Query 034006
Match_columns 106
No_of_seqs 105 out of 213
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 08:45:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034006.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034006hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3464 60S ribosomal protein 100.0 2.5E-53 5.4E-58 300.4 -0.1 103 2-106 1-105 (106)
2 PRK05767 rpl44e 50S ribosomal 100.0 8.1E-52 1.8E-56 288.1 6.1 91 3-96 1-91 (92)
3 PTZ00157 60S ribosomal protein 100.0 2E-48 4.3E-53 267.4 5.7 84 2-87 1-84 (84)
4 COG1631 RPL42A Ribosomal prote 100.0 2.5E-47 5.5E-52 266.2 5.5 93 3-97 1-94 (94)
5 PF00935 Ribosomal_L44: Riboso 100.0 3.2E-42 6.8E-47 233.3 3.8 77 20-96 1-77 (77)
6 PRK00504 rpmG 50S ribosomal pr 94.3 0.024 5.1E-07 35.7 1.4 17 8-26 32-48 (50)
7 PF00471 Ribosomal_L33: Riboso 93.8 0.045 9.7E-07 34.0 1.8 16 8-25 30-45 (48)
8 CHL00104 rpl33 ribosomal prote 93.5 0.04 8.8E-07 36.5 1.4 17 8-26 47-63 (66)
9 TIGR01023 rpmG_bact ribosomal 93.3 0.048 1E-06 34.7 1.4 17 8-26 36-52 (54)
10 PRK00595 rpmG 50S ribosomal pr 93.1 0.052 1.1E-06 34.3 1.4 17 8-26 35-51 (53)
11 COG0267 RpmG Ribosomal protein 93.1 0.051 1.1E-06 34.5 1.3 17 8-26 32-48 (50)
12 PF08772 NOB1_Zn_bind: Nin one 79.6 1.2 2.5E-05 30.0 1.4 23 6-30 20-42 (73)
13 PF06107 DUF951: Bacterial pro 52.7 13 0.00029 24.1 2.1 16 70-85 29-44 (57)
14 PF14205 Cys_rich_KTR: Cystein 50.0 11 0.00024 24.4 1.5 18 11-30 29-46 (55)
15 PF03811 Zn_Tnp_IS1: InsA N-te 47.4 24 0.00052 20.6 2.5 29 8-45 3-31 (36)
16 smart00659 RPOLCX RNA polymera 43.3 25 0.00054 21.2 2.2 22 72-93 19-42 (44)
17 COG4481 Uncharacterized protei 42.7 21 0.00046 23.4 1.9 16 70-85 32-47 (60)
18 COG1326 Uncharacterized archae 41.8 15 0.00033 29.2 1.4 20 8-29 4-24 (201)
19 KOG3507 DNA-directed RNA polym 38.7 6.8 0.00015 26.0 -0.8 12 70-81 18-29 (62)
20 PF06353 DUF1062: Protein of u 34.2 30 0.00066 25.7 1.9 18 69-86 10-27 (142)
21 KOG1597 Transcription initiati 32.9 26 0.00057 29.5 1.5 21 12-34 2-22 (308)
22 PF01096 TFIIS_C: Transcriptio 32.5 49 0.0011 19.2 2.2 14 69-82 25-38 (39)
23 PHA02768 hypothetical protein; 31.5 16 0.00035 23.4 0.1 15 70-84 3-17 (55)
24 PF11415 Toxin_37: Antifungal 30.4 20 0.00043 21.4 0.3 12 8-19 18-29 (35)
25 PF00096 zf-C2H2: Zinc finger, 30.4 34 0.00073 16.7 1.1 11 73-83 1-11 (23)
26 smart00440 ZnF_C2C2 C2C2 Zinc 28.1 55 0.0012 19.1 1.9 14 69-82 25-38 (40)
27 PF13465 zf-H2C2_2: Zinc-finge 25.5 48 0.001 17.3 1.2 10 73-82 15-24 (26)
28 PF15494 SRCR_2: Scavenger rec 25.3 47 0.001 22.1 1.5 13 69-81 85-97 (98)
29 KOG2463 Predicted RNA-binding 24.9 76 0.0016 27.5 2.9 59 10-72 257-315 (376)
30 TIGR00416 sms DNA repair prote 22.4 48 0.001 28.4 1.3 18 72-89 7-24 (454)
31 PRK11823 DNA repair protein Ra 22.3 48 0.001 28.2 1.3 20 71-90 6-25 (446)
32 PF14803 Nudix_N_2: Nudix N-te 21.5 53 0.0011 18.9 1.0 14 12-27 2-15 (34)
33 PF09526 DUF2387: Probable met 21.4 57 0.0012 21.6 1.3 17 71-87 29-45 (71)
34 PF13912 zf-C2H2_6: C2H2-type 21.3 61 0.0013 16.4 1.1 11 73-83 2-12 (27)
35 PF00301 Rubredoxin: Rubredoxi 21.0 67 0.0015 19.7 1.4 13 72-84 1-13 (47)
36 TIGR03831 YgiT_finger YgiT-typ 20.5 1.1E+02 0.0023 17.0 2.2 23 75-97 1-23 (46)
No 1
>KOG3464 consensus 60S ribosomal protein L44 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-53 Score=300.44 Aligned_cols=103 Identities=78% Similarity=1.206 Sum_probs=100.5
Q ss_pred ccccCceeeeeccCCCCCCccceEEEEeecCccchhhccceeeeccccCCCCcccceecCCCCccceeEEEEEec--CCC
Q 034006 2 DVNVPKTKKTYCKSKECRKHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYGGQTKPVFHKKAKTTKKIVLRLQCQ--GCK 79 (106)
Q Consensus 2 mv~vPK~~~tyC~~~~C~kHt~HkVtqyKkGK~s~~aqG~Rrydrkq~GygGq~kpi~~k~aKtTKKi~Lrl~C~--~C~ 79 (106)
|||||++++||| ++|++||+|+|+||++|++|++|||+|||||+|+||||||+|||+++|||||||||||||. +|.
T Consensus 1 mvnvpkT~~tfc--~kc~kh~~hkVtq~k~gk~s~~aQgkr~YdrkqsGygGQTKpIf~KkaKtTKKiVlrLec~e~~Ck 78 (106)
T KOG3464|consen 1 MVNVPKTRKTFC--KKCGKHTAHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRLECCEPKCK 78 (106)
T ss_pred CCccCCCCcchh--hhhcccchhhhhhhhhcccchHhhcCcccccccCCCCccccHHHHHHhhhhhhheeeeeeeccccc
Confidence 899999999999 8999999999999999999999999999999999999999999999999999999999964 699
Q ss_pred ceeeecceeeeeeEEeeeeccCCccCC
Q 034006 80 HVSQHPIKRCKHFEIGGDKKGKGTSLF 106 (106)
Q Consensus 80 ~~~~~~~kR~KkfEl~~~kk~kg~~~~ 106 (106)
+++|++|+||+|||||||++++|++|+
T Consensus 79 sk~~l~iKrcKhfelGg~kk~kg~~iq 105 (106)
T KOG3464|consen 79 SKRQLAIKRCKHFELGGDKKRKGQAIQ 105 (106)
T ss_pred chhhhhhhhhceeeecCcccccccccc
Confidence 999999999999999999999999984
No 2
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=100.00 E-value=8.1e-52 Score=288.11 Aligned_cols=91 Identities=43% Similarity=0.706 Sum_probs=89.9
Q ss_pred cccCceeeeeccCCCCCCccceEEEEeecCccchhhccceeeeccccCCCCcccceecCCCCccceeEEEEEecCCCcee
Q 034006 3 VNVPKTKKTYCKSKECRKHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYGGQTKPVFHKKAKTTKKIVLRLQCQGCKHVS 82 (106)
Q Consensus 3 v~vPK~~~tyC~~~~C~kHt~HkVtqyKkGK~s~~aqG~Rrydrkq~GygGq~kpi~~k~aKtTKKi~Lrl~C~~C~~~~ 82 (106)
||||++++||| |+|++||+|+|||||+|++|++|||+|||||+|+|||||++|||+ +|||||||||+|+|++|++++
T Consensus 1 m~~PK~~~tyC--p~CkkHt~HkV~qyKkGK~s~~a~G~Rry~Rkq~GygGq~kpv~~-~aK~TKKi~Lr~~C~~C~~~~ 77 (92)
T PRK05767 1 MKMPKKIRTYC--PYCKTHTEHEVEKVKKGKRSELKWGQRQYRRKTIGYGGKFSPVPG-GAKPTKKVDLRYRCTECGKAH 77 (92)
T ss_pred CCCCccccccC--cCCCCcccEEEEEEecCCcChhHHhhhHHHhhccccCCcCCcccC-CCccceeEEEEEEecccChhh
Confidence 89999999999 999999999999999999999999999999999999999999997 999999999999999999999
Q ss_pred eecceeeeeeEEee
Q 034006 83 QHPIKRCKHFEIGG 96 (106)
Q Consensus 83 ~~~~kR~KkfEl~~ 96 (106)
+++++||++|||++
T Consensus 78 ~~~~~R~k~fEl~e 91 (92)
T PRK05767 78 TREGFRAKKFELVE 91 (92)
T ss_pred ccccceeeeEEEec
Confidence 99999999999986
No 3
>PTZ00157 60S ribosomal protein L36a; Provisional
Probab=100.00 E-value=2e-48 Score=267.44 Aligned_cols=84 Identities=75% Similarity=1.174 Sum_probs=82.4
Q ss_pred ccccCceeeeeccCCCCCCccceEEEEeecCccchhhccceeeeccccCCCCcccceecCCCCccceeEEEEEecCCCce
Q 034006 2 DVNVPKTKKTYCKSKECRKHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYGGQTKPVFHKKAKTTKKIVLRLQCQGCKHV 81 (106)
Q Consensus 2 mv~vPK~~~tyC~~~~C~kHt~HkVtqyKkGK~s~~aqG~Rrydrkq~GygGq~kpi~~k~aKtTKKi~Lrl~C~~C~~~ 81 (106)
|||||++++||| |+|++||+|+|||||+|++|++|||+|||||+|+|||||++|||+++|||||||||+|+|++|+++
T Consensus 1 mv~~PK~~~tyC--~~C~kHt~HkV~qyKkGK~s~~aqG~Rry~Rkq~GygGq~kpv~~~kaK~TKKi~Lrl~C~~C~~~ 78 (84)
T PTZ00157 1 MVNVPKNRKTYC--KKCGKHTSHKVSQYKKGKESLFAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLKLECTKCKSK 78 (84)
T ss_pred CCcccccccccC--cCCCCCccEEEEEeccCCcChhHHhhhhhhhhccCcCCcCccccCccccccceeEEEEEecccCce
Confidence 999999999999 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecce
Q 034006 82 SQHPIK 87 (106)
Q Consensus 82 ~~~~~k 87 (106)
++++++
T Consensus 79 ~~~~~k 84 (84)
T PTZ00157 79 RQKVLK 84 (84)
T ss_pred eEeccC
Confidence 999874
No 4
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-47 Score=266.17 Aligned_cols=93 Identities=54% Similarity=0.900 Sum_probs=90.9
Q ss_pred cccCceeeeeccCCCCCCccceEEEEeecCccchhhccceeeeccccCCCCcccceecCCCCccceeEEEEEecCCCcee
Q 034006 3 VNVPKTKKTYCKSKECRKHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYGGQTKPVFHKKAKTTKKIVLRLQCQGCKHVS 82 (106)
Q Consensus 3 v~vPK~~~tyC~~~~C~kHt~HkVtqyKkGK~s~~aqG~Rrydrkq~GygGq~kpi~~k~aKtTKKi~Lrl~C~~C~~~~ 82 (106)
|||||+++||| |+|++||.|+|++|++|++|++|||+|||+|+|+|||||++|+|.++||+||+|||+|+|++||++|
T Consensus 1 mkiPK~~~tyC--p~CkkhT~H~V~~~kkgk~s~l~~gqRr~~R~~~GyGg~~rp~p~g~~KptKKv~Lr~~Ct~Cgkah 78 (94)
T COG1631 1 MKIPKKRRTYC--PYCKKHTIHKVERVKKGKASELAWGQRRYRRKQSGYGGQPRPVPKGKAKPTKKVDLRLRCTECGKAH 78 (94)
T ss_pred CCCCcceeecC--cccccceeeeeeehhcCCcchhhHHHHHHHHHhcccCCcCCcccCccCCccceEEEEEEehhhcccc
Confidence 89999999999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ee-cceeeeeeEEeee
Q 034006 83 QH-PIKRCKHFEIGGD 97 (106)
Q Consensus 83 ~~-~~kR~KkfEl~~~ 97 (106)
++ +++|+++|||++.
T Consensus 79 ~~~~~~Rakr~Elve~ 94 (94)
T COG1631 79 QRTPGFRAKRFELVEE 94 (94)
T ss_pred ccCcceeeeeEEEecC
Confidence 99 5999999999874
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=3.2e-42 Score=233.29 Aligned_cols=77 Identities=73% Similarity=1.091 Sum_probs=62.2
Q ss_pred CccceEEEEeecCccchhhccceeeeccccCCCCcccceecCCCCccceeEEEEEecCCCceeeecceeeeeeEEee
Q 034006 20 KHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYGGQTKPVFHKKAKTTKKIVLRLQCQGCKHVSQHPIKRCKHFEIGG 96 (106)
Q Consensus 20 kHt~HkVtqyKkGK~s~~aqG~Rrydrkq~GygGq~kpi~~k~aKtTKKi~Lrl~C~~C~~~~~~~~kR~KkfEl~~ 96 (106)
+||+|+|+||++|++|++|||+|||||+|+|||||++|||+++|||||||||+|+|++|+++++++++||++|||+.
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 59999999999999999999999999999999999999999999999999999999999999999999999999974
No 6
>PRK00504 rpmG 50S ribosomal protein L33; Validated
Probab=94.35 E-value=0.024 Score=35.72 Aligned_cols=17 Identities=53% Similarity=1.024 Sum_probs=14.7
Q ss_pred eeeeeccCCCCCCccceEE
Q 034006 8 TKKTYCKSKECRKHTLHKV 26 (106)
Q Consensus 8 ~~~tyC~~~~C~kHt~HkV 26 (106)
+.+-|| |.|++||.|+=
T Consensus 32 elkKyc--p~c~khtlhkE 48 (50)
T PRK00504 32 ELKKFC--PRCNKHTLHKE 48 (50)
T ss_pred EEECcC--CCCCCeEeeee
Confidence 467899 99999999973
No 7
>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=93.77 E-value=0.045 Score=34.03 Aligned_cols=16 Identities=69% Similarity=1.275 Sum_probs=14.3
Q ss_pred eeeeeccCCCCCCccceE
Q 034006 8 TKKTYCKSKECRKHTLHK 25 (106)
Q Consensus 8 ~~~tyC~~~~C~kHt~Hk 25 (106)
+.+-|| |.|++||.|+
T Consensus 30 ~lkKyc--p~~~khtlhk 45 (48)
T PF00471_consen 30 ELKKYC--PRCRKHTLHK 45 (48)
T ss_dssp EEEEEE--TSSSSEEEEE
T ss_pred eEeccC--CCCCCEecEE
Confidence 467899 9999999996
No 8
>CHL00104 rpl33 ribosomal protein L33
Probab=93.53 E-value=0.04 Score=36.52 Aligned_cols=17 Identities=47% Similarity=0.899 Sum_probs=14.7
Q ss_pred eeeeeccCCCCCCccceEE
Q 034006 8 TKKTYCKSKECRKHTLHKV 26 (106)
Q Consensus 8 ~~~tyC~~~~C~kHt~HkV 26 (106)
+.+-|| |.|++||.|+=
T Consensus 47 elkKyc--p~c~kHtlhkE 63 (66)
T CHL00104 47 ELKKFC--PYCYKHTIHKE 63 (66)
T ss_pred EEECcC--CCCCCEeeEee
Confidence 467899 99999999974
No 9
>TIGR01023 rpmG_bact ribosomal protein L33, bacterial type. This model describes bacterial ribosomal protein L33 and its chloroplast and mitochondrial equivalents.
Probab=93.31 E-value=0.048 Score=34.70 Aligned_cols=17 Identities=53% Similarity=1.060 Sum_probs=14.9
Q ss_pred eeeeeccCCCCCCccceEE
Q 034006 8 TKKTYCKSKECRKHTLHKV 26 (106)
Q Consensus 8 ~~~tyC~~~~C~kHt~HkV 26 (106)
+.+-|| |.|++|+.|+-
T Consensus 36 ~lkKyc--p~~~khtlhkE 52 (54)
T TIGR01023 36 ELRKYC--PVCRKHVLHKE 52 (54)
T ss_pred EEECcC--CCCCCeEeEEe
Confidence 567899 99999999974
No 10
>PRK00595 rpmG 50S ribosomal protein L33; Validated
Probab=93.15 E-value=0.052 Score=34.31 Aligned_cols=17 Identities=47% Similarity=0.528 Sum_probs=14.7
Q ss_pred eeeeeccCCCCCCccceEE
Q 034006 8 TKKTYCKSKECRKHTLHKV 26 (106)
Q Consensus 8 ~~~tyC~~~~C~kHt~HkV 26 (106)
+.+-|| |.|++||.|+=
T Consensus 35 ~lkKyc--p~~~khtlhkE 51 (53)
T PRK00595 35 ELKKYD--PVLRKHVLHKE 51 (53)
T ss_pred EEECcC--CCCCCEEeEEe
Confidence 457899 99999999974
No 11
>COG0267 RpmG Ribosomal protein L33 [Translation, ribosomal structure and biogenesis]
Probab=93.13 E-value=0.051 Score=34.45 Aligned_cols=17 Identities=65% Similarity=1.118 Sum_probs=14.7
Q ss_pred eeeeeccCCCCCCccceEE
Q 034006 8 TKKTYCKSKECRKHTLHKV 26 (106)
Q Consensus 8 ~~~tyC~~~~C~kHt~HkV 26 (106)
+.+-|| |.|++||.|+=
T Consensus 32 elkKyc--p~~~khtlhkE 48 (50)
T COG0267 32 ELKKYC--PVCRKHTLHKE 48 (50)
T ss_pred EEEecC--cccccEEEEee
Confidence 467899 99999999973
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=79.60 E-value=1.2 Score=30.00 Aligned_cols=23 Identities=26% Similarity=0.579 Sum_probs=10.9
Q ss_pred CceeeeeccCCCCCCccceEEEEee
Q 034006 6 PKTKKTYCKSKECRKHTLHKVTQYK 30 (106)
Q Consensus 6 PK~~~tyC~~~~C~kHt~HkVtqyK 30 (106)
+..-+-|| |+|+.+|..+|+-+=
T Consensus 20 ~~~~k~FC--p~CGn~TL~rvsvsv 42 (73)
T PF08772_consen 20 KDMTKQFC--PKCGNATLKRVSVSV 42 (73)
T ss_dssp S-SS--S---SSS--S--EEEE-B-
T ss_pred CCCCceeC--cccCCCcceEEEEEE
Confidence 34557899 999999999998764
No 13
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=52.73 E-value=13 Score=24.13 Aligned_cols=16 Identities=25% Similarity=0.746 Sum_probs=14.5
Q ss_pred EEEEEecCCCceeeec
Q 034006 70 VLRLQCQGCKHVSQHP 85 (106)
Q Consensus 70 ~Lrl~C~~C~~~~~~~ 85 (106)
+++++|..|+...|.+
T Consensus 29 DikikC~gCg~~imlp 44 (57)
T PF06107_consen 29 DIKIKCLGCGRQIMLP 44 (57)
T ss_pred cEEEEECCCCCEEEEe
Confidence 8999999999998875
No 14
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=49.97 E-value=11 Score=24.40 Aligned_cols=18 Identities=44% Similarity=0.905 Sum_probs=15.4
Q ss_pred eeccCCCCCCccceEEEEee
Q 034006 11 TYCKSKECRKHTLHKVTQYK 30 (106)
Q Consensus 11 tyC~~~~C~kHt~HkVtqyK 30 (106)
-|| |+|+.-+.-.|.+.+
T Consensus 29 lyC--pKCK~EtlI~v~~~~ 46 (55)
T PF14205_consen 29 LYC--PKCKQETLIDVKQLK 46 (55)
T ss_pred ccC--CCCCceEEEEeeccE
Confidence 699 999999988888764
No 15
>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=47.41 E-value=24 Score=20.57 Aligned_cols=29 Identities=28% Similarity=0.527 Sum_probs=18.2
Q ss_pred eeeeeccCCCCCCccceEEEEeecCccchhhccceeee
Q 034006 8 TKKTYCKSKECRKHTLHKVTQYKKGKDSLAAQGKRRYD 45 (106)
Q Consensus 8 ~~~tyC~~~~C~kHt~HkVtqyKkGK~s~~aqG~Rryd 45 (106)
++.-.| |+|..... -||.|+.+. |.+||+
T Consensus 3 ~i~v~C--P~C~s~~~----v~k~G~~~~---G~qryr 31 (36)
T PF03811_consen 3 KIDVHC--PRCQSTEG----VKKNGKSPS---GHQRYR 31 (36)
T ss_pred cEeeeC--CCCCCCCc----ceeCCCCCC---CCEeEe
Confidence 345789 99987651 356676543 555654
No 16
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=43.32 E-value=25 Score=21.20 Aligned_cols=22 Identities=18% Similarity=0.294 Sum_probs=14.2
Q ss_pred EEEecCCCceeeec--ceeeeeeE
Q 034006 72 RLQCQGCKHVSQHP--IKRCKHFE 93 (106)
Q Consensus 72 rl~C~~C~~~~~~~--~kR~KkfE 93 (106)
-++|.+||+..+.. ..+.+.|+
T Consensus 19 ~irC~~CG~rIlyK~R~~~~~~~~ 42 (44)
T smart00659 19 VVRCRECGYRILYKKRTKRLVEVK 42 (44)
T ss_pred ceECCCCCceEEEEeCCCceEEEE
Confidence 47899999987732 24445544
No 17
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.73 E-value=21 Score=23.44 Aligned_cols=16 Identities=25% Similarity=0.837 Sum_probs=14.6
Q ss_pred EEEEEecCCCceeeec
Q 034006 70 VLRLQCQGCKHVSQHP 85 (106)
Q Consensus 70 ~Lrl~C~~C~~~~~~~ 85 (106)
+++..|+.|+...|.+
T Consensus 32 DIkikC~nC~h~vm~p 47 (60)
T COG4481 32 DIKIKCENCGHSVMMP 47 (60)
T ss_pred cEEEEecCCCcEEEec
Confidence 8999999999998876
No 18
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=41.78 E-value=15 Score=29.20 Aligned_cols=20 Identities=20% Similarity=0.373 Sum_probs=15.4
Q ss_pred eeeeeccCCCCC-CccceEEEEe
Q 034006 8 TKKTYCKSKECR-KHTLHKVTQY 29 (106)
Q Consensus 8 ~~~tyC~~~~C~-kHt~HkVtqy 29 (106)
.+.-+| |.|+ .-++|.|-.-
T Consensus 4 ~iy~~C--p~Cg~eev~hEVik~ 24 (201)
T COG1326 4 EIYIEC--PSCGSEEVSHEVIKE 24 (201)
T ss_pred eEEEEC--CCCCcchhhHHHHHh
Confidence 567899 9999 5777887654
No 19
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=38.72 E-value=6.8 Score=25.96 Aligned_cols=12 Identities=17% Similarity=0.523 Sum_probs=5.8
Q ss_pred EEEEEecCCCce
Q 034006 70 VLRLQCQGCKHV 81 (106)
Q Consensus 70 ~Lrl~C~~C~~~ 81 (106)
.+.|-|-+|+..
T Consensus 18 ~miYiCgdC~~e 29 (62)
T KOG3507|consen 18 TMIYICGDCGQE 29 (62)
T ss_pred cEEEEecccccc
Confidence 445555544443
No 20
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=34.24 E-value=30 Score=25.69 Aligned_cols=18 Identities=22% Similarity=0.477 Sum_probs=16.1
Q ss_pred eEEEEEecCCCceeeecc
Q 034006 69 IVLRLQCQGCKHVSQHPI 86 (106)
Q Consensus 69 i~Lrl~C~~C~~~~~~~~ 86 (106)
|=|.|.|+.|++.+..++
T Consensus 10 VWLIYrC~~C~~TwN~ti 27 (142)
T PF06353_consen 10 VWLIYRCEKCDYTWNMTI 27 (142)
T ss_pred EEEEEEcccCcCccccce
Confidence 568999999999998877
No 21
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=32.89 E-value=26 Score=29.50 Aligned_cols=21 Identities=24% Similarity=0.632 Sum_probs=18.8
Q ss_pred eccCCCCCCccceEEEEeecCcc
Q 034006 12 YCKSKECRKHTLHKVTQYKKGKD 34 (106)
Q Consensus 12 yC~~~~C~kHt~HkVtqyKkGK~ 34 (106)
+| +.|+.|+++-|+.|..|-.
T Consensus 2 ~c--~~C~~~~~~~V~d~~~gdt 22 (308)
T KOG1597|consen 2 TC--PDCKRHPENLVEDHSAGDT 22 (308)
T ss_pred CC--CCCCCCCCCeeeeccCCce
Confidence 58 9999999999999998843
No 22
>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=32.50 E-value=49 Score=19.16 Aligned_cols=14 Identities=29% Similarity=0.534 Sum_probs=11.4
Q ss_pred eEEEEEecCCCcee
Q 034006 69 IVLRLQCQGCKHVS 82 (106)
Q Consensus 69 i~Lrl~C~~C~~~~ 82 (106)
.+|-|.|.+|+..+
T Consensus 25 ~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 25 MTLFYVCCNCGHRW 38 (39)
T ss_dssp SEEEEEESSSTEEE
T ss_pred CeEEEEeCCCCCee
Confidence 47889999999764
No 23
>PHA02768 hypothetical protein; Provisional
Probab=31.52 E-value=16 Score=23.39 Aligned_cols=15 Identities=20% Similarity=0.534 Sum_probs=11.3
Q ss_pred EEEEEecCCCceeee
Q 034006 70 VLRLQCQGCKHVSQH 84 (106)
Q Consensus 70 ~Lrl~C~~C~~~~~~ 84 (106)
.|-|+|++||+....
T Consensus 3 ~~~y~C~~CGK~Fs~ 17 (55)
T PHA02768 3 LLGYECPICGEIYIK 17 (55)
T ss_pred ccccCcchhCCeecc
Confidence 467899999987553
No 24
>PF11415 Toxin_37: Antifungal peptide termicin; InterPro: IPR024723 Termicin is a cysteine-rich antifungal peptide, which also exhibits weak antibacterial activity. The global fold of termicin consists of an alpha-helical segment and a two-stranded antiparallel beta-sheet forming a cysteine stabilised alphabeta motif that is also found in antibacterial and antifungal defensins from insects and from plants. The antifungal properties of termicin may be related to its marked hydrophobicity and its amphipatic structure compared to the antibacterial defensins [].; PDB: 1MM0_A.
Probab=30.36 E-value=20 Score=21.37 Aligned_cols=12 Identities=25% Similarity=1.074 Sum_probs=9.7
Q ss_pred eeeeeccCCCCC
Q 034006 8 TKKTYCKSKECR 19 (106)
Q Consensus 8 ~~~tyC~~~~C~ 19 (106)
.+++||+|+.|.
T Consensus 18 FRRAyCdGs~C~ 29 (35)
T PF11415_consen 18 FRRAYCDGSRCK 29 (35)
T ss_dssp EEEEEEETTEEE
T ss_pred hhhhhccCCeeE
Confidence 478999998874
No 25
>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=30.35 E-value=34 Score=16.70 Aligned_cols=11 Identities=18% Similarity=0.477 Sum_probs=8.8
Q ss_pred EEecCCCceee
Q 034006 73 LQCQGCKHVSQ 83 (106)
Q Consensus 73 l~C~~C~~~~~ 83 (106)
++|..|++...
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 26
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=28.06 E-value=55 Score=19.08 Aligned_cols=14 Identities=21% Similarity=0.503 Sum_probs=11.4
Q ss_pred eEEEEEecCCCcee
Q 034006 69 IVLRLQCQGCKHVS 82 (106)
Q Consensus 69 i~Lrl~C~~C~~~~ 82 (106)
.+|-|.|.+|+...
T Consensus 25 mT~fy~C~~C~~~w 38 (40)
T smart00440 25 MTVFYVCTKCGHRW 38 (40)
T ss_pred CeEEEEeCCCCCEe
Confidence 47899999999764
No 27
>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=25.48 E-value=48 Score=17.34 Aligned_cols=10 Identities=20% Similarity=0.534 Sum_probs=8.4
Q ss_pred EEecCCCcee
Q 034006 73 LQCQGCKHVS 82 (106)
Q Consensus 73 l~C~~C~~~~ 82 (106)
++|..|++..
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 28
>PF15494 SRCR_2: Scavenger receptor cysteine-rich domain
Probab=25.33 E-value=47 Score=22.13 Aligned_cols=13 Identities=38% Similarity=0.787 Sum_probs=10.6
Q ss_pred eEEEEEecCCCce
Q 034006 69 IVLRLQCQGCKHV 81 (106)
Q Consensus 69 i~Lrl~C~~C~~~ 81 (106)
-++-|+|++||..
T Consensus 85 ~vVsL~C~~CG~r 97 (98)
T PF15494_consen 85 SVVSLQCSDCGKR 97 (98)
T ss_pred CEEEEECcccCCc
Confidence 3788999999974
No 29
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=24.85 E-value=76 Score=27.46 Aligned_cols=59 Identities=25% Similarity=0.400 Sum_probs=34.3
Q ss_pred eeeccCCCCCCccceEEEEeecCccchhhccceeeeccccCCCCcccceecCCCCccceeEEE
Q 034006 10 KTYCKSKECRKHTLHKVTQYKKGKDSLAAQGKRRYDRKQSGYGGQTKPVFHKKAKTTKKIVLR 72 (106)
Q Consensus 10 ~tyC~~~~C~kHt~HkVtqyKkGK~s~~aqG~Rrydrkq~GygGq~kpi~~k~aKtTKKi~Lr 72 (106)
+-|| |.|+--|.|+|+--=......-+.=+.|+.++..|+- ..=|.| ++.|.++-..|+
T Consensus 257 k~FC--p~CG~~TL~K~aVsv~~dG~~~~h~k~r~~~n~RG~~-YSlp~P-kGgk~~kN~~Lr 315 (376)
T KOG2463|consen 257 KDFC--PSCGHKTLTKCAVSVDEDGNGQTHFKKRFQWNNRGLQ-YSLPKP-KGGKVAKNPILR 315 (376)
T ss_pred hhcc--cccCCCeeeEEEEEecCCCceeEEeecccccccCcce-eecCCC-CCCccccCcccc
Confidence 6799 9999999999875432221222223334444555552 122555 457777766665
No 30
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=22.36 E-value=48 Score=28.37 Aligned_cols=18 Identities=28% Similarity=0.584 Sum_probs=15.5
Q ss_pred EEEecCCCceeeecceee
Q 034006 72 RLQCQGCKHVSQHPIKRC 89 (106)
Q Consensus 72 rl~C~~C~~~~~~~~kR~ 89 (106)
.|.|++||+....-.+||
T Consensus 7 ~y~C~~Cg~~~~~~~g~C 24 (454)
T TIGR00416 7 KFVCQHCGADSPKWQGKC 24 (454)
T ss_pred eEECCcCCCCCccccEEC
Confidence 599999999988877776
No 31
>PRK11823 DNA repair protein RadA; Provisional
Probab=22.32 E-value=48 Score=28.22 Aligned_cols=20 Identities=30% Similarity=0.544 Sum_probs=16.5
Q ss_pred EEEEecCCCceeeecceeee
Q 034006 71 LRLQCQGCKHVSQHPIKRCK 90 (106)
Q Consensus 71 Lrl~C~~C~~~~~~~~kR~K 90 (106)
-.|.|++||+....-.+||-
T Consensus 6 ~~y~C~~Cg~~~~~~~g~Cp 25 (446)
T PRK11823 6 TAYVCQECGAESPKWLGRCP 25 (446)
T ss_pred CeEECCcCCCCCcccCeeCc
Confidence 46999999999888777763
No 32
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=21.52 E-value=53 Score=18.93 Aligned_cols=14 Identities=14% Similarity=0.676 Sum_probs=5.5
Q ss_pred eccCCCCCCccceEEE
Q 034006 12 YCKSKECRKHTLHKVT 27 (106)
Q Consensus 12 yC~~~~C~kHt~HkVt 27 (106)
|| |.|+...++.|-
T Consensus 2 fC--~~CG~~l~~~ip 15 (34)
T PF14803_consen 2 FC--PQCGGPLERRIP 15 (34)
T ss_dssp B---TTT--B-EEE--
T ss_pred cc--ccccChhhhhcC
Confidence 77 778777665543
No 33
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=21.38 E-value=57 Score=21.60 Aligned_cols=17 Identities=18% Similarity=0.481 Sum_probs=13.6
Q ss_pred EEEEecCCCceeeecce
Q 034006 71 LRLQCQGCKHVSQHPIK 87 (106)
Q Consensus 71 Lrl~C~~C~~~~~~~~k 87 (106)
=..||++||+.-.++..
T Consensus 29 e~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 29 EYVECVECGYTERQPDQ 45 (71)
T ss_pred eEEEecCCCCeeccCCc
Confidence 35799999999887765
No 34
>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=21.34 E-value=61 Score=16.36 Aligned_cols=11 Identities=18% Similarity=0.718 Sum_probs=8.8
Q ss_pred EEecCCCceee
Q 034006 73 LQCQGCKHVSQ 83 (106)
Q Consensus 73 l~C~~C~~~~~ 83 (106)
++|..|+....
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 35
>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=21.00 E-value=67 Score=19.68 Aligned_cols=13 Identities=31% Similarity=0.588 Sum_probs=10.2
Q ss_pred EEEecCCCceeee
Q 034006 72 RLQCQGCKHVSQH 84 (106)
Q Consensus 72 rl~C~~C~~~~~~ 84 (106)
|++|+.|++...-
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 36
>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=20.47 E-value=1.1e+02 Score=17.02 Aligned_cols=23 Identities=22% Similarity=0.485 Sum_probs=16.0
Q ss_pred ecCCCceeeecceeeeeeEEeee
Q 034006 75 CQGCKHVSQHPIKRCKHFEIGGD 97 (106)
Q Consensus 75 C~~C~~~~~~~~kR~KkfEl~~~ 97 (106)
|..|+...+....+.-.|++++.
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~~~ 23 (46)
T TIGR03831 1 CPICGGEELEGKTTTETYEYGGE 23 (46)
T ss_pred CCCCCCceecceEEEEEEEeCCE
Confidence 67787666666666777877554
Done!