 95.7 0.025 5.3E-07 36.4 4.4 31 2-33 6-36 (103)
19 PRK04019 rplP0 acidic ribosoma 95.6 0.014 3.1E-07 43.9 3.6 20 18-37 270-290 (330)
20 KOG1762 60s acidic ribosomal p 95.6 0.0077 1.7E-07 39.8 1.7 30 2-32 11-40 (114)
21 cd05832 Ribosomal_L12p Ribosom 95.5 0.021 4.6E-07 37.2 3.6 30 2-32 5-34 (106)
22 cd04411 Ribosomal_P1_P2_L12p R 89.1 0.55 1.2E-05 30.3 3.1 30 3-33 6-35 (105)
23 PF02084 Bindin: Bindin; Inte 45.6 22 0.00047 26.3 2.5 34 3-38 109-147 (238)
24 PF08671 SinI: Anti-repressor 45.3 34 0.00075 17.3 2.6 22 14-35 1-23 (30)
25 PF10815 ComZ: ComZ; InterPro 43.4 35 0.00076 19.8 2.7 24 3-26 17-40 (56)
26 PF09682 Holin_LLH: Phage holi 39.8 42 0.0009 21.2 3.0 24 2-25 76-99 (108)
27 PF03540 TFIID_30kDa: Transcri 37.5 29 0.00063 19.7 1.8 34 3-36 8-41 (51)
28 PF14788 EF-hand_10: EF hand; 36.8 56 0.0012 18.6 2.9 24 3-26 7-30 (51)
29 PF08585 DUF1767: Domain of un 33.1 38 0.00083 20.3 1.9 23 5-27 2-24 (90)
30 PF11116 DUF2624: Protein of u 30.9 60 0.0013 20.3 2.5 28 5-32 22-49 (85)
31 PF06144 DNA_pol3_delta: DNA p 30.5 87 0.0019 20.1 3.4 34 2-36 132-165 (172)
32 cd07979 TAF9 TATA Binding Prot 29.7 72 0.0016 20.6 2.9 25 2-26 6-31 (117)
33 KOG4576 Sulfite oxidase, heme- 29.5 25 0.00054 24.4 0.7 17 4-20 119-135 (167)
34 PF13443 HTH_26: Cro/C1-type H 28.0 62 0.0013 17.6 2.1 23 13-36 37-59 (63)
35 PF14265 DUF4355: Domain of un 23.9 79 0.0017 20.0 2.3 30 2-37 73-102 (125)
36 PF07308 DUF1456: Protein of u 23.1 88 0.0019 18.5 2.2 22 4-25 20-41 (68)
37 PHA02770 hypothetical protein; 22.1 71 0.0015 19.4 1.7 20 18-37 3-22 (81)
38 TIGR01128 holA DNA polymerase 21.9 1.6E+02 0.0035 20.6 3.8 35 2-37 119-153 (302)
39 PRK05574 holA DNA polymerase I 21.7 1.7E+02 0.0038 20.9 4.0 35 2-37 154-188 (340)
40 PF10987 DUF2806: Protein of u 21.4 90 0.0019 22.2 2.3 27 9-35 34-63 (219)
41 TIGR01044 rplV_bact ribosomal 20.3 1.8E+02 0.0038 18.3 3.3 27 11-37 5-31 (103)
No 1
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=99.94 E-value=7.6e-27 Score=152.09 Aligned_cols=78 Identities=56% Similarity=0.810 Sum_probs=59.7
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccccccccccCCCCC----C-C--cc--hhhhhhhhhhhhcccccC
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAA----A-A--PA--AEAKKEEKVEEKEESDDD 73 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~~~~~g~a----a-a--~a--~~~~~~~k~eeeEE~ddD 73 (80)
+++||+++|++|+++|+.+|++.|+||||++||++|..+++++|+++++ + + ++ .++++++|+|++||+|||
T Consensus 23 I~~IL~AaGveVe~~~~~lf~~~L~GKdi~eLIa~g~~kl~s~~~~~~~aa~a~~~~a~aa~~~~~e~kkee~eee~ddD 102 (109)
T cd05833 23 VKKILGSVGVEVDDEKLNKVISELEGKDVEELIAAGKEKLASVPAGAGGAAPAAAAAAAAAAAAKKEEKKEESEEESDDD 102 (109)
T ss_pred HHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHhhhcCCCccccccccccccccccccchhhhhhccCCccccccc
Confidence 5799999999999999999999999999999999999998875432211 1 1 11 122344445555667999
Q ss_pred CCCCCCC
Q 034868 74 MGFSLFD 80 (80)
Q Consensus 74 mgfgLFd 80 (80)
|||||||
T Consensus 103 mGf~LFd 109 (109)
T cd05833 103 MGFGLFD 109 (109)
T ss_pred cCCCCCC
Confidence 9999998
No 2
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=99.93 E-value=8.4e-27 Score=152.61 Aligned_cols=78 Identities=45% Similarity=0.614 Sum_probs=60.0
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccccccccccCCCCC------C--C--cchhhhhhhhhhhhccccc
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAA------A--A--PAAEAKKEEKVEEKEESDD 72 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~~~~~g~a------a--a--~a~~~~~~~k~eeeEE~dd 72 (80)
+++||+++|++|+++|+++|++.|+||||++||++|..+|++++.++++ + + +++++++++|+|++||+||
T Consensus 25 I~kIL~AaGveVd~~~~~l~~~~L~GKdI~ELIa~G~~kl~svgg~~~aa~a~a~~~~~~~~~~~~~~e~k~ee~ee~dd 104 (112)
T PTZ00373 25 VKNVLSAVNADVEDDVLDNFFKSLEGKTPHELIAAGMKKLQNIGGGVAAAAAPAAGAATAGAKAEAKKEEKKEEEEEEED 104 (112)
T ss_pred HHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHHhHHHHhcccCcccccccccccccccccchhhhhhhcccccccccc
Confidence 6899999999999999999999999999999999999999886222111 1 1 1112333344555678889
Q ss_pred CCCCCCCC
Q 034868 73 DMGFSLFD 80 (80)
Q Consensus 73 DmgfgLFd 80 (80)
||||||||
T Consensus 105 Dmgf~LFd 112 (112)
T PTZ00373 105 DLGFSLFG 112 (112)
T ss_pred cccccccC
Confidence 99999998
No 3
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=1.5e-26 Score=150.67 Aligned_cols=78 Identities=73% Similarity=0.946 Sum_probs=64.5
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccccccccccCCCCC--C----C----c--chhhhhhhhhhhhccc
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAA--A----A----P--AAEAKKEEKVEEKEES 70 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~~~~~g~a--a----a----~--a~~~~~~~k~eeeEE~ 70 (80)
+++||.++|++++++|+++|++.|+||||.+||+.|..+|+++|++|++ + + + ..++++++|+|++||+
T Consensus 23 ikkIl~sVG~E~d~e~i~~visel~GK~i~ElIA~G~eklAsvpsGGa~~aaa~~aaggaa~aa~~a~~~e~keEe~ees 102 (112)
T KOG3449|consen 23 IKKILESVGAEIDDERINLVLSELKGKDIEELIAAGREKLASVPSGGAVAAAAAPAAGGAAGAAPAAAKEEEKEEEKEES 102 (112)
T ss_pred HHHHHHHhCcccCHHHHHHHHHHhcCCCHHHHHHHhHHHHhcCCCCCccccccCcCCCCCccCCccchhhhhhhhhcccc
Confidence 5899999999999999999999999999999999999999999988872 1 1 1 1112344555556899
Q ss_pred ccCCCCCCCC
Q 034868 71 DDDMGFSLFD 80 (80)
Q Consensus 71 ddDmgfgLFd 80 (80)
||||||+|||
T Consensus 103 ddDmgf~lFd 112 (112)
T KOG3449|consen 103 DDDMGFGLFD 112 (112)
T ss_pred cccccccccC
Confidence 9999999998
No 4
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=99.93 E-value=4.4e-26 Score=147.62 Aligned_cols=77 Identities=42% Similarity=0.629 Sum_probs=60.9
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccccccccccCCCCC---C---C-cchhhhhhhhhhhhcccccCCC
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAA---A---A-PAAEAKKEEKVEEKEESDDDMG 75 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~~~~~g~a---a---a-~a~~~~~~~k~eeeEE~ddDmg 75 (80)
+++||+++|++|+++|+++|+++|+||||++||++|..+++++|++|++ + + +++++++++|+|++||+|||||
T Consensus 22 I~~IL~aaGveVe~~~~~~~~~aLaGk~V~eli~~g~~kl~~~~~~~~a~~~a~~~~~~~~~~~~e~k~ee~eE~dddmg 101 (105)
T cd04411 22 IKELLSAAGAEIEPERVKLFLSALNGKNIDEVISKGKELMSSQAAAAAAPAATAAATAEPAEKAEEAKEEEEEEEDEDFG 101 (105)
T ss_pred HHHHHHHcCCCcCHHHHHHHHHHHcCCCHHHHHHHHHhhccCCCCccccccccccccccchhhhhhhhcccccccccccC
Confidence 6899999999999999999999999999999999999998877655432 1 1 1112333444556677899999
Q ss_pred CCCC
Q 034868 76 FSLF 79 (80)
Q Consensus 76 fgLF 79 (80)
||||
T Consensus 102 f~LF 105 (105)
T cd04411 102 FGLF 105 (105)
T ss_pred cccC
Confidence 9999
No 5
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=99.92 E-value=8.1e-26 Score=148.10 Aligned_cols=78 Identities=83% Similarity=1.046 Sum_probs=60.9
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccccccccccCCCCC-----C---C--cc--h-hhhhhhhhhhhcc
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAA-----A---A--PA--A-EAKKEEKVEEKEE 69 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~~~~~g~a-----a---a--~a--~-~~~~~~k~eeeEE 69 (80)
+++||+++|++|+++|+++|++.|+||||++||++|..+|+++|++|++ + + ++ + +++++++++++||
T Consensus 23 I~~IL~AaGvevd~~~~~~f~~~L~gK~i~eLIa~G~~kl~sv~~gg~aa~a~a~a~~~~~~~~~~~~~~~e~k~e~eeE 102 (113)
T PLN00138 23 LKDILGSVGADADDDRIELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAAAPAAGGAAAPAAEAKKEEKVEEKEE 102 (113)
T ss_pred HHHHHHHcCCcccHHHHHHHHHHHcCCCHHHHHHhchhccccCCCCCccccccccccccccccccccchhhhhhcccccc
Confidence 6899999999999999999999999999999999999999887765431 1 0 11 1 1123333455577
Q ss_pred cccCCCCCCCC
Q 034868 70 SDDDMGFSLFD 80 (80)
Q Consensus 70 ~ddDmgfgLFd 80 (80)
+||||||+|||
T Consensus 103 ~ddDmGfgLFd 113 (113)
T PLN00138 103 SDDDMGFSLFD 113 (113)
T ss_pred ccccccccccC
Confidence 88999999998
No 6
>cd05831 Ribosomal_P1 Ribosomal protein P1. This subfamily represents the eukaryotic large ribosomal protein P1. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P1 is located in the L12 stalk, with proteins P2, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers) and bacteria may have four or six copies (two or three homodimers), depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and
Probab=99.86 E-value=5.4e-22 Score=128.07 Aligned_cols=77 Identities=38% Similarity=0.494 Sum_probs=55.2
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccccccc-cccCCCCCCCc---chhhhhhhhhhhhcccccCCCCCC
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLA-SVPSGGAAAAP---AAEAKKEEKVEEKEESDDDMGFSL 78 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~-~~~~~g~aaa~---a~~~~~~~k~eeeEE~ddDmgfgL 78 (80)
+++||+++|++|+++|+++|++.|+||+|++||.+++...+ +.|++++++++ ++++++++|++++||+|+||||||
T Consensus 23 I~~ilkAaGveve~~~~~~f~~~L~gk~i~elIa~~~~~~~~aap~a~~a~~~~~~~~~~~~~kk~e~eee~d~dmgfgl 102 (103)
T cd05831 23 INALLKAAGVNVEPYWPGLFAKALEGKDIKDLLSNVGGGGGGAAPAAAAAAAAAAAAEAKKEEKKEEEEEESDDDMGFGL 102 (103)
T ss_pred HHHHHHHcCCcccHHHHHHHHHHHcCCCHHHHhhccccccccccccccccccccccccchhhhccccccccccccccccc
Confidence 58999999999999999999999999999999988653211 13322222111 112234445566677899999999
Q ss_pred C
Q 034868 79 F 79 (80)
Q Consensus 79 F 79 (80)
|
T Consensus 103 F 103 (103)
T cd05831 103 F 103 (103)
T ss_pred C
Confidence 9
No 7
>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=99.82 E-value=1.6e-21 Score=121.97 Aligned_cols=77 Identities=45% Similarity=0.611 Sum_probs=53.8
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHcccccccc---ccCCCCCCCcchhh-hhhhhhhhh-cccccCCCCC
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLAS---VPSGGAAAAPAAEA-KKEEKVEEK-EESDDDMGFS 77 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~---~~~~g~aaa~a~~~-~~~~k~eee-EE~ddDmgfg 77 (80)
+++||+++|++|+++|+.+|++.|+|++|++||+++..++++ ++++++++.+++++ ++++|++++ ||+|+|||||
T Consensus 7 i~~vl~aag~~v~~~~~~~~~~~l~~~~i~~li~~~~~~~~~~aaa~aaa~aa~~~a~a~~e~kkEeeeeEEed~dmGf~ 86 (88)
T PF00428_consen 7 IKKVLKAAGVEVEAIWLELFAKALEGKDIKELIANGSAGMAAAAAAAAAAAAAAAAAAAAEEEKKEEEEEEEEDDDMGFG 86 (88)
T ss_dssp HHHHHHHHTHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHHHSTTHHHHT--SS-SSSSSTT
T ss_pred HHHHHHHhCCchhHHHHHHHHHHHcCCcHHHHHhcccccccccccccccccccccccccchhcccccccccccccccCcC
Confidence 578999999999999999999999999999999998876532 12222111122222 222333333 5889999999
Q ss_pred CC
Q 034868 78 LF 79 (80)
Q Consensus 78 LF 79 (80)
||
T Consensus 87 LF 88 (88)
T PF00428_consen 87 LF 88 (88)
T ss_dssp TT
T ss_pred CC
Confidence 99
No 8
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=99.82 E-value=2.3e-20 Score=121.43 Aligned_cols=78 Identities=37% Similarity=0.495 Sum_probs=59.2
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccccccccccCCCCCC---C-----cc--hhhhhhhhhhhhccccc
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLASVPSGGAAA---A-----PA--AEAKKEEKVEEKEESDD 72 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~~~~~g~aa---a-----~a--~~~~~~~k~eeeEE~dd 72 (80)
.++||+++|++|++.|++.|+++|+||||+++|.++..++++++++++++ + +. .+++++++++.+||+++
T Consensus 22 l~~vl~aaGveve~~r~k~lvaaLeg~~idE~i~~~~~~~~a~a~a~aaaa~~A~~~~a~~~~ea~eEe~eEe~~EE~~~ 101 (109)
T COG2058 22 LKSVLEAAGVEVEEARAKALVAALEGVDIDEVIKNAAEAPAAAAAAGAAAAAAAGAEAAAEADEAEEEEKEEEAEEESDD 101 (109)
T ss_pred HHHHHHHcCCCccHHHHHHHHHHhcCCCHHHHHHHhcccccccCCcccccccccccccccchhhHHHHHhhhchhhcccc
Confidence 57899999999999999999999999999999999988776655444421 1 11 11222234455577889
Q ss_pred CCCCCCCC
Q 034868 73 DMGFSLFD 80 (80)
Q Consensus 73 DmgfgLFd 80 (80)
||+|+|||
T Consensus 102 ~~lf~LF~ 109 (109)
T COG2058 102 DMLFGLFG 109 (109)
T ss_pred cchhhccC
Confidence 99999998
No 9
>KOG1762 consensus 60s acidic ribosomal protein P1 [Translation, ribosomal structure and biogenesis]
Probab=99.81 E-value=3.6e-20 Score=121.30 Aligned_cols=77 Identities=42% Similarity=0.542 Sum_probs=55.1
Q ss_pred hhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHcccccccc-----ccCCCCC----CCcchhhhhhhhhhhhcccccCC
Q 034868 4 WVFGFAVGAEADDERIEFLLSEVKGKDITELIASGREKLAS-----VPSGGAA----AAPAAEAKKEEKVEEKEESDDDM 74 (80)
Q Consensus 4 ~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~~~~~-----~~~~g~a----aa~a~~~~~~~k~eeeEE~ddDm 74 (80)
.+|++++|++|+++|+.+|+++|.++||.+||.+.+.+... +|+++++ ++++++++++.|+|+.||+||||
T Consensus 29 ~tl~kaa~v~ve~~Wp~lfakale~vni~~li~n~gag~~a~a~~~~~~~~aa~~~~aA~~~Ekk~eak~EeseesddDm 108 (114)
T KOG1762|consen 29 NTLTKAAGVNVEPYWPGLFAKALEGVNIKELICNVGAGGGALAAGAAAAGGAAAAGGAAAAEEKKEEAKKEESEESDDDM 108 (114)
T ss_pred hhHHHhccCcccccchhHHHHHhccCChHHHHHhcccCCccCCCccccccccccccccccchHHHHHhhhhhhccccccc
Confidence 46788999999999999999999999999999985542211 1111111 12233344445566678899999
Q ss_pred CCCCCC
Q 034868 75 GFSLFD 80 (80)
Q Consensus 75 gfgLFd 80 (80)
||||||
T Consensus 109 gfGLfd 114 (114)
T KOG1762|consen 109 GFGLFD 114 (114)
T ss_pred ccCCCC
Confidence 999997
No 10
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=99.63 E-value=4.4e-16 Score=101.19 Aligned_cols=38 Identities=24% Similarity=0.282 Sum_probs=35.0
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHcccc
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGRE 40 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~~ 40 (80)
+++||+++|++|+++|+++|+++|+|+||++||.+.+.
T Consensus 22 I~~IL~AAGveVee~~~k~~v~aL~GkdIeElI~~a~~ 59 (106)
T PRK06402 22 LKKVLEAAGVEVDEARVKALVAALEDVNIEEAIKKAAA 59 (106)
T ss_pred HHHHHHHcCCCccHHHHHHHHHHHcCCCHHHHHHhccc
Confidence 68999999999999999999999999999999986443
No 11
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=99.40 E-value=4.2e-13 Score=86.98 Aligned_cols=37 Identities=27% Similarity=0.364 Sum_probs=34.5
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccc
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGR 39 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~ 39 (80)
+++||+++||+|+++|+..|++.|+|++|.+||.+-.
T Consensus 22 I~~IL~AAGv~ve~~~~~~la~~L~gk~i~eli~~~~ 58 (105)
T TIGR03685 22 LKAVLEAAGVEVDEARVKALVAALEGVNIEEAIKKAA 58 (105)
T ss_pred HHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHHhhh
Confidence 5799999999999999999999999999999997644
No 12
>cd05832 Ribosomal_L12p Ribosomal protein L12p. This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera
Probab=99.32 E-value=2.5e-12 Score=83.60 Aligned_cols=37 Identities=24% Similarity=0.274 Sum_probs=34.7
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHccc
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIASGR 39 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~g~ 39 (80)
+++||+++|++|++.|++.|++.|+|+||++||++..
T Consensus 22 I~~IL~AAGveVd~~~~~ala~aL~gkdIeElIa~~~ 58 (106)
T cd05832 22 LKKVLEAAGIEVDEARVKALVAALEEVNIDEAIKKAA 58 (106)
T ss_pred HHHHHHHhCCcccHHHHHHHHHHHcCCCHHHHHHhcc
Confidence 6899999999999999999999999999999998744
No 13
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=98.86 E-value=2.4e-09 Score=80.00 Aligned_cols=74 Identities=30% Similarity=0.381 Sum_probs=42.9
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHhCC---------C---ChHHHH---HccccccccccCCCCCCCcchhhhhhhhhhhh
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEVKG---------K---DITELI---ASGREKLASVPSGGAAAAPAAEAKKEEKVEEK 67 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL~g---------k---~i~eLI---~~g~~~~~~~~~~g~aaa~a~~~~~~~k~eee 67 (80)
+.+|..++|+++.+.|+..|++++++ - .+..++ +... +.+++|+++ ++++++++++++++|
T Consensus 222 i~als~aag~pt~~s~p~~ia~a~k~~~a~a~~~~~~~~~~~~~~~~~a~~~-~~~~~~~~~---~~~~~~~~~~~~~~~ 297 (310)
T PTZ00135 222 VAAISLAAGYPTEASAPHSILNAFKNLAAIGLESGFTFPLAEKIKEALANPS-AAAAAAAAA---AAAAAAAAAAPAEEE 297 (310)
T ss_pred HHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHhhcCCCChhhHHHHHhhcCch-hhccCcccc---Ccccccccccccccc
Confidence 46788999999999999999986532 1 111111 1111 112222211 111112233345667
Q ss_pred cccccCCCCCCCC
Q 034868 68 EESDDDMGFSLFD 80 (80)
Q Consensus 68 EE~ddDmgfgLFd 80 (80)
||+||||||||||
T Consensus 298 ee~~~~~g~~lf~ 310 (310)
T PTZ00135 298 EEEEDDMGFGLFD 310 (310)
T ss_pred cCcchhccccCCC
Confidence 7889999999998
No 14
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=97.87 E-value=1.3e-05 Score=60.49 Aligned_cols=18 Identities=50% Similarity=0.876 Sum_probs=13.0
Q ss_pred hhhhhhcccccCCCCC-CC
Q 034868 62 EKVEEKEESDDDMGFS-LF 79 (80)
Q Consensus 62 ~k~eeeEE~ddDmgfg-LF 79 (80)
++++++||+|+||||| ||
T Consensus 305 ~~~~~~e~~~~d~~~~~~~ 323 (323)
T PTZ00240 305 AKEEEEESDEDDFGMGALF 323 (323)
T ss_pred cccCCccCcccccCccccC
Confidence 3355667788899997 55
No 15
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=96.87 E-value=0.0019 Score=42.05 Aligned_cols=31 Identities=16% Similarity=0.443 Sum_probs=26.0
Q ss_pred hHhhhhhhcCCCcCHHHHHHHHHHhCCCChHH
Q 034868 2 FSWVFGFAVGAEADDERIEFLLSEVKGKDITE 33 (80)
Q Consensus 2 ~~~~iL~aaGveV~~~~~~~~~kaL~gk~i~e 33 (80)
+.-.||+..|.+|+.+.|+.++++. |.+|++
T Consensus 5 yAaLLL~~~g~~it~e~I~~IL~AA-GveVee 35 (106)
T PRK06402 5 YAALLLHSAGKEINEDNLKKVLEAA-GVEVDE 35 (106)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHHc-CCCccH
Confidence 3457899999999999999999987 666654
No 16
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=96.04 E-value=0.009 Score=38.69 Aligned_cols=31 Identities=19% Similarity=0.463 Sum_probs=25.2
Q ss_pred hHhhhhhhcCCCcCHHHHHHHHHHhCCCChHH
Q 034868 2 FSWVFGFAVGAEADDERIEFLLSEVKGKDITE 33 (80)
Q Consensus 2 ~~~~iL~aaGveV~~~~~~~~~kaL~gk~i~e 33 (80)
+.-.||+..|.+|+.+.++.++++- |.+|++
T Consensus 5 yA~Lll~~~g~~iT~e~I~~IL~AA-Gv~ve~ 35 (105)
T TIGR03685 5 YAALLLHSAGKEINEENLKAVLEAA-GVEVDE 35 (105)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHHh-CCcccH
Confidence 3457899999999999999999987 555543
No 17
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=95.96 E-value=0.014 Score=38.27 Aligned_cols=29 Identities=14% Similarity=0.415 Sum_probs=24.1
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHhCCCChH
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEVKGKDIT 32 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~ 32 (80)
.-.+|+.+|-+++.++|..++++. |.+|+
T Consensus 6 a~llL~~agkei~e~~l~~vl~aa-Gveve 34 (109)
T COG2058 6 AYLLLHLAGKEITEDNLKSVLEAA-GVEVE 34 (109)
T ss_pred HHHHHHHccCcCCHHHHHHHHHHc-CCCcc
Confidence 346899999999999999999976 66654
No 18
>cd05831 Ribosomal_P1 Ribosomal protein P1. This subfamily represents the eukaryotic large ribosomal protein P1. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P1 is located in the L12 stalk, with proteins P2, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers) and bacteria may have four or six copies (two or three homodimers), depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and
Probab=95.71 E-value=0.025 Score=36.44 Aligned_cols=31 Identities=19% Similarity=0.318 Sum_probs=26.6
Q ss_pred hHhhhhhhcCCCcCHHHHHHHHHHhCCCChHH
Q 034868 2 FSWVFGFAVGAEADDERIEFLLSEVKGKDITE 33 (80)
Q Consensus 2 ~~~~iL~aaGveV~~~~~~~~~kaL~gk~i~e 33 (80)
|.-.||++.|++|+.+.|+.++++. |.+++.
T Consensus 6 yAaLiL~d~~~~~Tae~I~~ilkAa-Gveve~ 36 (103)
T cd05831 6 YAALILHDDGIEITADNINALLKAA-GVNVEP 36 (103)
T ss_pred HHHHHHccCCCCCCHHHHHHHHHHc-CCcccH
Confidence 5678999999999999999999987 566653
No 19
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=95.62 E-value=0.014 Score=43.85 Aligned_cols=20 Identities=10% Similarity=0.126 Sum_probs=14.2
Q ss_pred HHHHHHHHhCC-CChHHHHHc
Q 034868 18 RIEFLLSEVKG-KDITELIAS 37 (80)
Q Consensus 18 ~~~~~~kaL~g-k~i~eLI~~ 37 (80)
++..++..+.+ .++.+-|.+
T Consensus 270 ~~~ala~~~~~~~~~~~~~~~ 290 (330)
T PRK04019 270 QALALAAALADKDALDEELKE 290 (330)
T ss_pred HHHHHHHHhcCcccccHHHHh
Confidence 44455567888 888888875
No 20
>KOG1762 consensus 60s acidic ribosomal protein P1 [Translation, ribosomal structure and biogenesis]
Probab=95.58 E-value=0.0077 Score=39.77 Aligned_cols=30 Identities=13% Similarity=0.231 Sum_probs=25.3
Q ss_pred hHhhhhhhcCCCcCHHHHHHHHHHhCCCChH
Q 034868 2 FSWVFGFAVGAEADDERIEFLLSEVKGKDIT 32 (80)
Q Consensus 2 ~~~~iL~aaGveV~~~~~~~~~kaL~gk~i~ 32 (80)
+.-.||++.+++|+.++++.++|+. |.|+.
T Consensus 11 yaalIL~d~~i~it~dki~tl~kaa-~v~ve 40 (114)
T KOG1762|consen 11 YAALILHDDEIEVTADKINTLTKAA-GVNVE 40 (114)
T ss_pred hhhhhccccceeeehhhhhhHHHhc-cCccc
Confidence 3457999999999999999999988 55554
No 21
>cd05832 Ribosomal_L12p Ribosomal protein L12p. This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera
Probab=95.51 E-value=0.021 Score=37.17 Aligned_cols=30 Identities=17% Similarity=0.387 Sum_probs=24.6
Q ss_pred hHhhhhhhcCCCcCHHHHHHHHHHhCCCChH
Q 034868 2 FSWVFGFAVGAEADDERIEFLLSEVKGKDIT 32 (80)
Q Consensus 2 ~~~~iL~aaGveV~~~~~~~~~kaL~gk~i~ 32 (80)
+.-.||+..|.+|+.+.++.++++- |.+++
T Consensus 5 yAaLLL~~~G~eITae~I~~IL~AA-GveVd 34 (106)
T cd05832 5 YAALLLHYAGKEINEENLKKVLEAA-GIEVD 34 (106)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHHh-CCccc
Confidence 3457899999999999999999986 54444
No 22
>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=89.10 E-value=0.55 Score=30.31 Aligned_cols=30 Identities=27% Similarity=0.461 Sum_probs=24.7
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHhCCCChHH
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEVKGKDITE 33 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~e 33 (80)
.-.||+..|.+|+.+.|+.+++.. |.+|++
T Consensus 6 A~Lll~~~g~~~ta~~I~~IL~aa-GveVe~ 35 (105)
T cd04411 6 AYLLLHKGGKELTEDKIKELLSAA-GAEIEP 35 (105)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHc-CCCcCH
Confidence 456899999999999999999987 566653
No 23
>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=45.59 E-value=22 Score=26.28 Aligned_cols=34 Identities=18% Similarity=0.134 Sum_probs=23.1
Q ss_pred HhhhhhhcCCC--c---CHHHHHHHHHHhCCCChHHHHHcc
Q 034868 3 SWVFGFAVGAE--A---DDERIEFLLSEVKGKDITELIASG 38 (80)
Q Consensus 3 ~~~iL~aaGve--V---~~~~~~~~~kaL~gk~i~eLI~~g 38 (80)
+|+||-+..|+ | |++-|-+|++.|... ..||++.
T Consensus 109 ikavLgaTKiDLPVDINDPYDlGLLLRhLRHH--SNLLAnI 147 (238)
T PF02084_consen 109 IKAVLGATKIDLPVDINDPYDLGLLLRHLRHH--SNLLANI 147 (238)
T ss_pred HHHHhcccccccccccCChhhHHHHHHHHHHH--HHHHhhc
Confidence 46677776664 2 688889999988543 3667653
No 24
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=45.28 E-value=34 Score=17.34 Aligned_cols=22 Identities=23% Similarity=0.350 Sum_probs=13.7
Q ss_pred cCHHHHHHHHHHh-CCCChHHHH
Q 034868 14 ADDERIEFLLSEV-KGKDITELI 35 (80)
Q Consensus 14 V~~~~~~~~~kaL-~gk~i~eLI 35 (80)
.|++|+.++..+. .|.+++++-
T Consensus 1 LD~EW~~Li~eA~~~Gls~eeir 23 (30)
T PF08671_consen 1 LDEEWVELIKEAKESGLSKEEIR 23 (30)
T ss_dssp --HHHHHHHHHHHHTT--HHHHH
T ss_pred CCHHHHHHHHHHHHcCCCHHHHH
Confidence 3788998888877 677776653
No 25
>PF10815 ComZ: ComZ; InterPro: IPR024558 ComZ, which contains a leucine zipper motif, negatively regulates transcription of the ComG operon [].
Probab=43.40 E-value=35 Score=19.84 Aligned_cols=24 Identities=17% Similarity=-0.065 Sum_probs=20.6
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHh
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEV 26 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL 26 (80)
.+..|...||+.+.+.+.-|+..|
T Consensus 17 ak~~L~k~GIeLsme~~qP~m~L~ 40 (56)
T PF10815_consen 17 AKEELDKKGIELSMEMLQPLMQLL 40 (56)
T ss_pred HHHHHHHcCccCCHHHHHHHHHHH
Confidence 367899999999999999888765
No 26
>PF09682 Holin_LLH: Phage holin protein (Holin_LLH); InterPro: IPR010026 This entry represents the Bacteriophage LL-H, Orf107, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=39.79 E-value=42 Score=21.22 Aligned_cols=24 Identities=21% Similarity=0.097 Sum_probs=20.6
Q ss_pred hHhhhhhhcCCCcCHHHHHHHHHH
Q 034868 2 FSWVFGFAVGAEADDERIEFLLSE 25 (80)
Q Consensus 2 ~~~~iL~aaGveV~~~~~~~~~ka 25 (80)
+++..|+..|+.+++..++.++.+
T Consensus 76 ~v~~~L~~~gi~~t~~~i~~~IEa 99 (108)
T PF09682_consen 76 YVKERLKKKGIKVTDEQIEGAIEA 99 (108)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHH
Confidence 567889999999999999998863
No 27
>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=37.50 E-value=29 Score=19.73 Aligned_cols=34 Identities=21% Similarity=0.198 Sum_probs=28.9
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHH
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEVKGKDITELIA 36 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~ 36 (80)
+.-+|+.+|.+.+.-++..+++...-|=|.+++.
T Consensus 8 ~~~yL~~~G~~~~D~rv~RLvSLaaQKFisdI~~ 41 (51)
T PF03540_consen 8 TDYYLERSGFQTSDPRVKRLVSLAAQKFISDIAN 41 (51)
T ss_pred HHHHHHHCCCCCCCHhHHHHHHHHHHHHHHHHHH
Confidence 5678999999999999999998887777777775
No 28
>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=36.83 E-value=56 Score=18.56 Aligned_cols=24 Identities=25% Similarity=0.134 Sum_probs=17.8
Q ss_pred HhhhhhhcCCCcCHHHHHHHHHHh
Q 034868 3 SWVFGFAVGAEADDERIEFLLSEV 26 (80)
Q Consensus 3 ~~~iL~aaGveV~~~~~~~~~kaL 26 (80)
++++|+-.+|+++...+..+++.+
T Consensus 7 vk~lLk~~NI~~~~~yA~~LFq~~ 30 (51)
T PF14788_consen 7 VKKLLKMMNIEMDDEYARQLFQEC 30 (51)
T ss_dssp HHHHHHHTT----HHHHHHHHHHH
T ss_pred HHHHHHHHccCcCHHHHHHHHHHh
Confidence 678999999999999999988876
No 29
>PF08585 DUF1767: Domain of unknown function (DUF1767); InterPro: IPR013894 This domain is present in eukaryotic proteins of unknown function, and is sometimes found to the N terminus of ubiquitin-binding and nucleic acid-binding domains. ; PDB: 3NBI_A.
Probab=33.13 E-value=38 Score=20.25 Aligned_cols=23 Identities=13% Similarity=-0.006 Sum_probs=15.0
Q ss_pred hhhhhcCCCcCHHHHHHHHHHhC
Q 034868 5 VFGFAVGAEADDERIEFLLSEVK 27 (80)
Q Consensus 5 ~iL~aaGveV~~~~~~~~~kaL~ 27 (80)
.+|+.-|+.+.++|++.++..+.
T Consensus 2 ~~L~~~g~~l~~~wl~~c~~~~~ 24 (90)
T PF08585_consen 2 EWLNKRGWHLSPEWLEECVEYLQ 24 (90)
T ss_dssp HHHHHH-----HHHHHHHHHHHH
T ss_pred hHHHhcCCCcCHHHHHHHHHHHH
Confidence 36888899999999999998863
No 30
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=30.93 E-value=60 Score=20.32 Aligned_cols=28 Identities=14% Similarity=0.268 Sum_probs=24.1
Q ss_pred hhhhhcCCCcCHHHHHHHHHHhCCCChH
Q 034868 5 VFGFAVGAEADDERIEFLLSEVKGKDIT 32 (80)
Q Consensus 5 ~iL~aaGveV~~~~~~~~~kaL~gk~i~ 32 (80)
+..+.-|+.++...+..++..|.|+++.
T Consensus 22 kyskqy~i~it~~QA~~I~~~lr~k~in 49 (85)
T PF11116_consen 22 KYSKQYNISITKKQAEQIANILRGKNIN 49 (85)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHhcCCCC
Confidence 4556779999999999999999999874
No 31
>PF06144 DNA_pol3_delta: DNA polymerase III, delta subunit; InterPro: IPR010372 DNA polymerase III, delta subunit (2.7.7.7 from EC) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction []. The delta subunit is also known as HolA.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0009360 DNA polymerase III complex; PDB: 3GLG_F 1XXH_A 1JQL_B 3GLF_F 1JQJ_C 3GLI_F.
Probab=30.53 E-value=87 Score=20.10 Aligned_cols=34 Identities=21% Similarity=0.314 Sum_probs=24.3
Q ss_pred hHhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHH
Q 034868 2 FSWVFGFAVGAEADDERIEFLLSEVKGKDITELIA 36 (80)
Q Consensus 2 ~~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~ 36 (80)
|++..+...|+.+++.-+..|+..+ |.|+..+..
T Consensus 132 ~i~~~~~~~g~~i~~~a~~~L~~~~-~~d~~~l~~ 165 (172)
T PF06144_consen 132 WIKERAKKNGLKIDPDAAQYLIERV-GNDLSLLQN 165 (172)
T ss_dssp HHHHHHHHTT-EE-HHHHHHHHHHH-TT-HHHHHH
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHHh-ChHHHHHHH
Confidence 6788899999999999999999887 555555443
No 32
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=29.65 E-value=72 Score=20.61 Aligned_cols=25 Identities=20% Similarity=0.070 Sum_probs=20.8
Q ss_pred hHhhhhhhcCC-CcCHHHHHHHHHHh
Q 034868 2 FSWVFGFAVGA-EADDERIEFLLSEV 26 (80)
Q Consensus 2 ~~~~iL~aaGv-eV~~~~~~~~~kaL 26 (80)
++..||++.|+ ++++.-+..|+..+
T Consensus 6 ~v~~iLk~~Gv~~~~~~v~~~Lle~~ 31 (117)
T cd07979 6 VIAAILKSMGITEYEPRVINQLLEFA 31 (117)
T ss_pred HHHHHHHHCCCCccCHHHHHHHHHHH
Confidence 67899999999 59999888888643
No 33
>KOG4576 consensus Sulfite oxidase, heme-binding component [Energy production and conversion]
Probab=29.45 E-value=25 Score=24.36 Aligned_cols=17 Identities=18% Similarity=-0.095 Sum_probs=14.7
Q ss_pred hhhhhhcCCCcCHHHHH
Q 034868 4 WVFGFAVGAEADDERIE 20 (80)
Q Consensus 4 ~~iL~aaGveV~~~~~~ 20 (80)
.|||=++|..+||+|.-
T Consensus 119 dKillAAG~a~dPFWal 135 (167)
T KOG4576|consen 119 DKILLAAGGALDPFWAL 135 (167)
T ss_pred ceeeeecCCCcCcHHHH
Confidence 37899999999999963
No 34
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=28.02 E-value=62 Score=17.57 Aligned_cols=23 Identities=13% Similarity=0.159 Sum_probs=13.4
Q ss_pred CcCHHHHHHHHHHhCCCChHHHHH
Q 034868 13 EADDERIEFLLSEVKGKDITELIA 36 (80)
Q Consensus 13 eV~~~~~~~~~kaL~gk~i~eLI~ 36 (80)
.++...+..++++| |.++.+||.
T Consensus 37 ~~~~~~l~~ia~~l-~~~~~el~~ 59 (63)
T PF13443_consen 37 NPSLDTLEKIAKAL-NCSPEELFE 59 (63)
T ss_dssp ---HHHHHHHHHHH-T--HHHCTE
T ss_pred cccHHHHHHHHHHc-CCCHHHHhh
Confidence 56677777888888 677777763
No 35
>PF14265 DUF4355: Domain of unknown function (DUF4355)
Probab=23.94 E-value=79 Score=19.99 Aligned_cols=30 Identities=23% Similarity=0.066 Sum_probs=21.6
Q ss_pred hHhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHc
Q 034868 2 FSWVFGFAVGAEADDERIEFLLSEVKGKDITELIAS 37 (80)
Q Consensus 2 ~~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~ 37 (80)
.+..+|...|++++ |+..|-|-|-+++..+
T Consensus 73 ~~~~~l~e~GLp~~------l~~~l~g~d~e~~~~~ 102 (125)
T PF14265_consen 73 EAKKVLAEKGLPAE------LADFLVGDDEEETKAN 102 (125)
T ss_pred HHHHHHHHcCCCHH------HHHHHhCCCHHHHHHH
Confidence 35788999999877 5666667777766654
No 36
>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=23.07 E-value=88 Score=18.46 Aligned_cols=22 Identities=14% Similarity=0.049 Sum_probs=19.0
Q ss_pred hhhhhhcCCCcCHHHHHHHHHH
Q 034868 4 WVFGFAVGAEADDERIEFLLSE 25 (80)
Q Consensus 4 ~~iL~aaGveV~~~~~~~~~ka 25 (80)
-.|++.+|.+|++..+..+++.
T Consensus 20 ~~if~l~~~~vs~~el~a~lrk 41 (68)
T PF07308_consen 20 IEIFALAGFEVSKAELSAWLRK 41 (68)
T ss_pred HHHHHHcCCccCHHHHHHHHCC
Confidence 4688999999999999998864
No 37
>PHA02770 hypothetical protein; Provisional
Probab=22.10 E-value=71 Score=19.42 Aligned_cols=20 Identities=30% Similarity=0.576 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCCChHHHHHc
Q 034868 18 RIEFLLSEVKGKDITELIAS 37 (80)
Q Consensus 18 ~~~~~~kaL~gk~i~eLI~~ 37 (80)
++...++.|..|||.++|..
T Consensus 3 qieeiik~lnkkdikdiitk 22 (81)
T PHA02770 3 QIEEIIKTLNKKDIKDIITK 22 (81)
T ss_pred HHHHHHHHhhhhhHHHHHhc
Confidence 56778999999999999974
No 38
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=21.88 E-value=1.6e+02 Score=20.64 Aligned_cols=35 Identities=14% Similarity=0.237 Sum_probs=27.1
Q ss_pred hHhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHc
Q 034868 2 FSWVFGFAVGAEADDERIEFLLSEVKGKDITELIAS 37 (80)
Q Consensus 2 ~~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~ 37 (80)
++...+...|+.++++-+..++..+.| |+..+..+
T Consensus 119 ~i~~~~~~~g~~i~~~a~~~l~~~~~~-d~~~l~~e 153 (302)
T TIGR01128 119 WIQARLKKLGLRIDPDAVQLLAELVEG-NLLAIAQE 153 (302)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHHhCc-HHHHHHHH
Confidence 567888899999999999999987744 65555443
No 39
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=21.69 E-value=1.7e+02 Score=20.91 Aligned_cols=35 Identities=17% Similarity=0.222 Sum_probs=27.5
Q ss_pred hHhhhhhhcCCCcCHHHHHHHHHHhCCCChHHHHHc
Q 034868 2 FSWVFGFAVGAEADDERIEFLLSEVKGKDITELIAS 37 (80)
Q Consensus 2 ~~~~iL~aaGveV~~~~~~~~~kaL~gk~i~eLI~~ 37 (80)
+++..+...|+.++++-+..++..+.+ |+..+..+
T Consensus 154 ~i~~~~~~~g~~i~~~a~~~L~~~~~~-d~~~l~~E 188 (340)
T PRK05574 154 WIQQRLKQQGLQIDAAALQLLAERVEG-NLLALAQE 188 (340)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHHhCc-hHHHHHHH
Confidence 577889999999999999999887743 66655543
No 40
>PF10987 DUF2806: Protein of unknown function (DUF2806); InterPro: IPR021254 This bacterial family of proteins has no known function.
Probab=21.39 E-value=90 Score=22.18 Aligned_cols=27 Identities=15% Similarity=0.293 Sum_probs=18.5
Q ss_pred hcCCCcCHHHHHHHHHHh---CCCChHHHH
Q 034868 9 AVGAEADDERIEFLLSEV---KGKDITELI 35 (80)
Q Consensus 9 aaGveV~~~~~~~~~kaL---~gk~i~eLI 35 (80)
..+-+||++|+..|.... .+..+..|=
T Consensus 34 ~~~~~vD~DWl~~f~~~A~~isn~~mQ~LW 63 (219)
T PF10987_consen 34 VTGEPVDPDWLYRFFDMAEDISNEEMQELW 63 (219)
T ss_pred cCCCCCChHHHHHHHHHHHhcCcHHHHHHH
Confidence 456789999999999644 444444443
No 41
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=20.32 E-value=1.8e+02 Score=18.25 Aligned_cols=27 Identities=7% Similarity=0.239 Sum_probs=23.7
Q ss_pred CCCcCHHHHHHHHHHhCCCChHHHHHc
Q 034868 11 GAEADDERIEFLLSEVKGKDITELIAS 37 (80)
Q Consensus 11 GveV~~~~~~~~~kaL~gk~i~eLI~~ 37 (80)
.+.+.+-++..++..+.|+++.+-|..
T Consensus 5 ~~r~SpkK~~~va~~IrG~~v~~A~~~ 31 (103)
T TIGR01044 5 FVRISPRKARLVADLIRGKSVSQALDI 31 (103)
T ss_pred ccccCHHHHHHHHHHHcCCcHHHHHHH
Confidence 467889999999999999999988764
Done!