Query 032380
Match_columns 142
No_of_seqs 152 out of 441
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 13:20:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032380.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032380hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1722 60s ribosomal protein 100.0 2.5E-45 5.5E-50 283.6 8.8 134 2-139 21-155 (155)
2 PTZ00033 60S ribosomal protein 100.0 6.5E-40 1.4E-44 248.4 8.9 100 1-101 20-123 (125)
3 PF01246 Ribosomal_L24e: Ribos 99.9 4E-24 8.7E-29 148.7 -1.9 51 1-51 20-70 (71)
4 COG2075 RPL24A Ribosomal prote 99.9 1.8E-22 3.8E-27 138.7 3.3 46 1-46 20-65 (66)
5 PRK14891 50S ribosomal protein 99.9 2.8E-22 6.1E-27 153.1 3.7 44 1-44 21-64 (131)
6 KOG1723 60s ribosomal protein 99.8 8.1E-20 1.8E-24 144.1 3.8 99 1-99 20-132 (162)
7 cd00472 Ribosomal_L24e_L24 Rib 99.7 5.9E-19 1.3E-23 117.1 1.6 35 1-35 20-54 (54)
8 PRK00807 50S ribosomal protein 99.7 1E-17 2.2E-22 110.1 1.5 34 1-34 18-51 (52)
9 smart00746 TRASH metallochaper 95.9 0.0057 1.2E-07 33.3 1.9 21 4-24 18-38 (39)
10 PF04945 YHS: YHS domain; Int 93.5 0.059 1.3E-06 33.7 2.1 21 3-23 18-38 (47)
11 COG3350 Uncharacterized conser 91.9 0.13 2.8E-06 34.4 2.1 21 5-27 23-43 (53)
12 PF08394 Arc_trans_TRASH: Arch 86.6 0.54 1.2E-05 29.2 1.8 23 2-24 14-36 (37)
13 PF06467 zf-FCS: MYM-type Zinc 68.4 2.1 4.5E-05 25.7 0.4 19 3-21 25-43 (43)
14 cd01057 AAMH_A Aromatic and Al 51.5 9.2 0.0002 34.9 1.7 32 5-38 406-439 (465)
15 PF09889 DUF2116: Uncharacteri 51.2 3.8 8.3E-05 27.6 -0.6 24 10-33 17-41 (59)
16 TIGR03666 Rv2061_F420 PPOX cla 37.6 18 0.00038 27.1 1.1 27 2-28 33-59 (132)
17 PF15279 SOBP: Sine oculis-bin 26.0 24 0.00052 30.8 0.2 16 8-23 22-37 (306)
18 PF05573 NosL: NosL; InterPro 24.8 54 0.0012 24.9 1.9 20 4-23 47-67 (149)
19 TIGR03667 Rv3369 PPOX class pr 22.1 50 0.0011 24.2 1.2 27 3-29 36-62 (130)
No 1
>KOG1722 consensus 60s ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-45 Score=283.63 Aligned_cols=134 Identities=49% Similarity=0.716 Sum_probs=123.8
Q ss_pred cccccCceEeeechHHHHHhhccCCCcchhHHHHHHHhhhhhHHHHHHHhHhccCCCccccchhhhcHHHHHHHHhcChH
Q 032380 2 LPWLWVKVFLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKDIAAEAVKKKRRSTKKPYSRSIVGATLEVIQKRRTEKPE 81 (142)
Q Consensus 2 ~vr~Dgkvf~FcssKC~~~f~~krnPRKl~WT~~yRr~~kK~~~~e~~~krrR~~~~k~~Raivg~SLe~I~~kR~qk~e 81 (142)
|||-||+||.|+|+||+++|++++|||+|.||++||+.|+||+++|.+++++|+++.+|||+|||+||++|+++|||+||
T Consensus 21 ~vR~D~Kvf~Fln~Kc~~~f~~rrnPr~l~WTvLyR~khkKg~~ee~~kkrtrrt~k~~qRaI~GasL~~I~~KRn~kpe 100 (155)
T KOG1722|consen 21 FVRGDGKVFRFLNSKCESLFLQRRNPRRLAWTVLYRKKHKKGIQEEAAKKRTRRTVKKFQRAIVGASLDVILEKRNQKPE 100 (155)
T ss_pred EEecCCeeeeehhhhhHHHHHhccChhhhhHHHHHHHHhhcchhHHHHHHHhhhhhhhhhhhhccccHHHHHHHhccChH
Confidence 89999999999999999999999999999999999999999999999999999999889999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhhccccCC-CCCCCCCCCCCCCCCCCC
Q 032380 82 VRDAAREAALREIKERIKKTKDEKRAKKAEVTSKSKTQSK-GSMPKGAAPKGPKLGGGG 139 (142)
Q Consensus 82 ~r~a~re~a~~e~Kek~k~~~a~kka~ka~~~~~~k~~~k-~~~~k~~~~~~~~~~g~~ 139 (142)
+|+++||++++++||++++..+++++.++..++ +|+ +++.++++.++|+|||+.
T Consensus 101 vR~a~Re~alK~aKe~~ka~k~ak~A~K~~~as----~~k~qk~~k~~k~aaprVggkr 155 (155)
T KOG1722|consen 101 VRKAAREAALKKAKEKKKATKAAKKAKKAKSAS----APKKQKAKKNAKVAAPRVGGKR 155 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhccccccc----cccccchhhhhhhhcccccCCC
Confidence 999999999999999999998888665554333 333 889999999999999974
No 2
>PTZ00033 60S ribosomal protein L24; Provisional
Probab=100.00 E-value=6.5e-40 Score=248.42 Aligned_cols=100 Identities=27% Similarity=0.390 Sum_probs=94.1
Q ss_pred Cccc----ccCceEeeechHHHHHhhccCCCcchhHHHHHHHhhhhhHHHHHHHhHhccCCCccccchhhhcHHHHHHHH
Q 032380 1 MLPW----LWVKVFLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKDIAAEAVKKKRRSTKKPYSRSIVGATLEVIQKRR 76 (142)
Q Consensus 1 m~vr----~Dgkvf~FcssKC~~~f~~krnPRKl~WT~~yRr~~kK~~~~e~~~krrR~~~~k~~Raivg~SLe~I~~kR 76 (142)
|||+ +||+||+||||||+++|++++|||+|.||++||++|+||+++++ .+++++++++|||+|||+|||+|+++|
T Consensus 20 ~~Vr~~~~~Dgkv~~F~~sKc~~~~~~krnPRkl~WT~~yRr~~kK~~~e~~-~kkR~~rtvK~qRaivg~sLe~I~~kR 98 (125)
T PTZ00033 20 RYVPFAFLSTKPVLTFLRPKCFALYMRKKNPRFLPWTRTYRRINRKTTTDRV-QRRRAARTVKVQRAIVGADLSYIQEVR 98 (125)
T ss_pred EeeecccCCCCCEEEEecHHHHHHHHCcCCCccchHHHHHHHHhCCcchhHH-HHHHhcCCccchHHHHHHHHHHHHHHH
Confidence 7999 99999999999999999999999999999999999999987776 577777788999999999999999999
Q ss_pred hcChHHHHHHHHHHHHHHHHHhhhh
Q 032380 77 TEKPEVRDAAREAALREIKERIKKT 101 (142)
Q Consensus 77 ~qk~e~r~a~re~a~~e~Kek~k~~ 101 (142)
||+||++.++++++++++||+.++.
T Consensus 99 ~~k~evr~aar~~a~r~~Ke~~~~~ 123 (125)
T PTZ00033 99 AYVQKVDRSAKAKAVRAEKAERKAA 123 (125)
T ss_pred hcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999988754
No 3
>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=99.87 E-value=4e-24 Score=148.67 Aligned_cols=51 Identities=47% Similarity=0.718 Sum_probs=39.6
Q ss_pred CcccccCceEeeechHHHHHhhccCCCcchhHHHHHHHhhhhhHHHHHHHh
Q 032380 1 MLPWLWVKVFLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKDIAAEAVKK 51 (142)
Q Consensus 1 m~vr~Dgkvf~FcssKC~~~f~~krnPRKl~WT~~yRr~~kK~~~~e~~~k 51 (142)
|||++||+||+|||+||++||.+++|||+|.||.+||++|+|++++|++++
T Consensus 20 ~~Vr~DG~v~~F~s~Kc~~~~~~krnPrkl~WT~~~Rr~~kK~~~~~~~kk 70 (71)
T PF01246_consen 20 MYVRNDGKVFYFCSSKCEKLFKLKRNPRKLKWTVAYRRQHKKGQSEEAAKK 70 (71)
T ss_dssp EEE-TTS-EEEESSHHHHHHHHTT--GGGSTTSTTTCHHH-----SSSSSS
T ss_pred EEEecCCCeEEEeCHHHHHHHHccCCcccchhHHHHHHHhCchhhhhHhhc
Confidence 799999999999999999999999999999999999999999999887643
No 4
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=99.86 E-value=1.8e-22 Score=138.73 Aligned_cols=46 Identities=43% Similarity=0.658 Sum_probs=44.3
Q ss_pred CcccccCceEeeechHHHHHhhccCCCcchhHHHHHHHhhhhhHHH
Q 032380 1 MLPWLWVKVFLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKDIAA 46 (142)
Q Consensus 1 m~vr~Dgkvf~FcssKC~~~f~~krnPRKl~WT~~yRr~~kK~~~~ 46 (142)
|||+|||+||+||||||+++|.++||||+|.||..||+++++++.+
T Consensus 20 m~Vr~Dg~v~~FcssKc~k~~~~~rnPRk~~WT~~~~~~~~k~~~~ 65 (66)
T COG2075 20 MYVRNDGKVLRFCSSKCEKLFKLGRNPRKLKWTKKYRKMHKKEIKE 65 (66)
T ss_pred EEEecCCeEEEEechhHHHHHHccCCCccchhHHHHHHHHHhhhcc
Confidence 8999999999999999999999999999999999999999998764
No 5
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=99.85 E-value=2.8e-22 Score=153.07 Aligned_cols=44 Identities=23% Similarity=0.347 Sum_probs=42.7
Q ss_pred CcccccCceEeeechHHHHHhhccCCCcchhHHHHHHHhhhhhH
Q 032380 1 MLPWLWVKVFLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKDI 44 (142)
Q Consensus 1 m~vr~Dgkvf~FcssKC~~~f~~krnPRKl~WT~~yRr~~kK~~ 44 (142)
|||||||+||+||||||++||+++||||+|.||++||+.+++..
T Consensus 21 ~fVR~DGkvf~FcssKC~k~f~~kRnPRKlkWT~~yRk~~g~~~ 64 (131)
T PRK14891 21 MFVRKDGTVLHFVDSKCEKNYDLGREARDLEWTEAGRAEKGPAA 64 (131)
T ss_pred EEEecCCCEEEEecHHHHHHHHccCCCccchhHHHHHHHcCchh
Confidence 89999999999999999999999999999999999999999963
No 6
>KOG1723 consensus 60s ribosomal protein L30 isolog [Translation, ribosomal structure and biogenesis]
Probab=99.78 E-value=8.1e-20 Score=144.06 Aligned_cols=99 Identities=26% Similarity=0.565 Sum_probs=87.3
Q ss_pred CcccccCceEeeechHHHHHhhccCCCcchhHHHHHHHhhhhhHHHHHH--HhHhccCCCccccchhhhcHHHHHH----
Q 032380 1 MLPWLWVKVFLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKDIAAEAV--KKKRRSTKKPYSRSIVGATLEVIQK---- 74 (142)
Q Consensus 1 m~vr~Dgkvf~FcssKC~~~f~~krnPRKl~WT~~yRr~~kK~~~~e~~--~krrR~~~~k~~Raivg~SLe~I~~---- 74 (142)
|||+||.++|.||.|+|+++|.+++|||++.||.++|+++++++..|.+ ++.+|+++++|+|+.++.||++|+.
T Consensus 20 ~Fv~Nd~k~f~Fc~skc~k~f~~k~nPrk~~~tka~rKaagre~~~d~~~e~~~rrn~~~~y~r~~~~~Ti~a~k~v~~i 99 (162)
T KOG1723|consen 20 MFVRNDCKVFRFCKSKCHKNFKQKKNPRKVGWTKAFRKAAGRELVTDSTFEFEKRRNVPRKYDRELINKTIDAMKRVLEI 99 (162)
T ss_pred EEEecCcchhHHHHhhhhhhhhhhcCCCccchHHHHHHHhhhhHhhhhhHHHHHhcCcchhhcccchhhHHHHHHHHHhh
Confidence 8999999999999999999999999999999999999999999999988 5779999999999999999999876
Q ss_pred --HHhcCh------HHHHHHHHHHHHHHHHHhh
Q 032380 75 --RRTEKP------EVRDAAREAALREIKERIK 99 (142)
Q Consensus 75 --kR~qk~------e~r~a~re~a~~e~Kek~k 99 (142)
+|.+.. ..++++...++.+++.+++
T Consensus 100 ~~~~~~~~i~~rL~~~ke~~~~~d~k~v~~n~~ 132 (162)
T KOG1723|consen 100 KQKREAHFIGNRLKKGKEAQLVQDIKEVKQNIH 132 (162)
T ss_pred cccchhhhhhhccCccchhccchhHHHHHhhhh
Confidence 333332 3677777788888887765
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=99.73 E-value=5.9e-19 Score=117.10 Aligned_cols=35 Identities=40% Similarity=0.620 Sum_probs=33.7
Q ss_pred CcccccCceEeeechHHHHHhhccCCCcchhHHHH
Q 032380 1 MLPWLWVKVFLFANSKCKRYFHNRLKPSKLTWTSM 35 (142)
Q Consensus 1 m~vr~Dgkvf~FcssKC~~~f~~krnPRKl~WT~~ 35 (142)
|||++||+||+|||+||++||.+++|||+|.||++
T Consensus 20 ~~Vr~Dgkv~~F~s~Kc~~~~~~krnPRkv~WT~~ 54 (54)
T cd00472 20 MYVRNDGKVFRFCSSKCEKNFLRKRNPRKLKWTVA 54 (54)
T ss_pred EEEecCCCEEEEECHHHHHHHHCcCCCCcceeecC
Confidence 89999999999999999999999999999999963
No 8
>PRK00807 50S ribosomal protein L24e; Validated
Probab=99.68 E-value=1e-17 Score=110.11 Aligned_cols=34 Identities=29% Similarity=0.498 Sum_probs=33.1
Q ss_pred CcccccCceEeeechHHHHHhhccCCCcchhHHH
Q 032380 1 MLPWLWVKVFLFANSKCKRYFHNRLKPSKLTWTS 34 (142)
Q Consensus 1 m~vr~Dgkvf~FcssKC~~~f~~krnPRKl~WT~ 34 (142)
|||++||+||+|||+||+++|++++|||+|.||.
T Consensus 18 ~~vr~Dgkv~~Fcs~KC~~~f~~~~nprk~~WT~ 51 (52)
T PRK00807 18 MYVKKDGTILYFCSSKCEKNYKLGRVPRKLKWTK 51 (52)
T ss_pred EEEEeCCcEEEEeCHHHHHHHHccCCCCcccccc
Confidence 6899999999999999999999999999999996
No 9
>smart00746 TRASH metallochaperone-like domain.
Probab=95.92 E-value=0.0057 Score=33.28 Aligned_cols=21 Identities=38% Similarity=0.501 Sum_probs=18.0
Q ss_pred cccCceEeeechHHHHHhhcc
Q 032380 4 WLWVKVFLFANSKCKRYFHNR 24 (142)
Q Consensus 4 r~Dgkvf~FcssKC~~~f~~k 24 (142)
..||++++|||..|...|...
T Consensus 18 ~~~g~~~~FCs~~c~~~~~~~ 38 (39)
T smart00746 18 VNDGKVFYFCSSKCLSKFKKK 38 (39)
T ss_pred EECCEEEEEeCHHHHHHHHhc
Confidence 378999999999999988653
No 10
>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=93.51 E-value=0.059 Score=33.71 Aligned_cols=21 Identities=19% Similarity=0.357 Sum_probs=18.0
Q ss_pred ccccCceEeeechHHHHHhhc
Q 032380 3 PWLWVKVFLFANSKCKRYFHN 23 (142)
Q Consensus 3 vr~Dgkvf~FcssKC~~~f~~ 23 (142)
+.-+|++|+|||.-|...|..
T Consensus 18 ~~y~G~~Y~FCS~~C~~~F~~ 38 (47)
T PF04945_consen 18 VEYNGRTYYFCSEGCKEKFEA 38 (47)
T ss_dssp EEETTEEEEESSHHHHHHHHC
T ss_pred EEECCEEEEEcCHHHHHHHHH
Confidence 346899999999999999863
No 11
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=91.92 E-value=0.13 Score=34.36 Aligned_cols=21 Identities=29% Similarity=0.569 Sum_probs=17.5
Q ss_pred ccCceEeeechHHHHHhhccCCC
Q 032380 5 LWVKVFLFANSKCKRYFHNRLKP 27 (142)
Q Consensus 5 ~Dgkvf~FcssKC~~~f~~krnP 27 (142)
-+|+.|+|||..|...|. .||
T Consensus 23 Y~GktYYFcse~~~~~F~--~~P 43 (53)
T COG3350 23 YGGKTYYFCSEECKEKFK--DNP 43 (53)
T ss_pred eCCEEEEEeCHHHHHHHH--HCH
Confidence 479999999999988884 455
No 12
>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=86.57 E-value=0.54 Score=29.18 Aligned_cols=23 Identities=22% Similarity=0.430 Sum_probs=19.8
Q ss_pred cccccCceEeeechHHHHHhhcc
Q 032380 2 LPWLWVKVFLFANSKCKRYFHNR 24 (142)
Q Consensus 2 ~vr~Dgkvf~FcssKC~~~f~~k 24 (142)
-++-++++|+||..-|.+-|..+
T Consensus 14 ~~k~~~~~y~fCC~tC~~~fk~k 36 (37)
T PF08394_consen 14 VVKIGNKVYYFCCPTCLSQFKKK 36 (37)
T ss_pred EEEECCeEEEEECHHHHHHHHhh
Confidence 36779999999999999998754
No 13
>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=68.37 E-value=2.1 Score=25.68 Aligned_cols=19 Identities=16% Similarity=0.142 Sum_probs=15.7
Q ss_pred ccccCceEeeechHHHHHh
Q 032380 3 PWLWVKVFLFANSKCKRYF 21 (142)
Q Consensus 3 vr~Dgkvf~FcssKC~~~f 21 (142)
+..||.+..|||.-|...|
T Consensus 25 ~~~~g~~~~FCS~~C~~~y 43 (43)
T PF06467_consen 25 VQYDGKMKQFCSQSCLSSY 43 (43)
T ss_dssp EE-TTTTSCCSSHHHHHHH
T ss_pred ccccCcccChhCHHHHhhC
Confidence 6678999999999998765
No 14
>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=51.47 E-value=9.2 Score=34.89 Aligned_cols=32 Identities=19% Similarity=0.522 Sum_probs=24.8
Q ss_pred ccCceEeeechHHHHHhhccCCCcch--hHHHHHHH
Q 032380 5 LWVKVFLFANSKCKRYFHNRLKPSKL--TWTSMYRK 38 (142)
Q Consensus 5 ~Dgkvf~FcssKC~~~f~~krnPRKl--~WT~~yRr 38 (142)
-||+.|+|||--|+..|.+ +|-+. .|+..-|-
T Consensus 406 y~G~~y~FCS~~C~~~F~~--ePerY~~~~~~~~~~ 439 (465)
T cd01057 406 YNGRKYHFCSEGCEWIFEQ--EPERYAGHWNPVDRF 439 (465)
T ss_pred ECCEEEEecCHHHHHHHHH--CHHHHhcCCCHHHHH
Confidence 4899999999999999986 77666 45554443
No 15
>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=51.19 E-value=3.8 Score=27.65 Aligned_cols=24 Identities=17% Similarity=0.401 Sum_probs=15.7
Q ss_pred EeeechHHHHHhh-ccCCCcchhHH
Q 032380 10 FLFANSKCKRYFH-NRLKPSKLTWT 33 (142)
Q Consensus 10 f~FcssKC~~~f~-~krnPRKl~WT 33 (142)
-.|||.+|+..+. ..+..++..|.
T Consensus 17 ~~fCS~~C~~~~~k~qk~~~~~~~i 41 (59)
T PF09889_consen 17 ESFCSPKCREEYRKRQKRMRKTQYI 41 (59)
T ss_pred hhhhCHHHHHHHHHHHHHHHHHHHH
Confidence 3699999988765 44444555543
No 16
>TIGR03666 Rv2061_F420 PPOX class probable F420-dependent enzyme, Rv2061 family. A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F420 in a cleft similar to that in which the homologous enzyme pyridoxamine phosphate oxidase (PPOX) binds FMN.
Probab=37.55 E-value=18 Score=27.05 Aligned_cols=27 Identities=11% Similarity=-0.048 Sum_probs=22.0
Q ss_pred cccccCceEeeechHHHHHhhccCCCc
Q 032380 2 LPWLWVKVFLFANSKCKRYFHNRLKPS 28 (142)
Q Consensus 2 ~vr~Dgkvf~FcssKC~~~f~~krnPR 28 (142)
|+.-||.+|+|++..-.+.-.+.+||+
T Consensus 33 ~~~d~g~l~f~t~~~~~K~~nl~~np~ 59 (132)
T TIGR03666 33 AAVDGDKLLVRTKEDSWKVKRIRNNPR 59 (132)
T ss_pred EEEECCEEEEEECCcCHHHHHHHhCCC
Confidence 677788888888887777777888887
No 17
>PF15279 SOBP: Sine oculis-binding protein
Probab=25.97 E-value=24 Score=30.76 Aligned_cols=16 Identities=19% Similarity=0.526 Sum_probs=13.2
Q ss_pred ceEeeechHHHHHhhc
Q 032380 8 KVFLFANSKCKRYFHN 23 (142)
Q Consensus 8 kvf~FcssKC~~~f~~ 23 (142)
.-+.|||.||-.-|+|
T Consensus 22 ~~lqfcs~kclnqykm 37 (306)
T PF15279_consen 22 RQLQFCSDKCLNQYKM 37 (306)
T ss_pred HHhhhccHHHHhHHHH
Confidence 3578999999987876
No 18
>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=24.79 E-value=54 Score=24.93 Aligned_cols=20 Identities=20% Similarity=0.277 Sum_probs=14.2
Q ss_pred cccC-ceEeeechHHHHHhhc
Q 032380 4 WLWV-KVFLFANSKCKRYFHN 23 (142)
Q Consensus 4 r~Dg-kvf~FcssKC~~~f~~ 23 (142)
-.|| ++++||+-.|--.|.+
T Consensus 47 ~~~g~~~~~Fdsi~c~~~~~~ 67 (149)
T PF05573_consen 47 YKDGEKVYKFDSIGCMFAYLK 67 (149)
T ss_dssp ETT-SSEEEES-HHHHHHHHT
T ss_pred ECCCCEEEEECCHHHHHHHHh
Confidence 3567 9999999999866654
No 19
>TIGR03667 Rv3369 PPOX class probable F420-dependent enzyme, Rv3369 family. A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F420 in a cleft similar to that in which the homologous enzyme pyridoxamine phosphate oxidase (PPOX) binds FMN.
Probab=22.05 E-value=50 Score=24.22 Aligned_cols=27 Identities=11% Similarity=0.315 Sum_probs=22.0
Q ss_pred ccccCceEeeechHHHHHhhccCCCcc
Q 032380 3 PWLWVKVFLFANSKCKRYFHNRLKPSK 29 (142)
Q Consensus 3 vr~Dgkvf~FcssKC~~~f~~krnPRK 29 (142)
+..||.+++|......+.-.+.+||+=
T Consensus 36 ~~~d~~l~~~t~~~s~K~~~l~~np~V 62 (130)
T TIGR03667 36 LWDGTEFLIYSRPQAAKLRNIRRNPRV 62 (130)
T ss_pred EEECCEEEEEeCCcCHHHHHHhhCCcE
Confidence 445888999988887888889999983
Done!