Query 030949
Match_columns 168
No_of_seqs 158 out of 395
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 06:59:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030949.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030949hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00033 60S ribosomal protein 100.0 3.6E-42 7.8E-47 269.0 11.1 93 1-132 1-97 (125)
2 KOG1723 60s ribosomal protein 100.0 1E-39 2.2E-44 264.1 4.2 114 1-150 1-114 (162)
3 KOG1722 60s ribosomal protein 100.0 1.9E-36 4.2E-41 242.8 7.2 93 1-132 1-94 (155)
4 PF01246 Ribosomal_L24e: Ribos 100.0 7.6E-36 1.7E-40 213.6 1.4 64 1-64 1-64 (71)
5 PRK14891 50S ribosomal protein 100.0 9.5E-35 2.1E-39 228.8 5.9 64 1-64 2-65 (131)
6 COG2075 RPL24A Ribosomal prote 100.0 7.5E-34 1.6E-38 202.2 5.5 64 1-64 1-64 (66)
7 cd00472 Ribosomal_L24e_L24 Rib 100.0 2.1E-32 4.5E-37 187.2 4.0 54 1-54 1-54 (54)
8 PRK00807 50S ribosomal protein 99.9 9.9E-29 2.1E-33 167.0 3.3 52 3-54 1-52 (52)
9 smart00746 TRASH metallochaper 98.4 3.2E-07 6.9E-12 51.2 3.7 37 6-43 1-38 (39)
10 PF08394 Arc_trans_TRASH: Arch 96.6 0.0026 5.7E-08 41.2 3.4 36 6-43 1-36 (37)
11 PF04945 YHS: YHS domain; Int 96.5 0.003 6.4E-08 40.8 2.9 36 6-42 3-38 (47)
12 PF06467 zf-FCS: MYM-type Zinc 95.4 0.0056 1.2E-07 38.1 0.6 37 3-40 6-43 (43)
13 PF09889 DUF2116: Uncharacteri 94.7 0.0054 1.2E-07 43.1 -0.9 26 4-41 4-29 (59)
14 PF05573 NosL: NosL; InterPro 91.2 0.15 3.3E-06 39.9 2.2 39 4-42 26-67 (149)
15 COG3350 Uncharacterized conser 89.9 0.45 9.7E-06 33.3 3.3 38 7-46 6-43 (53)
16 PF09943 DUF2175: Uncharacteri 87.1 0.25 5.5E-06 38.2 0.7 29 3-32 2-30 (101)
17 COG4068 Uncharacterized protei 71.0 1.4 3E-05 31.9 0.1 24 4-39 9-32 (64)
18 PHA03073 late transcription fa 68.2 3 6.4E-05 34.5 1.4 38 3-41 49-87 (150)
19 PF04570 DUF581: Protein of un 66.5 4.4 9.5E-05 28.4 1.8 34 4-40 17-50 (58)
20 cd01057 AAMH_A Aromatic and Al 65.4 5.9 0.00013 37.1 3.0 51 5-57 382-439 (465)
21 COG4847 Uncharacterized protei 55.4 4.7 0.0001 31.5 0.4 29 1-30 4-32 (103)
22 PF00412 LIM: LIM domain; Int 50.6 17 0.00037 22.9 2.4 21 5-28 28-48 (58)
23 COG4314 NosL Predicted lipopro 50.3 17 0.00037 30.8 3.0 46 4-49 36-85 (176)
24 PF06689 zf-C4_ClpX: ClpX C4-t 45.8 7.3 0.00016 25.0 0.1 13 4-16 2-14 (41)
25 PF15585 Imm46: Immunity prote 41.8 18 0.00039 29.2 1.8 26 12-37 79-113 (129)
26 PF08384 NPP: Pro-opiomelanoco 41.2 13 0.00028 25.3 0.8 11 10-20 31-41 (45)
27 TIGR00270 conserved hypothetic 39.1 24 0.00053 28.4 2.2 31 6-39 3-33 (154)
28 KOG3851 Sulfide:quinone oxidor 37.8 12 0.00026 35.3 0.3 71 26-123 185-261 (446)
29 smart00132 LIM Zinc-binding do 35.8 30 0.00065 19.6 1.7 25 5-31 1-25 (39)
30 PRK08359 transcription factor; 35.0 30 0.00065 28.8 2.2 30 5-37 8-37 (176)
31 PLN02469 hydroxyacylglutathion 33.2 41 0.00088 28.5 2.7 25 102-126 213-237 (258)
32 COG2888 Predicted Zn-ribbon RN 32.3 51 0.0011 23.8 2.7 37 3-39 9-47 (61)
33 PRK09710 lar restriction allev 31.4 38 0.00083 24.5 2.0 31 3-39 6-36 (64)
34 PF14353 CpXC: CpXC protein 27.7 69 0.0015 24.0 2.9 33 3-35 38-70 (128)
35 PF07754 DUF1610: Domain of un 27.2 41 0.00089 20.0 1.3 17 6-22 1-18 (24)
36 PF08789 PBCV_basic_adap: PBCV 24.3 45 0.00098 22.1 1.2 18 9-26 7-25 (40)
37 PRK14890 putative Zn-ribbon RN 22.9 54 0.0012 23.4 1.4 40 1-40 5-46 (59)
38 PF14447 Prok-RING_4: Prokaryo 22.3 43 0.00092 23.6 0.8 13 5-17 41-53 (55)
39 PF03884 DUF329: Domain of unk 22.1 50 0.0011 23.1 1.1 29 4-39 3-31 (57)
No 1
>PTZ00033 60S ribosomal protein L24; Provisional
Probab=100.00 E-value=3.6e-42 Score=269.05 Aligned_cols=93 Identities=32% Similarity=0.621 Sum_probs=89.0
Q ss_pred CceeeeecCCCCccCCccceEEe----eCCceEEEechhhhhhhhcccCCccchhhHHHHHHhCCcceeeecccchhhhh
Q 030949 1 MRLEKCWFCSSTVYPGHGIQFVR----NDAKIFRFCRSKCHKNFKMKRNPRKVKWTKAYRRLHGKDMTQVNMFGFSILFC 76 (168)
Q Consensus 1 Mkie~CsFcG~kIYPGhG~~fVR----nDGkvF~FcsSKC~k~fk~KRNPRKlkWT~~yRr~~KK~~~~~~~~~~~~~~~ 76 (168)
|+++.|+|||++||||||++||+ +||++|+||||||+++|++|+|||+|+||++||++|||+++
T Consensus 1 Mk~~~C~Fsg~~IyPG~G~~~Vr~~~~~Dgkv~~F~~sKc~~~~~~krnPRkl~WT~~yRr~~kK~~~------------ 68 (125)
T PTZ00033 1 MRTIACEFSHFAVHPGHGRRYVPFAFLSTKPVLTFLRPKCFALYMRKKNPRFLPWTRTYRRINRKTTT------------ 68 (125)
T ss_pred CceeEecCcCCcccCCCCcEeeecccCCCCCEEEEecHHHHHHHHCcCCCccchHHHHHHHHhCCcch------------
Confidence 89999999999999999999999 99999999999999999999999999999999999999977
Q ss_pred hHhhhhhHHhhhcCccccCCCcccCCchHHHHHhhCCCccccHHHHHHHHHHHHhH
Q 030949 77 NLFYLNMFMRISGDLFFSFPFSYRQDSTFEFERKRNRPERYDRNLAENTLKAIKKI 132 (168)
Q Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~~~d~t~e~ekrrn~~~ky~R~l~~~tl~aik~v 132 (168)
+| + +++|+|+|++|||+|||+|||+|++.
T Consensus 69 ------------------------e~-~--~kkR~~rtvK~qRaivg~sLe~I~~k 97 (125)
T PTZ00033 69 ------------------------DR-V--QRRRAARTVKVQRAIVGADLSYIQEV 97 (125)
T ss_pred ------------------------hH-H--HHHHhcCCccchHHHHHHHHHHHHHH
Confidence 44 4 49999999999999999999999986
No 2
>KOG1723 consensus 60s ribosomal protein L30 isolog [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1e-39 Score=264.05 Aligned_cols=114 Identities=58% Similarity=1.106 Sum_probs=112.4
Q ss_pred CceeeeecCCCCccCCccceEEeeCCceEEEechhhhhhhhcccCCccchhhHHHHHHhCCcceeeecccchhhhhhHhh
Q 030949 1 MRLEKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNPRKVKWTKAYRRLHGKDMTQVNMFGFSILFCNLFY 80 (168)
Q Consensus 1 Mkie~CsFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~k~fk~KRNPRKlkWT~~yRr~~KK~~~~~~~~~~~~~~~~~~~ 80 (168)
|++++|+||+++||||||+|||+||.++|.||+|||+++|++++|||++.||.++|++++|++.
T Consensus 1 Mri~kc~fcss~IyPgHgi~Fv~Nd~k~f~Fc~skc~k~f~~k~nPrk~~~tka~rKaagre~~---------------- 64 (162)
T KOG1723|consen 1 MRIEKCYFCSSPIYPGHGIMFVRNDCKVFRFCKSKCHKNFKQKKNPRKVGWTKAFRKAAGRELV---------------- 64 (162)
T ss_pred CceeeeeeecCcccCCCceEEEecCcchhHHHHhhhhhhhhhhcCCCccchHHHHHHHhhhhHh----------------
Confidence 8999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHhhhcCccccCCCcccCCchHHHHHhhCCCccccHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhhh
Q 030949 81 LNMFMRISGDLFFSFPFSYRQDSTFEFERKRNRPERYDRNLAENTLKAIKKIDKIRVAREERHHKLRFVI 150 (168)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~d~t~e~ekrrn~~~ky~R~l~~~tl~aik~v~~i~~~r~~~~~~~r~~~ 150 (168)
.|+++||++|||+|++|+|++++.|++||+++++|+++|++.++.+||..
T Consensus 65 --------------------~d~~~e~~~rrn~~~~y~r~~~~~Ti~a~k~v~~i~~~~~~~~i~~rL~~ 114 (162)
T KOG1723|consen 65 --------------------TDSTFEFEKRRNVPRKYDRELINKTIDAMKRVLEIKQKREAHFIGNRLKK 114 (162)
T ss_pred --------------------hhhhHHHHHhcCcchhhcccchhhHHHHHHHHHhhcccchhhhhhhccCc
Confidence 89999999999999999999999999999999999999999999999965
No 3
>KOG1722 consensus 60s ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-36 Score=242.80 Aligned_cols=93 Identities=38% Similarity=0.812 Sum_probs=86.5
Q ss_pred CceeeeecCCCCccCCccceEEeeCCceEEEechhhhhhhhcccCCccchhhHHHHHHhCCcceeeecccchhhhhhHhh
Q 030949 1 MRLEKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNPRKVKWTKAYRRLHGKDMTQVNMFGFSILFCNLFY 80 (168)
Q Consensus 1 Mkie~CsFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~k~fk~KRNPRKlkWT~~yRr~~KK~~~~~~~~~~~~~~~~~~~ 80 (168)
|++|.|+|||++||||||+.|||.||+||.|+|+||+++|++++|||+|.||++||+.|+||.+
T Consensus 1 MKvElCsFSG~KIyPG~G~r~vR~D~Kvf~Fln~Kc~~~f~~rrnPr~l~WTvLyR~khkKg~~---------------- 64 (155)
T KOG1722|consen 1 MKVELCSFSGYKIYPGHGRRFVRGDGKVFRFLNSKCESLFLQRRNPRRLAWTVLYRKKHKKGIQ---------------- 64 (155)
T ss_pred CceeEeeccCceecCCCceeEEecCCeeeeehhhhhHHHHHhccChhhhhHHHHHHHHhhcchh----------------
Confidence 8999999999999999999999999999999999999999999999999999999999999987
Q ss_pred hhhHHhhhcCccccCCCcccCCchHHHHHhhCCCcc-ccHHHHHHHHHHHHhH
Q 030949 81 LNMFMRISGDLFFSFPFSYRQDSTFEFERKRNRPER-YDRNLAENTLKAIKKI 132 (168)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~d~t~e~ekrrn~~~k-y~R~l~~~tl~aik~v 132 (168)
++.+ .+|++++++ |||+|+|+||++|++-
T Consensus 65 --------------------ee~~---kkrtrrt~k~~qRaI~GasL~~I~~K 94 (155)
T KOG1722|consen 65 --------------------EEAA---KKRTRRTVKKFQRAIVGASLDVILEK 94 (155)
T ss_pred --------------------HHHH---HHHhhhhhhhhhhhhccccHHHHHHH
Confidence 6544 667777665 9999999999999875
No 4
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 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 archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=100.00 E-value=7.6e-36 Score=213.57 Aligned_cols=64 Identities=61% Similarity=1.131 Sum_probs=51.8
Q ss_pred CceeeeecCCCCccCCccceEEeeCCceEEEechhhhhhhhcccCCccchhhHHHHHHhCCcce
Q 030949 1 MRLEKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNPRKVKWTKAYRRLHGKDMT 64 (168)
Q Consensus 1 Mkie~CsFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~k~fk~KRNPRKlkWT~~yRr~~KK~~~ 64 (168)
|++++|+|||++||||||++||++||++|+|||+||+++|++++|||+|+||++||++|||+++
T Consensus 1 mk~~~C~Fsg~~I~PG~G~~~Vr~DG~v~~F~s~Kc~~~~~~krnPrkl~WT~~~Rr~~kK~~~ 64 (71)
T PF01246_consen 1 MKTEKCSFSGYKIYPGHGKMYVRNDGKVFYFCSSKCEKLFKLKRNPRKLKWTVAYRRQHKKGQS 64 (71)
T ss_dssp SSSEE-TTT-SEE-SSSSEEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTSTTTCHHH-----
T ss_pred CceEEecccCCccCCCCCeEEEecCCCeEEEeCHHHHHHHHccCCcccchhHHHHHHHhCchhh
Confidence 8999999999999999999999999999999999999999999999999999999999999998
No 5
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=100.00 E-value=9.5e-35 Score=228.79 Aligned_cols=64 Identities=33% Similarity=0.703 Sum_probs=62.2
Q ss_pred CceeeeecCCCCccCCccceEEeeCCceEEEechhhhhhhhcccCCccchhhHHHHHHhCCcce
Q 030949 1 MRLEKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNPRKVKWTKAYRRLHGKDMT 64 (168)
Q Consensus 1 Mkie~CsFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~k~fk~KRNPRKlkWT~~yRr~~KK~~~ 64 (168)
|++++|+|||++||||||+|||||||++|+||||||+++|++|||||||+||++||+.++|...
T Consensus 2 m~~e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~k~f~~kRnPRKlkWT~~yRk~~g~~~~ 65 (131)
T PRK14891 2 VETRTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCEKNYDLGREARDLEWTEAGRAEKGPAAA 65 (131)
T ss_pred CceeeecCcCCcccCCCCcEEEecCCCEEEEecHHHHHHHHccCCCccchhHHHHHHHcCchhh
Confidence 7999999999999999999999999999999999999999999999999999999999999854
No 6
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.5e-34 Score=202.17 Aligned_cols=64 Identities=55% Similarity=1.152 Sum_probs=62.5
Q ss_pred CceeeeecCCCCccCCccceEEeeCCceEEEechhhhhhhhcccCCccchhhHHHHHHhCCcce
Q 030949 1 MRLEKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNPRKVKWTKAYRRLHGKDMT 64 (168)
Q Consensus 1 Mkie~CsFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~k~fk~KRNPRKlkWT~~yRr~~KK~~~ 64 (168)
|+++.|+|||.+||||||+|||||||++|+||||||+++|+++||||+|+||+.||+.++|+..
T Consensus 1 m~~~~CsFcG~~I~PGtG~m~Vr~Dg~v~~FcssKc~k~~~~~rnPRk~~WT~~~~~~~~k~~~ 64 (66)
T COG2075 1 MKVRVCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCEKLFKLGRNPRKLKWTKKYRKMHKKEIK 64 (66)
T ss_pred CceeEecCcCCccCCCceEEEEecCCeEEEEechhHHHHHHccCCCccchhHHHHHHHHHhhhc
Confidence 8899999999999999999999999999999999999999999999999999999999999875
No 7
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=99.97 E-value=2.1e-32 Score=187.20 Aligned_cols=54 Identities=67% Similarity=1.282 Sum_probs=52.7
Q ss_pred CceeeeecCCCCccCCccceEEeeCCceEEEechhhhhhhhcccCCccchhhHH
Q 030949 1 MRLEKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNPRKVKWTKA 54 (168)
Q Consensus 1 Mkie~CsFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~k~fk~KRNPRKlkWT~~ 54 (168)
|++++|+|||++||||||++|||+||++|+|||+||+++|++|||||||+||++
T Consensus 1 m~~~~C~f~g~~I~PG~G~~~Vr~Dgkv~~F~s~Kc~~~~~~krnPRkv~WT~~ 54 (54)
T cd00472 1 MKTEKCSFCGYKIYPGHGKMYVRNDGKVFRFCSSKCEKNFLRKRNPRKLKWTVA 54 (54)
T ss_pred CcEEEecCcCCeecCCCccEEEecCCCEEEEECHHHHHHHHCcCCCCcceeecC
Confidence 899999999999999999999999999999999999999999999999999973
No 8
>PRK00807 50S ribosomal protein L24e; Validated
Probab=99.95 E-value=9.9e-29 Score=167.00 Aligned_cols=52 Identities=50% Similarity=1.047 Sum_probs=50.0
Q ss_pred eeeeecCCCCccCCccceEEeeCCceEEEechhhhhhhhcccCCccchhhHH
Q 030949 3 LEKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNPRKVKWTKA 54 (168)
Q Consensus 3 ie~CsFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~k~fk~KRNPRKlkWT~~ 54 (168)
+++|+|||++||||||++||++||++|+|||+||+++|++|+|||||+||.+
T Consensus 1 ~~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~KC~~~f~~~~nprk~~WT~~ 52 (52)
T PRK00807 1 TRTCSFCGKEIEPGTGKMYVKKDGTILYFCSSKCEKNYKLGRVPRKLKWTKA 52 (52)
T ss_pred CcccCCCCCeEcCCCCeEEEEeCCcEEEEeCHHHHHHHHccCCCCccccccC
Confidence 4689999999999999999999999999999999999999999999999964
No 9
>smart00746 TRASH metallochaperone-like domain.
Probab=98.43 E-value=3.2e-07 Score=51.20 Aligned_cols=37 Identities=57% Similarity=1.186 Sum_probs=33.6
Q ss_pred eecCCCCcc-CCccceEEeeCCceEEEechhhhhhhhcc
Q 030949 6 CWFCSSTVY-PGHGIQFVRNDAKIFRFCRSKCHKNFKMK 43 (168)
Q Consensus 6 CsFcG~kIY-PGhG~~fVRnDGkvF~FcsSKC~k~fk~K 43 (168)
|.+||..|+ |+.+..++ .||++++|||..|...|..+
T Consensus 1 c~~C~~~~~~~~~~~~~~-~~g~~~~FCs~~c~~~~~~~ 38 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVV-NDGKVFYFCSSKCLSKFKKK 38 (39)
T ss_pred CCCCCCCccCCCCceEEE-ECCEEEEEeCHHHHHHHHhc
Confidence 889999999 88888888 99999999999999988654
No 10
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=96.63 E-value=0.0026 Score=41.21 Aligned_cols=36 Identities=31% Similarity=0.753 Sum_probs=31.4
Q ss_pred eecCCCCccCCccceEEeeCCceEEEechhhhhhhhcc
Q 030949 6 CWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMK 43 (168)
Q Consensus 6 CsFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~k~fk~K 43 (168)
|.+||.+|. |.++.+ +-++++++||..-|.+-|+.|
T Consensus 1 Cd~CG~~I~-~eP~~~-k~~~~~y~fCC~tC~~~fk~k 36 (37)
T PF08394_consen 1 CDYCGGEIT-GEPIVV-KIGNKVYYFCCPTCLSQFKKK 36 (37)
T ss_pred CCccCCccc-CCEEEE-EECCeEEEEECHHHHHHHHhh
Confidence 899999998 777764 559999999999999999865
No 11
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=96.46 E-value=0.003 Score=40.78 Aligned_cols=36 Identities=25% Similarity=0.611 Sum_probs=26.5
Q ss_pred eecCCCCccCCccceEEeeCCceEEEechhhhhhhhc
Q 030949 6 CWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKM 42 (168)
Q Consensus 6 CsFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~k~fk~ 42 (168)
..-||-.| ||.....+.-+|+.++|||..|...|..
T Consensus 3 DPvcg~~v-~~~~~~~~~y~G~~Y~FCS~~C~~~F~~ 38 (47)
T PF04945_consen 3 DPVCGMKV-PGNAAYSVEYNGRTYYFCSEGCKEKFEA 38 (47)
T ss_dssp B-GGG-BE------EEEEETTEEEEESSHHHHHHHHC
T ss_pred CCCCCCEE-ccCccEEEEECCEEEEEcCHHHHHHHHH
Confidence 45799999 9999999999999999999999999863
No 12
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=95.39 E-value=0.0056 Score=38.12 Aligned_cols=37 Identities=22% Similarity=0.556 Sum_probs=26.4
Q ss_pred eeeeecCCCCccCCc-cceEEeeCCceEEEechhhhhhh
Q 030949 3 LEKCWFCSSTVYPGH-GIQFVRNDAKIFRFCRSKCHKNF 40 (168)
Q Consensus 3 ie~CsFcG~kIYPGh-G~~fVRnDGkvF~FcsSKC~k~f 40 (168)
...|++|+..|+.+. + .-+..||+.-.|||.-|...|
T Consensus 6 ~~~C~~C~~~~~~~~~~-~~~~~~g~~~~FCS~~C~~~y 43 (43)
T PF06467_consen 6 MKTCSYCKKYIPNKPTM-IEVQYDGKMKQFCSQSCLSSY 43 (43)
T ss_dssp CEE-TTT--EEECCC-----EE-TTTTSCCSSHHHHHHH
T ss_pred CCcCcccCCcccCCCcc-ccccccCcccChhCHHHHhhC
Confidence 457999999999888 5 888899999999999997654
No 13
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=94.75 E-value=0.0054 Score=43.06 Aligned_cols=26 Identities=27% Similarity=0.871 Sum_probs=22.4
Q ss_pred eeeecCCCCccCCccceEEeeCCceEEEechhhhhhhh
Q 030949 4 EKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFK 41 (168)
Q Consensus 4 e~CsFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~k~fk 41 (168)
..|-.||.+|+|. -.|||.+|++.+.
T Consensus 4 kHC~~CG~~Ip~~------------~~fCS~~C~~~~~ 29 (59)
T PF09889_consen 4 KHCPVCGKPIPPD------------ESFCSPKCREEYR 29 (59)
T ss_pred CcCCcCCCcCCcc------------hhhhCHHHHHHHH
Confidence 4699999999994 5799999999875
No 14
>PF05573 NosL: NosL; InterPro: IPR008719 NosL is one of the accessory proteins of the nos (nitrous oxide reductase) gene cluster. NosL is a monomeric protein of 18,540 MW that specifically and stoichiometrically binds Cu(I). The copper ion in NosL is ligated by a Cys residue, and one Met and one His are thought to serve as the other ligands. It is possible that NosL is a copper chaperone involved in metallocentre assembly []. This entry also contains HTH-type transcriptional repressors, including YcnK. YcnK may act as a negative transcriptional regulator of YcnJ in the presence of copper and may use copper as a corepressor. The gene, ycnK, is significantly induced under copper-limiting conditions.; PDB: 2HQ3_A 2HPU_A.
Probab=91.24 E-value=0.15 Score=39.89 Aligned_cols=39 Identities=26% Similarity=0.694 Sum_probs=16.3
Q ss_pred eeeecCCCCc--cCCccceEEeeCC-ceEEEechhhhhhhhc
Q 030949 4 EKCWFCSSTV--YPGHGIQFVRNDA-KIFRFCRSKCHKNFKM 42 (168)
Q Consensus 4 e~CsFcG~kI--YPGhG~~fVRnDG-kvF~FcsSKC~k~fk~ 42 (168)
+.|.+||-.| |||.--..+-.|| ++++||+-+|--.|.+
T Consensus 26 ~~C~~CgM~i~d~p~~~aqi~~~~g~~~~~Fdsi~c~~~~~~ 67 (149)
T PF05573_consen 26 DRCPVCGMVISDYPGFAAQIIYKDGEKVYKFDSIGCMFAYLK 67 (149)
T ss_dssp -----------------EEEEETT-SSEEEES-HHHHHHHHT
T ss_pred CccCCCCCEeccCCCccEEEEECCCCEEEEECCHHHHHHHHh
Confidence 6799999999 6875444444555 9999999999877654
No 15
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=89.90 E-value=0.45 Score=33.27 Aligned_cols=38 Identities=26% Similarity=0.506 Sum_probs=29.5
Q ss_pred ecCCCCccCCccceEEeeCCceEEEechhhhhhhhcccCC
Q 030949 7 WFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNP 46 (168)
Q Consensus 7 sFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~k~fk~KRNP 46 (168)
.-||.+|.+-.-.-=.--+|+.++|||..|...|+ .||
T Consensus 6 PVcgm~v~~~~a~~k~~Y~GktYYFcse~~~~~F~--~~P 43 (53)
T COG3350 6 PVCGMKVDNENAEYKSSYGGKTYYFCSEECKEKFK--DNP 43 (53)
T ss_pred CCcCccccccccceeEEeCCEEEEEeCHHHHHHHH--HCH
Confidence 35788887766666666789999999999988874 455
No 16
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=87.10 E-value=0.25 Score=38.18 Aligned_cols=29 Identities=24% Similarity=0.684 Sum_probs=22.9
Q ss_pred eeeeecCCCCccCCccceEEeeCCceEEEe
Q 030949 3 LEKCWFCSSTVYPGHGIQFVRNDAKIFRFC 32 (168)
Q Consensus 3 ie~CsFcG~kIYPGhG~~fVRnDGkvF~Fc 32 (168)
..+|++||.+|+-|..-+|.++ |-|.+=|
T Consensus 2 kWkC~iCg~~I~~gqlFTF~~k-G~VH~~C 30 (101)
T PF09943_consen 2 KWKCYICGKPIYEGQLFTFTKK-GPVHYEC 30 (101)
T ss_pred ceEEEecCCeeeecceEEEecC-CcEeHHH
Confidence 3589999999999888888877 7765443
No 17
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=71.04 E-value=1.4 Score=31.90 Aligned_cols=24 Identities=21% Similarity=0.743 Sum_probs=20.5
Q ss_pred eeeecCCCCccCCccceEEeeCCceEEEechhhhhh
Q 030949 4 EKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKN 39 (168)
Q Consensus 4 e~CsFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~k~ 39 (168)
..|-.||..|+||. .|||-+|..-
T Consensus 9 ~HC~VCg~aIp~de------------~~CSe~C~ei 32 (64)
T COG4068 9 RHCVVCGKAIPPDE------------QVCSEECGEI 32 (64)
T ss_pred ccccccCCcCCCcc------------chHHHHHHHH
Confidence 46999999999985 6899999844
No 18
>PHA03073 late transcription factor VLTF-2; Provisional
Probab=68.24 E-value=3 Score=34.49 Aligned_cols=38 Identities=21% Similarity=0.607 Sum_probs=29.5
Q ss_pred eeeeecCCCCccCCccceEEeeCC-ceEEEechhhhhhhh
Q 030949 3 LEKCWFCSSTVYPGHGIQFVRNDA-KIFRFCRSKCHKNFK 41 (168)
Q Consensus 3 ie~CsFcG~kIYPGhG~~fVRnDG-kvF~FcsSKC~k~fk 41 (168)
...|+||++..-+-. ...=..+| .+=.|||.=|+-+|.
T Consensus 49 ~~~CwfC~q~~~~~~-~~iETl~g~~vg~FCS~ICRDSfa 87 (150)
T PHA03073 49 NDYCWFCKQDLIIAP-LFIETLKGGAVGYFCSKICRDSFA 87 (150)
T ss_pred CCcEEeeccccccCc-eEEEeecCchhhhHhHHHHHHHHH
Confidence 467999999988766 33333556 999999999999985
No 19
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=66.51 E-value=4.4 Score=28.45 Aligned_cols=34 Identities=29% Similarity=0.802 Sum_probs=27.9
Q ss_pred eeeecCCCCccCCccceEEeeCCceEEEechhhhhhh
Q 030949 4 EKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNF 40 (168)
Q Consensus 4 e~CsFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~k~f 40 (168)
..|++|..++-||..+-.-|-|. -|||.-|+...
T Consensus 17 ~~C~~C~k~L~~~~DiymYrGd~---aFCS~ECR~~q 50 (58)
T PF04570_consen 17 SFCYLCKKKLDPGKDIYMYRGDK---AFCSEECRSQQ 50 (58)
T ss_pred HHHHccCCCCCCCCCeeeecccc---ccccHHHHHHH
Confidence 46999999999999877666665 49999998764
No 20
>cd01057 AAMH_A Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain. Aromatic and Alkene Monooxygenase Hydroxylases, subunit A (AAMH_A). Subunit A of the soluble hydroxylase of multicomponent, aromatic and alkene monooxygenases are members of a superfamily of ferritin-like iron-storage proteins. AAMH exists as a hexamer (an alpha2-beta2-gamma2 homodimer) with each alpha-subunit housing one nonheme diiron center embedded in a four-helix bundle. The N-terminal domain of the alpha- and noncatalytic beta-subunits possess nearly identical folds, however, the beta-subunit lacks critical diiron ligands and a C-terminal domain found in the alpha-subunit. Methane monooxygenase is a multicomponent enzyme found in methanotrophic bacteria that catalyzes the hydroxylation of methane and higher alkenes (as large as octane). Phenol monooxygenase, found in a diverse group of bacteria, catalyses the hydroxylation of phenol, chloro- and methyl-phenol and naphtho
Probab=65.45 E-value=5.9 Score=37.09 Aligned_cols=51 Identities=20% Similarity=0.462 Sum_probs=38.2
Q ss_pred eeecCCCCccC----CccceEE-eeCCceEEEechhhhhhhhcccCCccc--hhhHHHHH
Q 030949 5 KCWFCSSTVYP----GHGIQFV-RNDAKIFRFCRSKCHKNFKMKRNPRKV--KWTKAYRR 57 (168)
Q Consensus 5 ~CsFcG~kIYP----GhG~~fV-RnDGkvF~FcsSKC~k~fk~KRNPRKl--kWT~~yRr 57 (168)
.|.-|+-+|-| +....++ --||+.+.|||.-|+.-|.+ +|-+- .|+..-|-
T Consensus 382 ~c~vC~~p~~~~~~~~~~~~~~~ey~G~~y~FCS~~C~~~F~~--ePerY~~~~~~~~~~ 439 (465)
T cd01057 382 LCNVCQVPCVFTEDLTAEAPRVLEYNGRKYHFCSEGCEWIFEQ--EPERYAGHWNPVDRF 439 (465)
T ss_pred CCCCCCCeeccccCcccccceEEEECCEEEEecCHHHHHHHHH--CHHHHhcCCCHHHHH
Confidence 69999999985 4444444 46999999999999999986 77765 45554443
No 21
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=55.43 E-value=4.7 Score=31.54 Aligned_cols=29 Identities=21% Similarity=0.618 Sum_probs=21.1
Q ss_pred CceeeeecCCCCccCCccceEEeeCCceEE
Q 030949 1 MRLEKCWFCSSTVYPGHGIQFVRNDAKIFR 30 (168)
Q Consensus 1 Mkie~CsFcG~kIYPGhG~~fVRnDGkvF~ 30 (168)
|+..+|+.||.+|--|.--+|.. .|.|.+
T Consensus 4 lkewkC~VCg~~iieGqkFTF~~-kGsVH~ 32 (103)
T COG4847 4 LKEWKCYVCGGTIIEGQKFTFTK-KGSVHY 32 (103)
T ss_pred cceeeEeeeCCEeeeccEEEEee-CCcchH
Confidence 67889999999998776666655 355433
No 22
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=50.57 E-value=17 Score=22.95 Aligned_cols=21 Identities=33% Similarity=0.632 Sum_probs=15.8
Q ss_pred eeecCCCCccCCccceEEeeCCce
Q 030949 5 KCWFCSSTVYPGHGIQFVRNDAKI 28 (168)
Q Consensus 5 ~CsFcG~kIYPGhG~~fVRnDGkv 28 (168)
.|+-|+.+|.++. |.-.||++
T Consensus 28 ~C~~C~~~l~~~~---~~~~~~~~ 48 (58)
T PF00412_consen 28 KCSKCGKPLNDGD---FYEKDGKP 48 (58)
T ss_dssp BETTTTCBTTTSS---EEEETTEE
T ss_pred ccCCCCCccCCCe---eEeECCEE
Confidence 5888898888777 66677753
No 23
>COG4314 NosL Predicted lipoprotein involved in nitrous oxide reduction [Energy production and conversion]
Probab=50.28 E-value=17 Score=30.76 Aligned_cols=46 Identities=15% Similarity=0.426 Sum_probs=36.8
Q ss_pred eeeecCCCCc--cCC-ccceEEeeCCceEEEechhhhhhhh-cccCCccc
Q 030949 4 EKCWFCSSTV--YPG-HGIQFVRNDAKIFRFCRSKCHKNFK-MKRNPRKV 49 (168)
Q Consensus 4 e~CsFcG~kI--YPG-hG~~fVRnDGkvF~FcsSKC~k~fk-~KRNPRKl 49 (168)
..|.+||-.| ||| +|..+..-+-+..||||.+--=+|. +--+||.|
T Consensus 36 s~g~ycgMnl~ehpGPKgQi~l~g~~qP~wfsst~e~f~~tllPEepk~i 85 (176)
T COG4314 36 SMGHYCGMNLLEHPGPKGQIILNGKPQPIWFSSTREMFGFTLLPEEPKGI 85 (176)
T ss_pred ccccccceeeecCCCCcceEeeCCCCCceeeecHHHHhhHhcCCcCcCce
Confidence 3699999887 688 5999999888899999999876654 66677655
No 24
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=45.83 E-value=7.3 Score=24.97 Aligned_cols=13 Identities=23% Similarity=0.598 Sum_probs=6.7
Q ss_pred eeeecCCCCccCC
Q 030949 4 EKCWFCSSTVYPG 16 (168)
Q Consensus 4 e~CsFcG~kIYPG 16 (168)
..|||||.+-...
T Consensus 2 ~~CSFCgr~~~~v 14 (41)
T PF06689_consen 2 KRCSFCGRPESEV 14 (41)
T ss_dssp -B-TTT--BTTTS
T ss_pred CCccCCCCCHHHH
Confidence 4799999986644
No 25
>PF15585 Imm46: Immunity protein 46
Probab=41.80 E-value=18 Score=29.19 Aligned_cols=26 Identities=27% Similarity=0.772 Sum_probs=21.0
Q ss_pred CccCCc-cceEEeeCC--------ceEEEechhhh
Q 030949 12 TVYPGH-GIQFVRNDA--------KIFRFCRSKCH 37 (168)
Q Consensus 12 kIYPGh-G~~fVRnDG--------kvF~FcsSKC~ 37 (168)
+|-||. |.+|+|.|- +|+.+++++|.
T Consensus 79 e~aPGSYGlLy~rDDEd~~~~neFrV~vl~RG~~t 113 (129)
T PF15585_consen 79 EIAPGSYGLLYIRDDEDPEHFNEFRVFVLARGELT 113 (129)
T ss_pred HhCCCceeEEEEecCCCCCCCCceEEEEEEccEEe
Confidence 355665 999999887 78999998884
No 26
>PF08384 NPP: Pro-opiomelanocortin, N-terminal region; InterPro: IPR013593 This domain represents the N-terminal peptide of pro-opiomelanocortin (NPP). It is thought to represent an important pituitary peptide, given its high yield from pituitary glands, and exhibits a potent in vitro aldosterone-stimulating activity [].
Probab=41.19 E-value=13 Score=25.29 Aligned_cols=11 Identities=45% Similarity=0.884 Sum_probs=9.3
Q ss_pred CCCccCCccce
Q 030949 10 SSTVYPGHGIQ 20 (168)
Q Consensus 10 G~kIYPGhG~~ 20 (168)
..+||||+|.+
T Consensus 31 EsPv~PGn~hl 41 (45)
T PF08384_consen 31 ESPVFPGNGHL 41 (45)
T ss_pred CCCccCCCccc
Confidence 67999999964
No 27
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=39.15 E-value=24 Score=28.37 Aligned_cols=31 Identities=23% Similarity=0.562 Sum_probs=25.7
Q ss_pred eecCCCCccCCccceEEeeCCceEEEechhhhhh
Q 030949 6 CWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKN 39 (168)
Q Consensus 6 CsFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~k~ 39 (168)
|--||.+|. |.| .-|+-||..+.-|.+ |.+.
T Consensus 3 CEiCG~~i~-~~~-~~v~iega~l~vC~~-C~k~ 33 (154)
T TIGR00270 3 CEICGRKIK-GKG-FKIVIEGSEMTVCGE-CRKF 33 (154)
T ss_pred cccCCCccC-CCC-eEEEEcCeEEehhhh-HHhc
Confidence 999999995 665 779999999999985 6543
No 28
>KOG3851 consensus Sulfide:quinone oxidoreductase/flavo-binding protein [Energy production and conversion]
Probab=37.84 E-value=12 Score=35.35 Aligned_cols=71 Identities=31% Similarity=0.540 Sum_probs=48.5
Q ss_pred CceEEEech--hhhhhhhcccCCccchh-hHHHHHHhCCcceeeec-ccchh--hhhhHhhhhhHHhhhcCccccCCCcc
Q 030949 26 AKIFRFCRS--KCHKNFKMKRNPRKVKW-TKAYRRLHGKDMTQVNM-FGFSI--LFCNLFYLNMFMRISGDLFFSFPFSY 99 (168)
Q Consensus 26 GkvF~FcsS--KC~k~fk~KRNPRKlkW-T~~yRr~~KK~~~~~~~-~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~ 99 (168)
.-+|.|=|. ||.- -|.|+-| |..|-|.+|+--. .|| |.-|. +|...-|.
T Consensus 185 NAIfTfPntpiKCAG------APQKi~yise~y~Rk~gvRd~-a~iiy~Tsl~~iFgVk~Y~------------------ 239 (446)
T KOG3851|consen 185 NAIFTFPNTPIKCAG------APQKIMYISESYFRKRGVRDN-ANIIYNTSLPTIFGVKHYA------------------ 239 (446)
T ss_pred ceEEecCCCccccCC------CchhhhhhhHHHHHHhCcccc-ccEEEecCccceecHHHHH------------------
Confidence 345666553 5543 4889999 5677777777654 344 66664 67777773
Q ss_pred cCCchHHHHHhhCCCccccHHHHH
Q 030949 100 RQDSTFEFERKRNRPERYDRNLAE 123 (168)
Q Consensus 100 ~~d~t~e~ekrrn~~~ky~R~l~~ 123 (168)
|+-.+..+.||..++|.|+|++
T Consensus 240 --~AL~k~~~~rni~vn~krnLiE 261 (446)
T KOG3851|consen 240 --DALEKVIQERNITVNYKRNLIE 261 (446)
T ss_pred --HHHHHHHHhcceEeeeccceEE
Confidence 4444556789999999999986
No 29
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=35.80 E-value=30 Score=19.65 Aligned_cols=25 Identities=24% Similarity=0.394 Sum_probs=18.7
Q ss_pred eeecCCCCccCCccceEEeeCCceEEE
Q 030949 5 KCWFCSSTVYPGHGIQFVRNDAKIFRF 31 (168)
Q Consensus 5 ~CsFcG~kIYPGhG~~fVRnDGkvF~F 31 (168)
.|.-|+.+|+|+ ...+..+|+.|.-
T Consensus 1 ~C~~C~~~i~~~--~~~~~~~~~~~H~ 25 (39)
T smart00132 1 KCAGCGKPIRGG--ELVLRALGKVWHP 25 (39)
T ss_pred CccccCCcccCC--cEEEEeCCccccc
Confidence 488899999998 5566667776653
No 30
>PRK08359 transcription factor; Validated
Probab=35.03 E-value=30 Score=28.81 Aligned_cols=30 Identities=23% Similarity=0.619 Sum_probs=25.4
Q ss_pred eeecCCCCccCCccceEEeeCCceEEEechhhh
Q 030949 5 KCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCH 37 (168)
Q Consensus 5 ~CsFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~ 37 (168)
.|--||.+|. |.| .-|+-||..+.-|++ |.
T Consensus 8 ~CEiCG~~i~-g~~-~~v~ieGael~VC~~-Ca 37 (176)
T PRK08359 8 YCEICGAEIR-GPG-HRIRIEGAELLVCDR-CY 37 (176)
T ss_pred eeecCCCccC-CCC-eEEEEcCeEEehHHH-HH
Confidence 4999999995 665 779999999999985 65
No 31
>PLN02469 hydroxyacylglutathione hydrolase
Probab=33.20 E-value=41 Score=28.50 Aligned_cols=25 Identities=28% Similarity=0.139 Sum_probs=16.6
Q ss_pred CchHHHHHhhCCCccccHHHHHHHH
Q 030949 102 DSTFEFERKRNRPERYDRNLAENTL 126 (168)
Q Consensus 102 d~t~e~ekrrn~~~ky~R~l~~~tl 126 (168)
=||...||+-|-=.|.+..-+.+.+
T Consensus 213 pstl~~E~~~Npflr~~~~~~~~~~ 237 (258)
T PLN02469 213 PSTIEEELETNPFMRVDLPEIQEKV 237 (258)
T ss_pred CccHHHHHhhCCeecCCCHHHHHHh
Confidence 4566778888877777665555444
No 32
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=32.32 E-value=51 Score=23.76 Aligned_cols=37 Identities=24% Similarity=0.407 Sum_probs=27.7
Q ss_pred eeeeecCCCCccCCccce-EE-eeCCceEEEechhhhhh
Q 030949 3 LEKCWFCSSTVYPGHGIQ-FV-RNDAKIFRFCRSKCHKN 39 (168)
Q Consensus 3 ie~CsFcG~kIYPGhG~~-fV-RnDGkvF~FcsSKC~k~ 39 (168)
...|.-||..|.||.+-. |. -|=|++...=..||+++
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~CRk~ 47 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKCRKL 47 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehhhhHHHc
Confidence 468999999999997643 32 36677777777888775
No 33
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=31.40 E-value=38 Score=24.46 Aligned_cols=31 Identities=19% Similarity=0.423 Sum_probs=24.5
Q ss_pred eeeeecCCCCccCCccceEEeeCCceEEEechhhhhh
Q 030949 3 LEKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKN 39 (168)
Q Consensus 3 ie~CsFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~k~ 39 (168)
++-|.|||.++ ..|+.++--++|+..+|...
T Consensus 6 lKPCPFCG~~~------~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 6 VKPCPFCGCPS------VTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred ccCCCCCCCce------eEEEecCceEEEEcCCCCcC
Confidence 56799998875 46677788888888899874
No 34
>PF14353 CpXC: CpXC protein
Probab=27.71 E-value=69 Score=23.97 Aligned_cols=33 Identities=9% Similarity=0.124 Sum_probs=29.4
Q ss_pred eeeeecCCCCccCCccceEEeeCCceEEEechh
Q 030949 3 LEKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSK 35 (168)
Q Consensus 3 ie~CsFcG~kIYPGhG~~fVRnDGkvF~FcsSK 35 (168)
.-+|.-||......+..+|...+.+.+.+....
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~~~~~~i~~~P~ 70 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDPEKKFMIYYFPD 70 (128)
T ss_pred EEECCCCCCceecCCCEEEEcCCCCEEEEEcCC
Confidence 357999999999999999999999988887766
No 35
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=27.25 E-value=41 Score=20.00 Aligned_cols=17 Identities=24% Similarity=0.657 Sum_probs=13.9
Q ss_pred eecCCCCccCCc-cceEE
Q 030949 6 CWFCSSTVYPGH-GIQFV 22 (168)
Q Consensus 6 CsFcG~kIYPGh-G~~fV 22 (168)
|.-||..|.|.. |..|.
T Consensus 1 C~sC~~~i~~r~~~v~f~ 18 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFP 18 (24)
T ss_pred CccCCCcccCcccCceEe
Confidence 778999999877 77775
No 36
>PF08789 PBCV_basic_adap: PBCV-specific basic adaptor domain; InterPro: IPR014897 The small PBCV-specific basic adaptor protein is found fused to S/T protein kinases and the 2-Cysteine domain [].
Probab=24.33 E-value=45 Score=22.12 Aligned_cols=18 Identities=22% Similarity=0.493 Sum_probs=15.3
Q ss_pred CCCCccCC-ccceEEeeCC
Q 030949 9 CSSTVYPG-HGIQFVRNDA 26 (168)
Q Consensus 9 cG~kIYPG-hG~~fVRnDG 26 (168)
-|..||-| .|..||..|+
T Consensus 7 kgR~i~~g~rGg~yV~~~~ 25 (40)
T PF08789_consen 7 KGRKIFKGPRGGTYVISDG 25 (40)
T ss_pred cCCEEEECCCCCEEEeCCC
Confidence 37789998 7999999985
No 37
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=22.87 E-value=54 Score=23.35 Aligned_cols=40 Identities=25% Similarity=0.511 Sum_probs=27.6
Q ss_pred CceeeeecCCCCccCCc-cceEEe-eCCceEEEechhhhhhh
Q 030949 1 MRLEKCWFCSSTVYPGH-GIQFVR-NDAKIFRFCRSKCHKNF 40 (168)
Q Consensus 1 Mkie~CsFcG~kIYPGh-G~~fVR-nDGkvF~FcsSKC~k~f 40 (168)
|....|.-||..|.|+. |..|-= |=|++...=-.||++..
T Consensus 5 ~~~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~ 46 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQS 46 (59)
T ss_pred ccCccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhcC
Confidence 34668999999999876 776654 44565344456777654
No 38
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=22.26 E-value=43 Score=23.55 Aligned_cols=13 Identities=23% Similarity=0.514 Sum_probs=11.0
Q ss_pred eeecCCCCccCCc
Q 030949 5 KCWFCSSTVYPGH 17 (168)
Q Consensus 5 ~CsFcG~kIYPGh 17 (168)
-|-|||.++.+|.
T Consensus 41 gCPfC~~~~~~~~ 53 (55)
T PF14447_consen 41 GCPFCGTPFEFDD 53 (55)
T ss_pred CCCCCCCcccCCC
Confidence 4899999999874
No 39
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=22.07 E-value=50 Score=23.08 Aligned_cols=29 Identities=24% Similarity=0.495 Sum_probs=14.7
Q ss_pred eeeecCCCCccCCccceEEeeCCceEEEechhhhhh
Q 030949 4 EKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKN 39 (168)
Q Consensus 4 e~CsFcG~kIYPGhG~~fVRnDGkvF~FcsSKC~k~ 39 (168)
..|.-||.++.+.. +....=|||.+|+-.
T Consensus 3 v~CP~C~k~~~~~~-------~n~~rPFCS~RCk~i 31 (57)
T PF03884_consen 3 VKCPICGKPVEWSP-------ENPFRPFCSERCKLI 31 (57)
T ss_dssp EE-TTT--EEE-SS-------SSS--SSSSHHHHHH
T ss_pred ccCCCCCCeecccC-------CCCcCCcccHhhccc
Confidence 35777777666532 223344999999743
Done!