Query psy6045
Match_columns 105
No_of_seqs 114 out of 212
Neff 4.0
Searched_HMMs 46136
Date Sat Aug 17 01:07:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6045.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6045hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05767 rpl44e 50S ribosomal 100.0 1E-52 2.2E-57 292.1 5.9 91 4-95 1-91 (92)
2 KOG3464|consensus 100.0 4.4E-52 9.6E-57 293.4 0.2 102 3-104 1-104 (106)
3 PTZ00157 60S ribosomal protein 100.0 3.5E-49 7.5E-54 270.6 5.3 84 3-86 1-84 (84)
4 COG1631 RPL42A Ribosomal prote 100.0 9.8E-49 2.1E-53 272.7 5.0 93 4-96 1-94 (94)
5 PF00935 Ribosomal_L44: Riboso 100.0 8E-42 1.7E-46 230.8 3.1 77 19-95 1-77 (77)
6 PRK00504 rpmG 50S ribosomal pr 96.1 0.0033 7.1E-08 39.5 1.4 16 9-24 32-47 (50)
7 CHL00104 rpl33 ribosomal prote 95.7 0.0056 1.2E-07 40.5 1.4 17 9-25 47-63 (66)
8 TIGR01023 rpmG_bact ribosomal 95.5 0.008 1.7E-07 38.2 1.5 17 9-25 36-52 (54)
9 COG0267 RpmG Ribosomal protein 95.4 0.0075 1.6E-07 38.2 1.3 17 9-25 32-48 (50)
10 PF00471 Ribosomal_L33: Riboso 95.4 0.0074 1.6E-07 37.5 1.2 16 9-24 30-45 (48)
11 PRK00595 rpmG 50S ribosomal pr 95.4 0.0086 1.9E-07 37.8 1.4 17 9-25 35-51 (53)
12 PF08772 NOB1_Zn_bind: Nin one 90.0 0.2 4.3E-06 33.7 1.6 23 7-29 20-42 (73)
13 COG2023 RPR2 RNase P subunit R 74.8 2.6 5.7E-05 30.3 2.2 19 70-88 81-99 (105)
14 PF14205 Cys_rich_KTR: Cystein 74.7 2.2 4.7E-05 27.6 1.6 19 11-29 28-46 (55)
15 COG1326 Uncharacterized archae 72.5 1.5 3.2E-05 34.7 0.6 21 8-28 3-24 (201)
16 PF04032 Rpr2: RNAse P Rpr2/Rp 68.9 8.2 0.00018 24.7 3.4 14 7-20 42-55 (85)
17 PRK03954 ribonuclease P protei 68.6 3.1 6.8E-05 30.3 1.5 22 69-90 91-112 (121)
18 PF03811 Zn_Tnp_IS1: InsA N-te 63.0 8.3 0.00018 22.5 2.3 29 9-44 3-31 (36)
19 COG4332 Uncharacterized protei 62.0 9.3 0.0002 30.3 3.1 50 12-89 18-68 (203)
20 KOG2463|consensus 60.5 10 0.00022 32.5 3.3 59 11-71 257-315 (376)
21 KOG3507|consensus 60.5 2.3 5E-05 28.1 -0.4 21 72-92 38-60 (62)
22 KOG1597|consensus 60.3 5.6 0.00012 33.3 1.7 22 13-34 2-23 (308)
23 PF14803 Nudix_N_2: Nudix N-te 58.2 5.5 0.00012 23.0 0.9 14 13-26 2-15 (34)
24 PF06107 DUF951: Bacterial pro 51.0 12 0.00025 24.3 1.7 17 69-85 29-45 (57)
25 PF09986 DUF2225: Uncharacteri 51.0 32 0.0007 26.4 4.5 57 11-84 5-61 (214)
26 PF06353 DUF1062: Protein of u 50.3 11 0.00024 27.9 1.7 22 68-89 10-32 (142)
27 PF13240 zinc_ribbon_2: zinc-r 48.8 9.1 0.0002 20.2 0.8 9 13-21 1-9 (23)
28 smart00659 RPOLCX RNA polymera 47.3 16 0.00034 22.0 1.8 22 71-92 19-42 (44)
29 PF13248 zf-ribbon_3: zinc-rib 46.4 7.1 0.00015 20.8 0.1 9 11-19 16-24 (26)
30 PRK03824 hypA hydrogenase nick 42.8 16 0.00034 26.5 1.5 14 12-25 108-121 (135)
31 PF09855 DUF2082: Nucleic-acid 42.5 36 0.00078 22.1 3.0 15 69-83 34-48 (64)
32 PF09297 zf-NADH-PPase: NADH p 40.6 11 0.00024 20.7 0.3 12 11-22 3-14 (32)
33 PHA02998 RNA polymerase subuni 40.2 50 0.0011 26.2 4.0 21 69-89 169-189 (195)
34 PHA02768 hypothetical protein; 38.9 9.6 0.00021 24.4 -0.1 15 69-83 3-17 (55)
35 PF00096 zf-C2H2: Zinc finger, 35.1 22 0.00048 17.3 0.9 11 72-82 1-11 (23)
36 PF10601 zf-LITAF-like: LITAF- 33.5 44 0.00096 21.2 2.4 25 9-34 5-29 (73)
37 PF15494 SRCR_2: Scavenger rec 32.8 28 0.0006 23.2 1.4 13 68-80 85-97 (98)
38 PF05876 Terminase_GpA: Phage 32.4 37 0.0008 29.7 2.4 14 69-82 227-240 (557)
39 COG4481 Uncharacterized protei 32.2 32 0.0007 22.5 1.6 17 69-85 32-48 (60)
40 PF04828 GFA: Glutathione-depe 31.6 20 0.00044 22.3 0.5 18 7-24 44-61 (92)
41 COG3634 AhpF Alkyl hydroperoxi 31.3 22 0.00047 31.5 0.8 18 3-20 327-350 (520)
42 smart00661 RPOL9 RNA polymeras 31.1 23 0.0005 20.6 0.7 12 71-82 20-31 (52)
43 PF01096 TFIIS_C: Transcriptio 30.8 40 0.00087 19.5 1.7 13 69-81 26-38 (39)
44 COG1998 RPS31 Ribosomal protei 30.2 25 0.00053 22.5 0.7 11 9-19 17-27 (51)
45 PRK00432 30S ribosomal protein 28.9 27 0.00058 21.5 0.7 10 10-19 19-28 (50)
46 PF13465 zf-H2C2_2: Zinc-finge 28.5 33 0.00073 17.9 1.0 10 72-81 15-24 (26)
47 COG1885 Uncharacterized protei 28.1 29 0.00062 25.4 0.9 13 11-23 49-61 (115)
48 PF02150 RNA_POL_M_15KD: RNA p 27.5 26 0.00055 20.0 0.4 8 73-80 22-29 (35)
49 PF00301 Rubredoxin: Rubredoxi 25.2 46 0.001 20.3 1.3 13 71-83 1-13 (47)
50 smart00440 ZnF_C2C2 C2C2 Zinc 25.0 56 0.0012 19.0 1.6 13 69-81 26-38 (40)
51 PF13912 zf-C2H2_6: C2H2-type 24.5 43 0.00093 16.9 0.9 11 72-82 2-12 (27)
52 PF14353 CpXC: CpXC protein 24.2 59 0.0013 22.5 1.9 48 13-83 3-50 (128)
53 PF14690 zf-ISL3: zinc-finger 23.6 45 0.00098 19.0 1.0 10 12-21 3-12 (47)
54 smart00355 ZnF_C2H2 zinc finge 21.8 26 0.00056 16.5 -0.2 11 72-82 1-11 (26)
55 PF11023 DUF2614: Protein of u 21.6 38 0.00082 24.8 0.5 11 11-21 69-79 (114)
56 PF08882 Acetone_carb_G: Aceto 21.6 51 0.0011 24.0 1.1 20 10-31 73-92 (112)
57 TIGR03831 YgiT_finger YgiT-typ 21.5 80 0.0017 17.5 1.8 23 74-96 1-23 (46)
58 PF13894 zf-C2H2_4: C2H2-type 21.2 51 0.0011 15.4 0.8 11 72-82 1-11 (24)
59 COG0375 HybF Zn finger protein 21.1 57 0.0012 23.6 1.3 19 7-25 82-100 (115)
60 PF06677 Auto_anti-p27: Sjogre 21.0 45 0.00097 19.9 0.6 9 9-17 32-40 (41)
61 PF12171 zf-C2H2_jaz: Zinc-fin 21.0 48 0.001 17.1 0.7 9 12-20 2-10 (27)
62 smart00714 LITAF Possible memb 20.3 52 0.0011 20.6 0.9 17 4-20 45-61 (67)
63 PF03716 WCCH: WCCH motif ; I 20.3 49 0.0011 17.9 0.6 10 12-21 6-15 (25)
64 PF04606 Ogr_Delta: Ogr/Delta- 20.0 49 0.0011 19.6 0.7 14 69-82 23-38 (47)
No 1
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=100.00 E-value=1e-52 Score=292.06 Aligned_cols=91 Identities=43% Similarity=0.690 Sum_probs=89.9
Q ss_pred cccCceeeecCcCCCCccceEEEEeecCccccccccceeeeeeccCCCCcccccccccccccceeEEEEEecccccccee
Q psy6045 4 VNVPKQRRTFCKKCKIHKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAKTTKKIVLRMECTECKYRKQL 83 (105)
Q Consensus 4 m~iPK~~~tyCp~C~kHt~HkV~qyKkGK~s~~aqG~Rry~Rkq~GygGq~kpv~~k~aK~TKKi~Lrl~C~eC~~~~~~ 83 (105)
||||++++||||+|++||+|+||||++|++|++|||+|||||+|+|||||++|||+ +|||||||||+|+|++|++++++
T Consensus 1 m~~PK~~~tyCp~CkkHt~HkV~qyKkGK~s~~a~G~Rry~Rkq~GygGq~kpv~~-~aK~TKKi~Lr~~C~~C~~~~~~ 79 (92)
T PRK05767 1 MKMPKKIRTYCPYCKTHTEHEVEKVKKGKRSELKWGQRQYRRKTIGYGGKFSPVPG-GAKPTKKVDLRYRCTECGKAHTR 79 (92)
T ss_pred CCCCccccccCcCCCCcccEEEEEEecCCcChhHHhhhHHHhhccccCCcCCcccC-CCccceeEEEEEEecccChhhcc
Confidence 89999999999999999999999999999999999999999999999999999998 99999999999999999999999
Q ss_pred cceeeeeeEecc
Q psy6045 84 PLKRCKHFELGG 95 (105)
Q Consensus 84 ~~~R~KkfElg~ 95 (105)
+++||++|||++
T Consensus 80 ~~~R~k~fEl~e 91 (92)
T PRK05767 80 EGFRAKKFELVE 91 (92)
T ss_pred ccceeeeEEEec
Confidence 999999999985
No 2
>KOG3464|consensus
Probab=100.00 E-value=4.4e-52 Score=293.40 Aligned_cols=102 Identities=75% Similarity=1.209 Sum_probs=100.1
Q ss_pred ccccCceeeecCcCCCCccceEEEEeecCccccccccceeeeeeccCCCCcccccccccccccceeEEEEEecc--cccc
Q psy6045 3 HVNVPKQRRTFCKKCKIHKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAKTTKKIVLRMECTE--CKYR 80 (105)
Q Consensus 3 mm~iPK~~~tyCp~C~kHt~HkV~qyKkGK~s~~aqG~Rry~Rkq~GygGq~kpv~~k~aK~TKKi~Lrl~C~e--C~~~ 80 (105)
|||||++++|||++|++|+.|+|+||++|++|++|||.|||||+|+||||||+|||+++|||||||||||||.| |.+.
T Consensus 1 mvnvpkT~~tfc~kc~kh~~hkVtq~k~gk~s~~aQgkr~YdrkqsGygGQTKpIf~KkaKtTKKiVlrLec~e~~Cksk 80 (106)
T KOG3464|consen 1 MVNVPKTRKTFCKKCGKHTAHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRLECCEPKCKSK 80 (106)
T ss_pred CCccCCCCcchhhhhcccchhhhhhhhhcccchHhhcCcccccccCCCCccccHHHHHHhhhhhhheeeeeeecccccch
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999664 9999
Q ss_pred ceecceeeeeeEeccceeccCccc
Q psy6045 81 KQLPLKRCKHFELGGDKKRKVQTK 104 (105)
Q Consensus 81 ~~~~~~R~KkfElg~~kk~~~~~~ 104 (105)
+|++++||+|||||||++++|++|
T Consensus 81 ~~l~iKrcKhfelGg~kk~kg~~i 104 (106)
T KOG3464|consen 81 RQLAIKRCKHFELGGDKKRKGQAI 104 (106)
T ss_pred hhhhhhhhceeeecCccccccccc
Confidence 999999999999999999999998
No 3
>PTZ00157 60S ribosomal protein L36a; Provisional
Probab=100.00 E-value=3.5e-49 Score=270.64 Aligned_cols=84 Identities=71% Similarity=1.147 Sum_probs=82.4
Q ss_pred ccccCceeeecCcCCCCccceEEEEeecCccccccccceeeeeeccCCCCcccccccccccccceeEEEEEeccccccce
Q psy6045 3 HVNVPKQRRTFCKKCKIHKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAKTTKKIVLRMECTECKYRKQ 82 (105)
Q Consensus 3 mm~iPK~~~tyCp~C~kHt~HkV~qyKkGK~s~~aqG~Rry~Rkq~GygGq~kpv~~k~aK~TKKi~Lrl~C~eC~~~~~ 82 (105)
|||||++++||||+|++||+|+||||++|++|++|||+|||||+|+|||||++|||+++|||||||||+|+|++|+++++
T Consensus 1 mv~~PK~~~tyC~~C~kHt~HkV~qyKkGK~s~~aqG~Rry~Rkq~GygGq~kpv~~~kaK~TKKi~Lrl~C~~C~~~~~ 80 (84)
T PTZ00157 1 MVNVPKNRKTYCKKCGKHTSHKVSQYKKGKESLFAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLKLECTKCKSKRQ 80 (84)
T ss_pred CCcccccccccCcCCCCCccEEEEEeccCCcChhHHhhhhhhhhccCcCCcCccccCccccccceeEEEEEecccCceeE
Confidence 99999999999999999999999999999999999999999999999999999999989999999999999999999999
Q ss_pred ecce
Q psy6045 83 LPLK 86 (105)
Q Consensus 83 ~~~~ 86 (105)
.+++
T Consensus 81 ~~~k 84 (84)
T PTZ00157 81 KVLK 84 (84)
T ss_pred eccC
Confidence 8874
No 4
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.8e-49 Score=272.65 Aligned_cols=93 Identities=51% Similarity=0.869 Sum_probs=90.9
Q ss_pred cccCceeeecCcCCCCccceEEEEeecCccccccccceeeeeeccCCCCcccccccccccccceeEEEEEecccccccee
Q psy6045 4 VNVPKQRRTFCKKCKIHKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAKTTKKIVLRMECTECKYRKQL 83 (105)
Q Consensus 4 m~iPK~~~tyCp~C~kHt~HkV~qyKkGK~s~~aqG~Rry~Rkq~GygGq~kpv~~k~aK~TKKi~Lrl~C~eC~~~~~~ 83 (105)
|||||+++||||+|++||.|+||+|++|++|+|+||+|||+|+|+|||||++|+|.++|||||||||+|+|++||++|++
T Consensus 1 mkiPK~~~tyCp~CkkhT~H~V~~~kkgk~s~l~~gqRr~~R~~~GyGg~~rp~p~g~~KptKKv~Lr~~Ct~Cgkah~~ 80 (94)
T COG1631 1 MKIPKKRRTYCPYCKKHTIHKVERVKKGKASELAWGQRRYRRKQSGYGGQPRPVPKGKAKPTKKVDLRLRCTECGKAHQR 80 (94)
T ss_pred CCCCcceeecCcccccceeeeeeehhcCCcchhhHHHHHHHHHhcccCCcCCcccCccCCccceEEEEEEehhhcccccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred -cceeeeeeEeccc
Q psy6045 84 -PLKRCKHFELGGD 96 (105)
Q Consensus 84 -~~~R~KkfElg~~ 96 (105)
+++|+++|||+++
T Consensus 81 ~~~~Rakr~Elve~ 94 (94)
T COG1631 81 TPGFRAKRFELVEE 94 (94)
T ss_pred CcceeeeeEEEecC
Confidence 5999999999864
No 5
>PF00935 Ribosomal_L44: Ribosomal protein L44; InterPro: IPR000552 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of mammalian [], Trypanosoma brucei, Caenorhabditis elegans and fungal L44, and Haloarcula marismortui LA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_r 1S1I_Z 3O5H_f 3O58_f 3IZR_r 1M1K_4 3CCQ_3 3CCL_3 3CME_3 1K73_4 ....
Probab=100.00 E-value=8e-42 Score=230.84 Aligned_cols=77 Identities=69% Similarity=1.052 Sum_probs=62.1
Q ss_pred CccceEEEEeecCccccccccceeeeeeccCCCCcccccccccccccceeEEEEEeccccccceecceeeeeeEecc
Q psy6045 19 IHKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAKTTKKIVLRMECTECKYRKQLPLKRCKHFELGG 95 (105)
Q Consensus 19 kHt~HkV~qyKkGK~s~~aqG~Rry~Rkq~GygGq~kpv~~k~aK~TKKi~Lrl~C~eC~~~~~~~~~R~KkfElg~ 95 (105)
+||+|+|+||++|++|++|||+|||||+|+|||||++|+|+++|||||||||+|+|++|+++++++++||++|||+.
T Consensus 1 kHt~HkV~~yKkgK~s~~a~G~Rry~Rk~~GygGq~kp~~~~kaK~TKKi~Lrl~C~~C~~~~~~~~~R~kkfEl~E 77 (77)
T PF00935_consen 1 KHTEHKVSQYKKGKASPLAQGKRRYDRKQKGYGGQTKPVFRKKAKTTKKIVLRLECTECGKAHMRPGKRCKKFELVE 77 (77)
T ss_dssp EEEEEEEEE---S--SSTSHHHHHHHHTSSSSSSCCSSS-S----SSEBBEEEEEETTTS-EEEEE-BBESS-EEC-
T ss_pred CCcceEEEEeccCCcChHHHhhhhhhhhccccCCccccccccCCcccccEEEEEEeCCCCcccccccceeEEEEecC
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999973
No 6
>PRK00504 rpmG 50S ribosomal protein L33; Validated
Probab=96.07 E-value=0.0033 Score=39.55 Aligned_cols=16 Identities=38% Similarity=1.045 Sum_probs=14.4
Q ss_pred eeeecCcCCCCccceE
Q psy6045 9 QRRTFCKKCKIHKVHK 24 (105)
Q Consensus 9 ~~~tyCp~C~kHt~Hk 24 (105)
..+-|||.|++||.|+
T Consensus 32 elkKycp~c~khtlhk 47 (50)
T PRK00504 32 ELKKFCPRCNKHTLHK 47 (50)
T ss_pred EEECcCCCCCCeEeee
Confidence 4678999999999997
No 7
>CHL00104 rpl33 ribosomal protein L33
Probab=95.70 E-value=0.0056 Score=40.53 Aligned_cols=17 Identities=35% Similarity=0.821 Sum_probs=14.7
Q ss_pred eeeecCcCCCCccceEE
Q psy6045 9 QRRTFCKKCKIHKVHKV 25 (105)
Q Consensus 9 ~~~tyCp~C~kHt~HkV 25 (105)
+.+-|||.|++||.|+=
T Consensus 47 elkKycp~c~kHtlhkE 63 (66)
T CHL00104 47 ELKKFCPYCYKHTIHKE 63 (66)
T ss_pred EEECcCCCCCCEeeEee
Confidence 46789999999999974
No 8
>TIGR01023 rpmG_bact ribosomal protein L33, bacterial type. This model describes bacterial ribosomal protein L33 and its chloroplast and mitochondrial equivalents.
Probab=95.47 E-value=0.008 Score=38.18 Aligned_cols=17 Identities=35% Similarity=0.864 Sum_probs=14.9
Q ss_pred eeeecCcCCCCccceEE
Q psy6045 9 QRRTFCKKCKIHKVHKV 25 (105)
Q Consensus 9 ~~~tyCp~C~kHt~HkV 25 (105)
..+-|||.|++|+.|+-
T Consensus 36 ~lkKycp~~~khtlhkE 52 (54)
T TIGR01023 36 ELRKYCPVCRKHVLHKE 52 (54)
T ss_pred EEECcCCCCCCeEeEEe
Confidence 46789999999999974
No 9
>COG0267 RpmG Ribosomal protein L33 [Translation, ribosomal structure and biogenesis]
Probab=95.45 E-value=0.0075 Score=38.15 Aligned_cols=17 Identities=29% Similarity=0.860 Sum_probs=14.7
Q ss_pred eeeecCcCCCCccceEE
Q psy6045 9 QRRTFCKKCKIHKVHKV 25 (105)
Q Consensus 9 ~~~tyCp~C~kHt~HkV 25 (105)
+.+-|||.|++||.|+=
T Consensus 32 elkKycp~~~khtlhkE 48 (50)
T COG0267 32 ELKKYCPVCRKHTLHKE 48 (50)
T ss_pred EEEecCcccccEEEEee
Confidence 46789999999999973
No 10
>PF00471 Ribosomal_L33: Ribosomal protein L33; InterPro: IPR001705 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 L33 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L33 has been shown to be on the surface of 50S subunit. L33 belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , ], groups: Eubacterial L33. Algal and plant chloroplast L33. Cyanelle L33. L33 is a small protein of 49 to 66 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3PIO_1 3PIP_1 3PYT_3 3MS1_3 3F1F_6 3F1H_6 3MRZ_3 3PYO_3 3D5B_6 3D5D_6 ....
Probab=95.43 E-value=0.0074 Score=37.45 Aligned_cols=16 Identities=31% Similarity=1.045 Sum_probs=14.2
Q ss_pred eeeecCcCCCCccceE
Q psy6045 9 QRRTFCKKCKIHKVHK 24 (105)
Q Consensus 9 ~~~tyCp~C~kHt~Hk 24 (105)
..+-|||.|++||.|+
T Consensus 30 ~lkKycp~~~khtlhk 45 (48)
T PF00471_consen 30 ELKKYCPRCRKHTLHK 45 (48)
T ss_dssp EEEEEETSSSSEEEEE
T ss_pred eEeccCCCCCCEecEE
Confidence 4678999999999996
No 11
>PRK00595 rpmG 50S ribosomal protein L33; Validated
Probab=95.40 E-value=0.0086 Score=37.80 Aligned_cols=17 Identities=18% Similarity=0.284 Sum_probs=14.7
Q ss_pred eeeecCcCCCCccceEE
Q psy6045 9 QRRTFCKKCKIHKVHKV 25 (105)
Q Consensus 9 ~~~tyCp~C~kHt~HkV 25 (105)
..+-|||.|++|+.|+-
T Consensus 35 ~lkKycp~~~khtlhkE 51 (53)
T PRK00595 35 ELKKYDPVLRKHVLHKE 51 (53)
T ss_pred EEECcCCCCCCEEeEEe
Confidence 45789999999999974
No 12
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=89.97 E-value=0.2 Score=33.65 Aligned_cols=23 Identities=22% Similarity=0.498 Sum_probs=10.9
Q ss_pred CceeeecCcCCCCccceEEEEee
Q psy6045 7 PKQRRTFCKKCKIHKVHKVTQYK 29 (105)
Q Consensus 7 PK~~~tyCp~C~kHt~HkV~qyK 29 (105)
+..-+-|||+|+.+|..+|+-+=
T Consensus 20 ~~~~k~FCp~CGn~TL~rvsvsv 42 (73)
T PF08772_consen 20 KDMTKQFCPKCGNATLKRVSVSV 42 (73)
T ss_dssp S-SS--S-SSS--S--EEEE-B-
T ss_pred CCCCceeCcccCCCcceEEEEEE
Confidence 34557899999999999998764
No 13
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=74.84 E-value=2.6 Score=30.28 Aligned_cols=19 Identities=26% Similarity=0.590 Sum_probs=14.8
Q ss_pred EEEEeccccccceecceee
Q psy6045 70 LRMECTECKYRKQLPLKRC 88 (105)
Q Consensus 70 Lrl~C~eC~~~~~~~~~R~ 88 (105)
|..+|.+||...--+..|.
T Consensus 81 v~vtC~~CG~~~R~p~~r~ 99 (105)
T COG2023 81 VVVTCLECGTIRRYPYGRE 99 (105)
T ss_pred EEEEecCCCcEEEeccccc
Confidence 8889999999866666543
No 14
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=74.67 E-value=2.2 Score=27.63 Aligned_cols=19 Identities=37% Similarity=0.698 Sum_probs=15.8
Q ss_pred eecCcCCCCccceEEEEee
Q psy6045 11 RTFCKKCKIHKVHKVTQYK 29 (105)
Q Consensus 11 ~tyCp~C~kHt~HkV~qyK 29 (105)
--|||+|+.-+.-.|.+.+
T Consensus 28 PlyCpKCK~EtlI~v~~~~ 46 (55)
T PF14205_consen 28 PLYCPKCKQETLIDVKQLK 46 (55)
T ss_pred cccCCCCCceEEEEeeccE
Confidence 3799999999988887754
No 15
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=72.46 E-value=1.5 Score=34.73 Aligned_cols=21 Identities=19% Similarity=0.309 Sum_probs=16.0
Q ss_pred ceeeecCcCCC-CccceEEEEe
Q psy6045 8 KQRRTFCKKCK-IHKVHKVTQY 28 (105)
Q Consensus 8 K~~~tyCp~C~-kHt~HkV~qy 28 (105)
..+..+||.|+ .-++|+|-.-
T Consensus 3 ~~iy~~Cp~Cg~eev~hEVik~ 24 (201)
T COG1326 3 EEIYIECPSCGSEEVSHEVIKE 24 (201)
T ss_pred ceEEEECCCCCcchhhHHHHHh
Confidence 35678999999 5777888654
No 16
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=68.92 E-value=8.2 Score=24.68 Aligned_cols=14 Identities=50% Similarity=1.009 Sum_probs=8.2
Q ss_pred CceeeecCcCCCCc
Q psy6045 7 PKQRRTFCKKCKIH 20 (105)
Q Consensus 7 PK~~~tyCp~C~kH 20 (105)
|...+++|++|+..
T Consensus 42 ~~~kr~~Ck~C~~~ 55 (85)
T PF04032_consen 42 PEIKRTICKKCGSL 55 (85)
T ss_dssp TTCCCTB-TTT--B
T ss_pred hHHhcccccCCCCE
Confidence 44567999999983
No 17
>PRK03954 ribonuclease P protein component 4; Validated
Probab=68.64 E-value=3.1 Score=30.25 Aligned_cols=22 Identities=23% Similarity=0.395 Sum_probs=16.8
Q ss_pred EEEEEeccccccceecceeeee
Q psy6045 69 VLRMECTECKYRKQLPLKRCKH 90 (105)
Q Consensus 69 ~Lrl~C~eC~~~~~~~~~R~Kk 90 (105)
.|.++|.+||...-.|..+-++
T Consensus 91 ~vvitCl~CG~~kR~P~~~~~k 112 (121)
T PRK03954 91 HVVITCLECGHIMRYPYLREVK 112 (121)
T ss_pred eEEEECccCCCEEeeccchhhh
Confidence 5789999999987666665554
No 18
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=63.04 E-value=8.3 Score=22.49 Aligned_cols=29 Identities=24% Similarity=0.523 Sum_probs=17.6
Q ss_pred eeeecCcCCCCccceEEEEeecCccccccccceeee
Q psy6045 9 QRRTFCKKCKIHKVHKVTQYKKSKERKACQGRRRYD 44 (105)
Q Consensus 9 ~~~tyCp~C~kHt~HkV~qyKkGK~s~~aqG~Rry~ 44 (105)
++.-.||+|..... -||.|+.+. |.+||+
T Consensus 3 ~i~v~CP~C~s~~~----v~k~G~~~~---G~qryr 31 (36)
T PF03811_consen 3 KIDVHCPRCQSTEG----VKKNGKSPS---GHQRYR 31 (36)
T ss_pred cEeeeCCCCCCCCc----ceeCCCCCC---CCEeEe
Confidence 34578999987641 356676543 445553
No 19
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.96 E-value=9.3 Score=30.31 Aligned_cols=50 Identities=24% Similarity=0.564 Sum_probs=36.0
Q ss_pred ecCcCCCCccceEEEEeecCccccccccceeeeeeccCCCCcccccccccccccceeEEEEEeccccccceecc-eeee
Q psy6045 12 TFCKKCKIHKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAKTTKKIVLRMECTECKYRKQLPL-KRCK 89 (105)
Q Consensus 12 tyCp~C~kHt~HkV~qyKkGK~s~~aqG~Rry~Rkq~GygGq~kpv~~k~aK~TKKi~Lrl~C~eC~~~~~~~~-~R~K 89 (105)
-.|+.|+.-+...-| |+-+..|||++ =-+.|.|+|+.|.+.+..++ -|+.
T Consensus 18 k~C~~Cg~kr~f~cS----g~fRvNAq~K~------------------------LDvWlIYkC~~Cd~tWN~~IfeR~~ 68 (203)
T COG4332 18 KRCNSCGVKRAFTCS----GKFRVNAQGKV------------------------LDVWLIYKCTHCDYTWNISIFERLN 68 (203)
T ss_pred hhCcccCCcceeeec----CcEEEcCCCcE------------------------EEEEEEEEeeccCCccchhhhhccC
Confidence 469999887766543 66666666651 13589999999999999877 3443
No 20
>KOG2463|consensus
Probab=60.49 E-value=10 Score=32.50 Aligned_cols=59 Identities=20% Similarity=0.367 Sum_probs=33.2
Q ss_pred eecCcCCCCccceEEEEeecCccccccccceeeeeeccCCCCcccccccccccccceeEEE
Q psy6045 11 RTFCKKCKIHKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAKTTKKIVLR 71 (105)
Q Consensus 11 ~tyCp~C~kHt~HkV~qyKkGK~s~~aqG~Rry~Rkq~GygGq~kpv~~k~aK~TKKi~Lr 71 (105)
+-|||.|+--|.|+|+--=......-+.=+-|+.+...|+- ..=|.| ++.|.++-..|+
T Consensus 257 k~FCp~CG~~TL~K~aVsv~~dG~~~~h~k~r~~~n~RG~~-YSlp~P-kGgk~~kN~~Lr 315 (376)
T KOG2463|consen 257 KDFCPSCGHKTLTKCAVSVDEDGNGQTHFKKRFQWNNRGLQ-YSLPKP-KGGKVAKNPILR 315 (376)
T ss_pred hhcccccCCCeeeEEEEEecCCCceeEEeecccccccCcce-eecCCC-CCCccccCcccc
Confidence 67999999999999875432221222222223333444441 112555 357777777765
No 21
>KOG3507|consensus
Probab=60.48 E-value=2.3 Score=28.11 Aligned_cols=21 Identities=43% Similarity=0.781 Sum_probs=10.6
Q ss_pred EEeccccccce--ecceeeeeeE
Q psy6045 72 MECTECKYRKQ--LPLKRCKHFE 92 (105)
Q Consensus 72 l~C~eC~~~~~--~~~~R~KkfE 92 (105)
++|.|||+.++ ...+|...||
T Consensus 38 irCReCG~RIlyKkRtkrlvqfe 60 (62)
T KOG3507|consen 38 IRCRECGYRILYKKRTKRLVQFE 60 (62)
T ss_pred EehhhcchHHHHHHHHhhhheee
Confidence 45556666555 2334444554
No 22
>KOG1597|consensus
Probab=60.26 E-value=5.6 Score=33.33 Aligned_cols=22 Identities=23% Similarity=0.374 Sum_probs=19.7
Q ss_pred cCcCCCCccceEEEEeecCccc
Q psy6045 13 FCKKCKIHKVHKVTQYKKSKER 34 (105)
Q Consensus 13 yCp~C~kHt~HkV~qyKkGK~s 34 (105)
+|+.|+.|+++-|+.|..|-.-
T Consensus 2 ~c~~C~~~~~~~V~d~~~gdtv 23 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAGDTV 23 (308)
T ss_pred CCCCCCCCCCCeeeeccCCcee
Confidence 6999999999999999999543
No 23
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=58.19 E-value=5.5 Score=23.02 Aligned_cols=14 Identities=21% Similarity=0.636 Sum_probs=6.1
Q ss_pred cCcCCCCccceEEE
Q psy6045 13 FCKKCKIHKVHKVT 26 (105)
Q Consensus 13 yCp~C~kHt~HkV~ 26 (105)
|||.|+...++.|-
T Consensus 2 fC~~CG~~l~~~ip 15 (34)
T PF14803_consen 2 FCPQCGGPLERRIP 15 (34)
T ss_dssp B-TTT--B-EEE--
T ss_pred ccccccChhhhhcC
Confidence 88888887766553
No 24
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=51.04 E-value=12 Score=24.30 Aligned_cols=17 Identities=24% Similarity=0.630 Sum_probs=14.9
Q ss_pred EEEEEeccccccceecc
Q psy6045 69 VLRMECTECKYRKQLPL 85 (105)
Q Consensus 69 ~Lrl~C~eC~~~~~~~~ 85 (105)
+++++|..||...|.+-
T Consensus 29 DikikC~gCg~~imlpR 45 (57)
T PF06107_consen 29 DIKIKCLGCGRQIMLPR 45 (57)
T ss_pred cEEEEECCCCCEEEEeH
Confidence 89999999999988653
No 25
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=51.04 E-value=32 Score=26.43 Aligned_cols=57 Identities=21% Similarity=0.355 Sum_probs=33.3
Q ss_pred eecCcCCCCccceEEEEeecCccccccccceeeeeeccCCCCcccccccccccccceeEEEEEeccccccceec
Q psy6045 11 RTFCKKCKIHKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAKTTKKIVLRMECTECKYRKQLP 84 (105)
Q Consensus 11 ~tyCp~C~kHt~HkV~qyKkGK~s~~aqG~Rry~Rkq~GygGq~kpv~~k~aK~TKKi~Lrl~C~eC~~~~~~~ 84 (105)
..-||-|++. .+++.++.|.-+.. ++-+| +.|.+. ...| =.-..-.|..||++-+-.
T Consensus 5 ~~~CPvC~~~--F~~~~vrs~~~r~~---~~d~D---------~~~~Y~-~vnP--~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 5 KITCPVCGKE--FKTKKVRSGKIRVI---RRDSD---------FCPRYK-GVNP--LFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred ceECCCCCCe--eeeeEEEcCCceEe---eecCC---------CccccC-CCCC--eeeeEEECCCCCCccccc
Confidence 4569999875 55667776665543 22222 333332 1222 124566899999997754
No 26
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=50.26 E-value=11 Score=27.92 Aligned_cols=22 Identities=23% Similarity=0.668 Sum_probs=18.0
Q ss_pred eEEEEEeccccccceecc-eeee
Q psy6045 68 IVLRMECTECKYRKQLPL-KRCK 89 (105)
Q Consensus 68 i~Lrl~C~eC~~~~~~~~-~R~K 89 (105)
|.|.|+|+.|++.+..++ -|+.
T Consensus 10 VWLIYrC~~C~~TwN~ti~eR~~ 32 (142)
T PF06353_consen 10 VWLIYRCEKCDYTWNMTIFERVN 32 (142)
T ss_pred EEEEEEcccCcCccccceEeecC
Confidence 679999999999998877 4443
No 27
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=48.82 E-value=9.1 Score=20.15 Aligned_cols=9 Identities=22% Similarity=0.914 Sum_probs=5.8
Q ss_pred cCcCCCCcc
Q psy6045 13 FCKKCKIHK 21 (105)
Q Consensus 13 yCp~C~kHt 21 (105)
|||+|+..-
T Consensus 1 ~Cp~CG~~~ 9 (23)
T PF13240_consen 1 YCPNCGAEI 9 (23)
T ss_pred CCcccCCCC
Confidence 677777643
No 28
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=47.33 E-value=16 Score=22.03 Aligned_cols=22 Identities=32% Similarity=0.581 Sum_probs=14.6
Q ss_pred EEEecccccccee--cceeeeeeE
Q psy6045 71 RMECTECKYRKQL--PLKRCKHFE 92 (105)
Q Consensus 71 rl~C~eC~~~~~~--~~~R~KkfE 92 (105)
-.+|.+||+..+. ...+.+.|+
T Consensus 19 ~irC~~CG~rIlyK~R~~~~~~~~ 42 (44)
T smart00659 19 VVRCRECGYRILYKKRTKRLVEVK 42 (44)
T ss_pred ceECCCCCceEEEEeCCCceEEEE
Confidence 4789999998773 234555554
No 29
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=46.37 E-value=7.1 Score=20.79 Aligned_cols=9 Identities=33% Similarity=1.028 Sum_probs=6.7
Q ss_pred eecCcCCCC
Q psy6045 11 RTFCKKCKI 19 (105)
Q Consensus 11 ~tyCp~C~k 19 (105)
-.|||+|+.
T Consensus 16 ~~fC~~CG~ 24 (26)
T PF13248_consen 16 AKFCPNCGA 24 (26)
T ss_pred cccChhhCC
Confidence 478888875
No 30
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.83 E-value=16 Score=26.46 Aligned_cols=14 Identities=29% Similarity=0.501 Sum_probs=9.7
Q ss_pred ecCcCCCCccceEE
Q psy6045 12 TFCKKCKIHKVHKV 25 (105)
Q Consensus 12 tyCp~C~kHt~HkV 25 (105)
..||.|+.+..+-+
T Consensus 108 ~~CP~Cgs~~~~i~ 121 (135)
T PRK03824 108 LKCPKCGSRDFEIV 121 (135)
T ss_pred cCCcCCCCCCcEEe
Confidence 34999998765443
No 31
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=42.45 E-value=36 Score=22.15 Aligned_cols=15 Identities=27% Similarity=0.709 Sum_probs=11.1
Q ss_pred EEEEEecccccccee
Q psy6045 69 VLRMECTECKYRKQL 83 (105)
Q Consensus 69 ~Lrl~C~eC~~~~~~ 83 (105)
-.-..|+.||+.-+-
T Consensus 34 f~~v~C~~CGYTE~Y 48 (64)
T PF09855_consen 34 FTTVSCTNCGYTEFY 48 (64)
T ss_pred EEEEECCCCCCEEEE
Confidence 445689999998654
No 32
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=40.55 E-value=11 Score=20.70 Aligned_cols=12 Identities=25% Similarity=0.761 Sum_probs=6.4
Q ss_pred eecCcCCCCccc
Q psy6045 11 RTFCKKCKIHKV 22 (105)
Q Consensus 11 ~tyCp~C~kHt~ 22 (105)
..||+.|+..|.
T Consensus 3 ~rfC~~CG~~t~ 14 (32)
T PF09297_consen 3 HRFCGRCGAPTK 14 (32)
T ss_dssp TSB-TTT--BEE
T ss_pred CcccCcCCcccc
Confidence 468999987654
No 33
>PHA02998 RNA polymerase subunit; Provisional
Probab=40.18 E-value=50 Score=26.18 Aligned_cols=21 Identities=33% Similarity=0.588 Sum_probs=17.5
Q ss_pred EEEEEeccccccceecceeee
Q psy6045 69 VLRMECTECKYRKQLPLKRCK 89 (105)
Q Consensus 69 ~Lrl~C~eC~~~~~~~~~R~K 89 (105)
++-|+|.+||..+..|-+|..
T Consensus 169 T~FYkC~~CG~~wkppkf~~~ 189 (195)
T PHA02998 169 LVRHACRDCKKHFKPPKFRDK 189 (195)
T ss_pred eEEEEcCCCCCccCCcccccc
Confidence 578999999999888877754
No 34
>PHA02768 hypothetical protein; Provisional
Probab=38.88 E-value=9.6 Score=24.38 Aligned_cols=15 Identities=27% Similarity=0.363 Sum_probs=11.6
Q ss_pred EEEEEecccccccee
Q psy6045 69 VLRMECTECKYRKQL 83 (105)
Q Consensus 69 ~Lrl~C~eC~~~~~~ 83 (105)
.|-|+|.+||+....
T Consensus 3 ~~~y~C~~CGK~Fs~ 17 (55)
T PHA02768 3 LLGYECPICGEIYIK 17 (55)
T ss_pred ccccCcchhCCeecc
Confidence 467899999987653
No 35
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=35.13 E-value=22 Score=17.35 Aligned_cols=11 Identities=18% Similarity=0.452 Sum_probs=8.9
Q ss_pred EEeccccccce
Q psy6045 72 MECTECKYRKQ 82 (105)
Q Consensus 72 l~C~eC~~~~~ 82 (105)
|+|.+|++...
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 68999998754
No 36
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=33.45 E-value=44 Score=21.19 Aligned_cols=25 Identities=24% Similarity=0.534 Sum_probs=17.4
Q ss_pred eeeecCcCCCCccceEEEEeecCccc
Q psy6045 9 QRRTFCKKCKIHKVHKVTQYKKSKER 34 (105)
Q Consensus 9 ~~~tyCp~C~kHt~HkV~qyKkGK~s 34 (105)
-...+||.|+....-.|+ ++.|...
T Consensus 5 p~~~~CP~C~~~~~T~v~-~~~g~~t 29 (73)
T PF10601_consen 5 PVRIYCPYCQQQVQTRVE-YKSGTMT 29 (73)
T ss_pred ceeeECCCCCCEEEEEEE-EEeChHH
Confidence 456899999988776664 4456544
No 37
>PF15494 SRCR_2: Scavenger receptor cysteine-rich domain
Probab=32.78 E-value=28 Score=23.20 Aligned_cols=13 Identities=31% Similarity=0.933 Sum_probs=10.7
Q ss_pred eEEEEEecccccc
Q psy6045 68 IVLRMECTECKYR 80 (105)
Q Consensus 68 i~Lrl~C~eC~~~ 80 (105)
-++-|+|++||..
T Consensus 85 ~vVsL~C~~CG~r 97 (98)
T PF15494_consen 85 SVVSLQCSDCGKR 97 (98)
T ss_pred CEEEEECcccCCc
Confidence 3788999999975
No 38
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=32.44 E-value=37 Score=29.74 Aligned_cols=14 Identities=21% Similarity=0.555 Sum_probs=11.9
Q ss_pred EEEEEeccccccce
Q psy6045 69 VLRMECTECKYRKQ 82 (105)
Q Consensus 69 ~Lrl~C~eC~~~~~ 82 (105)
..+|.|..||..+.
T Consensus 227 ~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 227 TARYVCPHCGCEIE 240 (557)
T ss_pred ceEEECCCCcCCCC
Confidence 67999999998765
No 39
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.23 E-value=32 Score=22.52 Aligned_cols=17 Identities=18% Similarity=0.630 Sum_probs=15.0
Q ss_pred EEEEEeccccccceecc
Q psy6045 69 VLRMECTECKYRKQLPL 85 (105)
Q Consensus 69 ~Lrl~C~eC~~~~~~~~ 85 (105)
+++..|+.|+...|.+-
T Consensus 32 DIkikC~nC~h~vm~pR 48 (60)
T COG4481 32 DIKIKCENCGHSVMMPR 48 (60)
T ss_pred cEEEEecCCCcEEEecH
Confidence 89999999999988763
No 40
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=31.59 E-value=20 Score=22.29 Aligned_cols=18 Identities=22% Similarity=0.455 Sum_probs=12.0
Q ss_pred CceeeecCcCCCCccceE
Q psy6045 7 PKQRRTFCKKCKIHKVHK 24 (105)
Q Consensus 7 PK~~~tyCp~C~kHt~Hk 24 (105)
+...+.||+.|+.+--..
T Consensus 44 ~~~~r~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 44 KGVERYFCPTCGSPLFSE 61 (92)
T ss_dssp SSCEEEEETTT--EEEEE
T ss_pred CcCcCcccCCCCCeeecc
Confidence 445679999999987654
No 41
>COG3634 AhpF Alkyl hydroperoxide reductase, large subunit [Posttranslational modification, protein turnover, chaperones]
Probab=31.29 E-value=22 Score=31.46 Aligned_cols=18 Identities=28% Similarity=0.719 Sum_probs=13.2
Q ss_pred ccccCce------eeecCcCCCCc
Q psy6045 3 HVNVPKQ------RRTFCKKCKIH 20 (105)
Q Consensus 3 mm~iPK~------~~tyCp~C~kH 20 (105)
-||||-+ -.+|||+|+-.
T Consensus 327 n~nvPGE~e~rnKGVayCPHCDGP 350 (520)
T COG3634 327 NMNVPGEDEYRNKGVAYCPHCDGP 350 (520)
T ss_pred cCCCCchHHHhhCCeeeCCCCCCc
Confidence 3788854 35899999864
No 42
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=31.09 E-value=23 Score=20.63 Aligned_cols=12 Identities=33% Similarity=1.013 Sum_probs=8.9
Q ss_pred EEEeccccccce
Q psy6045 71 RMECTECKYRKQ 82 (105)
Q Consensus 71 rl~C~eC~~~~~ 82 (105)
++.|..||+..-
T Consensus 20 ~~vC~~Cg~~~~ 31 (52)
T smart00661 20 RFVCRKCGYEEP 31 (52)
T ss_pred EEECCcCCCeEE
Confidence 678888887643
No 43
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=30.83 E-value=40 Score=19.48 Aligned_cols=13 Identities=31% Similarity=0.514 Sum_probs=10.9
Q ss_pred EEEEEeccccccc
Q psy6045 69 VLRMECTECKYRK 81 (105)
Q Consensus 69 ~Lrl~C~eC~~~~ 81 (105)
.|-|.|.+||..+
T Consensus 26 T~fy~C~~C~~~w 38 (39)
T PF01096_consen 26 TLFYVCCNCGHRW 38 (39)
T ss_dssp EEEEEESSSTEEE
T ss_pred eEEEEeCCCCCee
Confidence 7889999999764
No 44
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=30.16 E-value=25 Score=22.48 Aligned_cols=11 Identities=27% Similarity=0.990 Sum_probs=8.4
Q ss_pred eeeecCcCCCC
Q psy6045 9 QRRTFCKKCKI 19 (105)
Q Consensus 9 ~~~tyCp~C~k 19 (105)
..|.+||+|+-
T Consensus 17 rk~~~CPrCG~ 27 (51)
T COG1998 17 RKNRFCPRCGP 27 (51)
T ss_pred EccccCCCCCC
Confidence 45789999973
No 45
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=28.89 E-value=27 Score=21.53 Aligned_cols=10 Identities=30% Similarity=1.075 Sum_probs=7.5
Q ss_pred eeecCcCCCC
Q psy6045 10 RRTFCKKCKI 19 (105)
Q Consensus 10 ~~tyCp~C~k 19 (105)
.+.|||.|+.
T Consensus 19 ~~~fCP~Cg~ 28 (50)
T PRK00432 19 KNKFCPRCGS 28 (50)
T ss_pred ccCcCcCCCc
Confidence 3569999974
No 46
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=28.48 E-value=33 Score=17.90 Aligned_cols=10 Identities=20% Similarity=0.491 Sum_probs=8.5
Q ss_pred EEeccccccc
Q psy6045 72 MECTECKYRK 81 (105)
Q Consensus 72 l~C~eC~~~~ 81 (105)
|+|..|++..
T Consensus 15 ~~C~~C~k~F 24 (26)
T PF13465_consen 15 YKCPYCGKSF 24 (26)
T ss_dssp EEESSSSEEE
T ss_pred CCCCCCcCee
Confidence 8999999864
No 47
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.12 E-value=29 Score=25.40 Aligned_cols=13 Identities=31% Similarity=0.381 Sum_probs=10.7
Q ss_pred eecCcCCCCccce
Q psy6045 11 RTFCKKCKIHKVH 23 (105)
Q Consensus 11 ~tyCp~C~kHt~H 23 (105)
-|-||.|+.|.+-
T Consensus 49 ~t~CP~Cg~~~e~ 61 (115)
T COG1885 49 STSCPKCGEPFES 61 (115)
T ss_pred cccCCCCCCccce
Confidence 4789999999864
No 48
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=27.48 E-value=26 Score=20.04 Aligned_cols=8 Identities=38% Similarity=1.240 Sum_probs=4.1
Q ss_pred Eecccccc
Q psy6045 73 ECTECKYR 80 (105)
Q Consensus 73 ~C~eC~~~ 80 (105)
.|..|++.
T Consensus 22 ~C~~C~Y~ 29 (35)
T PF02150_consen 22 ACRTCGYE 29 (35)
T ss_dssp EESSSS-E
T ss_pred CCCCCCCc
Confidence 56666654
No 49
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=25.16 E-value=46 Score=20.35 Aligned_cols=13 Identities=23% Similarity=0.682 Sum_probs=10.3
Q ss_pred EEEecccccccee
Q psy6045 71 RMECTECKYRKQL 83 (105)
Q Consensus 71 rl~C~eC~~~~~~ 83 (105)
||+|+.|++...-
T Consensus 1 ky~C~~CgyvYd~ 13 (47)
T PF00301_consen 1 KYQCPVCGYVYDP 13 (47)
T ss_dssp EEEETTTSBEEET
T ss_pred CcCCCCCCEEEcC
Confidence 6899999987653
No 50
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=25.02 E-value=56 Score=19.01 Aligned_cols=13 Identities=31% Similarity=0.542 Sum_probs=10.8
Q ss_pred EEEEEeccccccc
Q psy6045 69 VLRMECTECKYRK 81 (105)
Q Consensus 69 ~Lrl~C~eC~~~~ 81 (105)
.|-|.|..|+...
T Consensus 26 T~fy~C~~C~~~w 38 (40)
T smart00440 26 TVFYVCTKCGHRW 38 (40)
T ss_pred eEEEEeCCCCCEe
Confidence 6889999999754
No 51
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=24.48 E-value=43 Score=16.92 Aligned_cols=11 Identities=36% Similarity=0.767 Sum_probs=8.9
Q ss_pred EEeccccccce
Q psy6045 72 MECTECKYRKQ 82 (105)
Q Consensus 72 l~C~eC~~~~~ 82 (105)
|+|.+|+....
T Consensus 2 ~~C~~C~~~F~ 12 (27)
T PF13912_consen 2 FECDECGKTFS 12 (27)
T ss_dssp EEETTTTEEES
T ss_pred CCCCccCCccC
Confidence 78999998754
No 52
>PF14353 CpXC: CpXC protein
Probab=24.20 E-value=59 Score=22.45 Aligned_cols=48 Identities=19% Similarity=0.322 Sum_probs=28.9
Q ss_pred cCcCCCCccceEEEEeecCccccccccceeeeeeccCCCCcccccccccccccceeEEEEEecccccccee
Q psy6045 13 FCKKCKIHKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAKTTKKIVLRMECTECKYRKQL 83 (105)
Q Consensus 13 yCp~C~kHt~HkV~qyKkGK~s~~aqG~Rry~Rkq~GygGq~kpv~~k~aK~TKKi~Lrl~C~eC~~~~~~ 83 (105)
-||.|+.+..-+|...=.....+ .. +.+.-.--.+.++|..||.....
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p---------------------~l--~e~il~g~l~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDP---------------------EL--KEKILDGSLFSFTCPSCGHKFRL 50 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCH---------------------HH--HHHHHcCCcCEEECCCCCCceec
Confidence 49999998888776654332221 11 00111112678999999998764
No 53
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=23.55 E-value=45 Score=19.00 Aligned_cols=10 Identities=20% Similarity=0.534 Sum_probs=8.2
Q ss_pred ecCcCCCCcc
Q psy6045 12 TFCKKCKIHK 21 (105)
Q Consensus 12 tyCp~C~kHt 21 (105)
..||.|+..+
T Consensus 3 ~~Cp~Cg~~~ 12 (47)
T PF14690_consen 3 PRCPHCGSPS 12 (47)
T ss_pred ccCCCcCCCc
Confidence 5799999666
No 54
>smart00355 ZnF_C2H2 zinc finger.
Probab=21.84 E-value=26 Score=16.49 Aligned_cols=11 Identities=27% Similarity=0.603 Sum_probs=8.2
Q ss_pred EEeccccccce
Q psy6045 72 MECTECKYRKQ 82 (105)
Q Consensus 72 l~C~eC~~~~~ 82 (105)
++|..|++...
T Consensus 1 ~~C~~C~~~f~ 11 (26)
T smart00355 1 YRCPECGKVFK 11 (26)
T ss_pred CCCCCCcchhC
Confidence 47899987754
No 55
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=21.64 E-value=38 Score=24.76 Aligned_cols=11 Identities=18% Similarity=0.573 Sum_probs=8.6
Q ss_pred eecCcCCCCcc
Q psy6045 11 RTFCKKCKIHK 21 (105)
Q Consensus 11 ~tyCp~C~kHt 21 (105)
.--||.|+++|
T Consensus 69 ~V~CP~C~K~T 79 (114)
T PF11023_consen 69 QVECPNCGKQT 79 (114)
T ss_pred eeECCCCCChH
Confidence 34599999887
No 56
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=21.60 E-value=51 Score=24.02 Aligned_cols=20 Identities=20% Similarity=0.416 Sum_probs=13.9
Q ss_pred eeecCcCCCCccceEEEEeecC
Q psy6045 10 RRTFCKKCKIHKVHKVTQYKKS 31 (105)
Q Consensus 10 ~~tyCp~C~kHt~HkV~qyKkG 31 (105)
+--|||.|++ .|.|+-.-.|
T Consensus 73 rEyyCP~Cgt--~levE~~~Pg 92 (112)
T PF08882_consen 73 REYYCPGCGT--QLEVEAPPPG 92 (112)
T ss_pred EEEECCCCcc--eeEEccCCCC
Confidence 3469999984 6777755544
No 57
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=21.50 E-value=80 Score=17.53 Aligned_cols=23 Identities=22% Similarity=0.489 Sum_probs=16.2
Q ss_pred eccccccceecceeeeeeEeccc
Q psy6045 74 CTECKYRKQLPLKRCKHFELGGD 96 (105)
Q Consensus 74 C~eC~~~~~~~~~R~KkfElg~~ 96 (105)
|..|+...+....+.-.|++++.
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~~~ 23 (46)
T TIGR03831 1 CPICGGEELEGKTTTETYEYGGE 23 (46)
T ss_pred CCCCCCceecceEEEEEEEeCCE
Confidence 67787776666666778888654
No 58
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=21.25 E-value=51 Score=15.40 Aligned_cols=11 Identities=18% Similarity=0.561 Sum_probs=6.8
Q ss_pred EEeccccccce
Q psy6045 72 MECTECKYRKQ 82 (105)
Q Consensus 72 l~C~eC~~~~~ 82 (105)
+.|..|+....
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 57999998754
No 59
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=21.09 E-value=57 Score=23.65 Aligned_cols=19 Identities=16% Similarity=0.312 Sum_probs=13.4
Q ss_pred CceeeecCcCCCCccceEE
Q psy6045 7 PKQRRTFCKKCKIHKVHKV 25 (105)
Q Consensus 7 PK~~~tyCp~C~kHt~HkV 25 (105)
|-...-+||.|+.+..+-+
T Consensus 82 ~e~~~~~CP~C~s~~~~i~ 100 (115)
T COG0375 82 LEELDYRCPKCGSINLRII 100 (115)
T ss_pred chhheeECCCCCCCceEEe
Confidence 3445667999998886544
No 60
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=21.01 E-value=45 Score=19.94 Aligned_cols=9 Identities=22% Similarity=1.054 Sum_probs=4.4
Q ss_pred eeeecCcCC
Q psy6045 9 QRRTFCKKC 17 (105)
Q Consensus 9 ~~~tyCp~C 17 (105)
.-+.||+.|
T Consensus 32 ~g~~~Cv~C 40 (41)
T PF06677_consen 32 DGKIYCVSC 40 (41)
T ss_pred CCCEECCCC
Confidence 334555555
No 61
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=20.96 E-value=48 Score=17.11 Aligned_cols=9 Identities=22% Similarity=0.822 Sum_probs=6.9
Q ss_pred ecCcCCCCc
Q psy6045 12 TFCKKCKIH 20 (105)
Q Consensus 12 tyCp~C~kH 20 (105)
-||.-|+++
T Consensus 2 ~~C~~C~k~ 10 (27)
T PF12171_consen 2 FYCDACDKY 10 (27)
T ss_dssp CBBTTTTBB
T ss_pred CCcccCCCC
Confidence 488888875
No 62
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=20.32 E-value=52 Score=20.57 Aligned_cols=17 Identities=18% Similarity=0.542 Sum_probs=13.1
Q ss_pred cccCceeeecCcCCCCc
Q psy6045 4 VNVPKQRRTFCKKCKIH 20 (105)
Q Consensus 4 m~iPK~~~tyCp~C~kH 20 (105)
|+--+...-|||.|+..
T Consensus 45 ~~~~kd~~H~Cp~C~~~ 61 (67)
T smart00714 45 LDSFKDVNHYCPNCGAF 61 (67)
T ss_pred cccccCccEECCCCCCE
Confidence 45557788999999874
No 63
>PF03716 WCCH: WCCH motif ; InterPro: IPR005159 The WCCH motif is found in a retrotransposons and Gemini viruses. A specific function has not been associated to this motif [].
Probab=20.30 E-value=49 Score=17.89 Aligned_cols=10 Identities=40% Similarity=0.929 Sum_probs=8.1
Q ss_pred ecCcCCCCcc
Q psy6045 12 TFCKKCKIHK 21 (105)
Q Consensus 12 tyCp~C~kHt 21 (105)
=+||+|-.|.
T Consensus 6 C~cphCprHk 15 (25)
T PF03716_consen 6 CCCPHCPRHK 15 (25)
T ss_pred cCCCCCcccc
Confidence 4789999994
No 64
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=20.02 E-value=49 Score=19.65 Aligned_cols=14 Identities=29% Similarity=0.458 Sum_probs=9.8
Q ss_pred EEEEEecc--ccccce
Q psy6045 69 VLRMECTE--CKYRKQ 82 (105)
Q Consensus 69 ~Lrl~C~e--C~~~~~ 82 (105)
.|-++|+. ||....
T Consensus 23 ~~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 23 ELYCQCTNPECGHTFV 38 (47)
T ss_pred EEEEEECCCcCCCEEE
Confidence 37778877 887654
Done!