Query 032100
Match_columns 147
No_of_seqs 116 out of 232
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 09:35:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032100.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032100hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04570 DUF581: Protein of un 99.9 2E-27 4.2E-32 162.1 3.8 50 61-110 9-58 (58)
2 PF09889 DUF2116: Uncharacteri 95.4 0.018 3.9E-07 39.6 3.1 27 69-104 4-30 (59)
3 COG4068 Uncharacterized protei 92.4 0.19 4.2E-06 35.5 3.5 36 69-115 9-44 (64)
4 PF12855 Ecl1: Life-span regul 92.0 0.071 1.5E-06 34.6 0.9 30 66-101 4-33 (43)
5 PF06467 zf-FCS: MYM-type Zinc 91.4 0.15 3.3E-06 31.0 1.9 34 68-101 6-42 (43)
6 COG2075 RPL24A Ribosomal prote 91.3 0.18 3.8E-06 35.9 2.4 32 69-100 4-38 (66)
7 PF04945 YHS: YHS domain; Int 80.8 0.99 2.1E-05 28.4 1.4 29 73-101 5-35 (47)
8 PRK00418 DNA gyrase inhibitor; 80.6 0.96 2.1E-05 31.6 1.3 38 68-111 6-43 (62)
9 PF03884 DUF329: Domain of unk 79.2 0.84 1.8E-05 31.3 0.7 27 70-100 4-30 (57)
10 smart00746 TRASH metallochaper 78.5 3.3 7.2E-05 21.7 2.9 32 71-102 1-35 (39)
11 PRK01343 zinc-binding protein; 77.5 1.8 3.9E-05 29.9 1.9 30 69-108 10-39 (57)
12 PRK00807 50S ribosomal protein 76.1 3.1 6.8E-05 27.6 2.7 33 69-101 2-37 (52)
13 PRK14891 50S ribosomal protein 70.2 4.4 9.5E-05 32.2 2.7 35 69-103 5-42 (131)
14 PF02069 Metallothio_Pro: Prok 69.6 3.7 8E-05 27.8 1.9 32 69-102 8-39 (52)
15 PF00412 LIM: LIM domain; Int 69.4 3.1 6.8E-05 25.9 1.5 25 70-96 28-52 (58)
16 cd00472 Ribosomal_L24e_L24 Rib 63.1 8.3 0.00018 26.0 2.6 35 69-103 4-41 (54)
17 PHA03073 late transcription fa 52.4 9.4 0.0002 31.0 1.7 35 66-101 47-85 (150)
18 PF06906 DUF1272: Protein of u 48.8 14 0.0003 25.7 1.9 27 69-95 6-33 (57)
19 PF12156 ATPase-cat_bd: Putati 46.7 39 0.00084 24.1 4.0 36 70-105 2-39 (88)
20 COG3024 Uncharacterized protei 45.0 11 0.00023 26.9 0.9 40 69-114 8-47 (65)
21 smart00132 LIM Zinc-binding do 38.9 32 0.00069 19.1 2.1 23 70-93 1-23 (39)
22 PF04181 RPAP2_Rtr1: Rtr1/RPAP 38.6 37 0.0008 23.4 2.8 12 92-103 60-71 (79)
23 PF01246 Ribosomal_L24e: Ribos 36.1 39 0.00084 24.0 2.6 34 69-102 4-40 (71)
24 PF08394 Arc_trans_TRASH: Arch 35.3 42 0.00092 21.3 2.4 31 71-101 1-32 (37)
25 PF04640 PLATZ: PLATZ transcri 34.6 31 0.00068 24.6 1.9 23 67-98 48-70 (72)
26 KOG4357 Uncharacterized conser 30.3 22 0.00048 28.9 0.6 16 78-93 111-127 (164)
27 PTZ00033 60S ribosomal protein 30.2 56 0.0012 25.8 2.9 35 69-103 4-45 (125)
28 PF10367 Vps39_2: Vacuolar sor 29.4 45 0.00097 22.8 2.0 25 68-93 78-102 (109)
29 PF11792 Baculo_LEF5_C: Baculo 25.0 24 0.00051 23.3 -0.0 17 60-76 26-42 (43)
30 PF01753 zf-MYND: MYND finger; 22.7 55 0.0012 19.4 1.3 15 89-103 16-30 (37)
31 PF10013 DUF2256: Uncharacteri 20.8 31 0.00067 22.7 -0.1 29 69-101 9-41 (42)
32 COG3350 Uncharacterized conser 20.6 40 0.00086 23.1 0.4 28 74-101 8-38 (53)
No 1
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=99.94 E-value=2e-27 Score=162.06 Aligned_cols=50 Identities=52% Similarity=0.982 Sum_probs=47.1
Q ss_pred CCchhhhhhccccccCCCCCCCceEEEcCCccccChhhHHHHHHHHHHHH
Q 032100 61 GDQYYCYLKSCYLCNKNLSLDKEVYMYRGDQGFCSIECRDRQIFLDEMKE 110 (147)
Q Consensus 61 g~~~~~FL~~C~lCkK~L~~~kDIyMYRGe~AFCS~ECR~~qI~~DE~~E 110 (147)
..++.+||++|++|+|+|.+|+||||||||+||||.|||++||++||++|
T Consensus 9 ~~~~~~FL~~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~~qi~~de~~E 58 (58)
T PF04570_consen 9 PFPSEHFLSFCYLCKKKLDPGKDIYMYRGDKAFCSEECRSQQILMDEEKE 58 (58)
T ss_pred CCCcHHHHHHHHccCCCCCCCCCeeeeccccccccHHHHHHHHHHHHhcC
Confidence 34679999999999999999999999999999999999999999999875
No 2
>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=95.39 E-value=0.018 Score=39.65 Aligned_cols=27 Identities=37% Similarity=0.818 Sum_probs=22.6
Q ss_pred hccccccCCCCCCCceEEEcCCccccChhhHHHHHH
Q 032100 69 KSCYLCNKNLSLDKEVYMYRGDQGFCSIECRDRQIF 104 (147)
Q Consensus 69 ~~C~lCkK~L~~~kDIyMYRGe~AFCS~ECR~~qI~ 104 (147)
+-|-.|.+++.+ |..|||.+|++....
T Consensus 4 kHC~~CG~~Ip~---------~~~fCS~~C~~~~~k 30 (59)
T PF09889_consen 4 KHCPVCGKPIPP---------DESFCSPKCREEYRK 30 (59)
T ss_pred CcCCcCCCcCCc---------chhhhCHHHHHHHHH
Confidence 458999999996 689999999987543
No 3
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=92.41 E-value=0.19 Score=35.49 Aligned_cols=36 Identities=31% Similarity=0.618 Sum_probs=26.8
Q ss_pred hccccccCCCCCCCceEEEcCCccccChhhHHHHHHHHHHHHHHHHH
Q 032100 69 KSCYLCNKNLSLDKEVYMYRGDQGFCSIECRDRQIFLDEMKELEASR 115 (147)
Q Consensus 69 ~~C~lCkK~L~~~kDIyMYRGe~AFCS~ECR~~qI~~DE~~E~~~s~ 115 (147)
+-|--|.+.+.+ |.-|||++|++ |+..|++.....+
T Consensus 9 ~HC~VCg~aIp~---------de~~CSe~C~e--il~ker~R~r~~~ 44 (64)
T COG4068 9 RHCVVCGKAIPP---------DEQVCSEECGE--ILNKERKRQRNFM 44 (64)
T ss_pred ccccccCCcCCC---------ccchHHHHHHH--HHHHHHHHHHHHH
Confidence 458899999996 46799999974 7777766554443
No 4
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=92.01 E-value=0.071 Score=34.63 Aligned_cols=30 Identities=27% Similarity=0.698 Sum_probs=24.5
Q ss_pred hhhhccccccCCCCCCCceEEEcCCccccChhhHHH
Q 032100 66 CYLKSCYLCNKNLSLDKEVYMYRGDQGFCSIECRDR 101 (147)
Q Consensus 66 ~FL~~C~lCkK~L~~~kDIyMYRGe~AFCS~ECR~~ 101 (147)
.|+.+|-.|-|.+.+.. .+..+||++||..
T Consensus 4 ~F~~yC~~Cdk~~~~~~------~~~lYCSe~Cr~~ 33 (43)
T PF12855_consen 4 AFNDYCIVCDKQIDPPD------DGSLYCSEECRLK 33 (43)
T ss_pred hhhhHHHHhhccccCCC------CCccccCHHHHhH
Confidence 79999999999995422 2467899999976
No 5
>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=91.43 E-value=0.15 Score=30.97 Aligned_cols=34 Identities=29% Similarity=0.695 Sum_probs=21.7
Q ss_pred hhccccccCCCCCCCc--eEEEcCC-ccccChhhHHH
Q 032100 68 LKSCYLCNKNLSLDKE--VYMYRGD-QGFCSIECRDR 101 (147)
Q Consensus 68 L~~C~lCkK~L~~~kD--IyMYRGe-~AFCS~ECR~~ 101 (147)
...|..|++.+....+ +..|.|. .-|||..|+..
T Consensus 6 ~~~C~~C~~~~~~~~~~~~~~~~g~~~~FCS~~C~~~ 42 (43)
T PF06467_consen 6 MKTCSYCKKYIPNKPTMIEVQYDGKMKQFCSQSCLSS 42 (43)
T ss_dssp CEE-TTT--EEECCC----EE-TTTTSCCSSHHHHHH
T ss_pred CCcCcccCCcccCCCccccccccCcccChhCHHHHhh
Confidence 4579999999975555 6777763 58999999875
No 6
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=91.31 E-value=0.18 Score=35.87 Aligned_cols=32 Identities=28% Similarity=0.741 Sum_probs=28.2
Q ss_pred hccccccCCCCCCCceEEEcCCcc---ccChhhHH
Q 032100 69 KSCYLCNKNLSLDKEVYMYRGDQG---FCSIECRD 100 (147)
Q Consensus 69 ~~C~lCkK~L~~~kDIyMYRGe~A---FCS~ECR~ 100 (147)
..|++|.++|.||.-|+.-++|.. |||..|+.
T Consensus 4 ~~CsFcG~~I~PGtG~m~Vr~Dg~v~~FcssKc~k 38 (66)
T COG2075 4 RVCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCEK 38 (66)
T ss_pred eEecCcCCccCCCceEEEEecCCeEEEEechhHHH
Confidence 469999999999998877788764 99999998
No 7
>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=80.81 E-value=0.99 Score=28.37 Aligned_cols=29 Identities=24% Similarity=0.598 Sum_probs=19.2
Q ss_pred cccCCC-CCCCceEEEcCCc-cccChhhHHH
Q 032100 73 LCNKNL-SLDKEVYMYRGDQ-GFCSIECRDR 101 (147)
Q Consensus 73 lCkK~L-~~~kDIyMYRGe~-AFCS~ECR~~ 101 (147)
-|...| ......+.|.|.. -|||.+|++.
T Consensus 5 vcg~~v~~~~~~~~~y~G~~Y~FCS~~C~~~ 35 (47)
T PF04945_consen 5 VCGMKVPGNAAYSVEYNGRTYYFCSEGCKEK 35 (47)
T ss_dssp GGG-BE-----EEEEETTEEEEESSHHHHHH
T ss_pred CCCCEEccCccEEEEECCEEEEEcCHHHHHH
Confidence 477788 2235677888854 7999999986
No 8
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=80.57 E-value=0.96 Score=31.61 Aligned_cols=38 Identities=29% Similarity=0.468 Sum_probs=24.7
Q ss_pred hhccccccCCCCCCCceEEEcCCccccChhhHHHHHHHHHHHHH
Q 032100 68 LKSCYLCNKNLSLDKEVYMYRGDQGFCSIECRDRQIFLDEMKEL 111 (147)
Q Consensus 68 L~~C~lCkK~L~~~kDIyMYRGe~AFCS~ECR~~qI~~DE~~E~ 111 (147)
...|--|+|... +..-.-| .+|||..|+. |.+-++...
T Consensus 6 ~v~CP~C~k~~~-w~~~~~~---rPFCS~RCk~--IDLg~W~~e 43 (62)
T PRK00418 6 TVNCPTCGKPVE-WGEISPF---RPFCSKRCQL--IDLGEWAAE 43 (62)
T ss_pred cccCCCCCCccc-ccCCCCc---CCcccHHHHh--hhHHHHHcC
Confidence 357999999875 2222223 4899999975 566555443
No 9
>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=79.18 E-value=0.84 Score=31.29 Aligned_cols=27 Identities=26% Similarity=0.562 Sum_probs=14.8
Q ss_pred ccccccCCCCCCCceEEEcCCccccChhhHH
Q 032100 70 SCYLCNKNLSLDKEVYMYRGDQGFCSIECRD 100 (147)
Q Consensus 70 ~C~lCkK~L~~~kDIyMYRGe~AFCS~ECR~ 100 (147)
.|--|+|.... .+-. .-.+|||..|+.
T Consensus 4 ~CP~C~k~~~~-~~~n---~~rPFCS~RCk~ 30 (57)
T PF03884_consen 4 KCPICGKPVEW-SPEN---PFRPFCSERCKL 30 (57)
T ss_dssp E-TTT--EEE--SSSS---S--SSSSHHHHH
T ss_pred cCCCCCCeecc-cCCC---CcCCcccHhhcc
Confidence 58889988873 1111 237999999994
No 10
>smart00746 TRASH metallochaperone-like domain.
Probab=78.48 E-value=3.3 Score=21.73 Aligned_cols=32 Identities=25% Similarity=0.567 Sum_probs=20.1
Q ss_pred cccccCCCC-CCCc-eEEEcC-CccccChhhHHHH
Q 032100 71 CYLCNKNLS-LDKE-VYMYRG-DQGFCSIECRDRQ 102 (147)
Q Consensus 71 C~lCkK~L~-~~kD-IyMYRG-e~AFCS~ECR~~q 102 (147)
|..|+..+. +... .+.+.| ..-|||.+|....
T Consensus 1 c~~C~~~~~~~~~~~~~~~~g~~~~FCs~~c~~~~ 35 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVVNDGKVFYFCSSKCLSKF 35 (39)
T ss_pred CCCCCCCccCCCCceEEEECCEEEEEeCHHHHHHH
Confidence 677888886 3322 223444 2369999998753
No 11
>PRK01343 zinc-binding protein; Provisional
Probab=77.47 E-value=1.8 Score=29.86 Aligned_cols=30 Identities=37% Similarity=0.668 Sum_probs=21.6
Q ss_pred hccccccCCCCCCCceEEEcCCccccChhhHHHHHHHHHH
Q 032100 69 KSCYLCNKNLSLDKEVYMYRGDQGFCSIECRDRQIFLDEM 108 (147)
Q Consensus 69 ~~C~lCkK~L~~~kDIyMYRGe~AFCS~ECR~~qI~~DE~ 108 (147)
..|--|+|.... -..+|||.-|+. |.+-.+
T Consensus 10 ~~CP~C~k~~~~--------~~rPFCS~RC~~--iDLg~W 39 (57)
T PRK01343 10 RPCPECGKPSTR--------EAYPFCSERCRD--IDLNRW 39 (57)
T ss_pred CcCCCCCCcCcC--------CCCcccCHHHhh--hhHHHH
Confidence 579999998652 235999999986 444443
No 12
>PRK00807 50S ribosomal protein L24e; Validated
Probab=76.07 E-value=3.1 Score=27.59 Aligned_cols=33 Identities=24% Similarity=0.635 Sum_probs=26.1
Q ss_pred hccccccCCCCCCCceEEEcCCc---cccChhhHHH
Q 032100 69 KSCYLCNKNLSLDKEVYMYRGDQ---GFCSIECRDR 101 (147)
Q Consensus 69 ~~C~lCkK~L~~~kDIyMYRGe~---AFCS~ECR~~ 101 (147)
..|..|..++.||.-+..++.|. -|||..|...
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~KC~~~ 37 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYFCSSKCEKN 37 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEEeCHHHHHH
Confidence 36999999999998776566543 5999999765
No 13
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=70.16 E-value=4.4 Score=32.18 Aligned_cols=35 Identities=14% Similarity=0.338 Sum_probs=26.3
Q ss_pred hccccccCCCCCCCceEEEcCCc---cccChhhHHHHH
Q 032100 69 KSCYLCNKNLSLDKEVYMYRGDQ---GFCSIECRDRQI 103 (147)
Q Consensus 69 ~~C~lCkK~L~~~kDIyMYRGe~---AFCS~ECR~~qI 103 (147)
..|++|..+|-||.-+-.-|.|. -|||..|....+
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~k~f~ 42 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCEKNYD 42 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEEEecHHHHHHHH
Confidence 46999999999997554445543 499999976543
No 14
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=69.55 E-value=3.7 Score=27.85 Aligned_cols=32 Identities=22% Similarity=0.432 Sum_probs=18.1
Q ss_pred hccccccCCCCCCCceEEEcCCccccChhhHHHH
Q 032100 69 KSCYLCNKNLSLDKEVYMYRGDQGFCSIECRDRQ 102 (147)
Q Consensus 69 ~~C~lCkK~L~~~kDIyMYRGe~AFCS~ECR~~q 102 (147)
-+|..|.=-+.. .+-++. +.++|||++|=+.+
T Consensus 8 CaC~~C~C~V~~-~~Ai~~-dGk~YCS~aCA~gH 39 (52)
T PF02069_consen 8 CACPSCSCVVSE-EEAIQK-DGKYYCSEACANGH 39 (52)
T ss_dssp -SSTT----B-T-TTSEES-SS-EESSHHHHHTS
T ss_pred ecCCCCEeEECc-hHhHHh-CCEeeecHHHhccC
Confidence 468888888885 455554 45999999997654
No 15
>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=69.43 E-value=3.1 Score=25.90 Aligned_cols=25 Identities=24% Similarity=0.599 Sum_probs=18.1
Q ss_pred ccccccCCCCCCCceEEEcCCccccCh
Q 032100 70 SCYLCNKNLSLDKEVYMYRGDQGFCSI 96 (147)
Q Consensus 70 ~C~lCkK~L~~~kDIyMYRGe~AFCS~ 96 (147)
.|..|++.|.++. .|+ ..++.||..
T Consensus 28 ~C~~C~~~l~~~~-~~~-~~~~~~C~~ 52 (58)
T PF00412_consen 28 KCSKCGKPLNDGD-FYE-KDGKPYCKD 52 (58)
T ss_dssp BETTTTCBTTTSS-EEE-ETTEEEEHH
T ss_pred ccCCCCCccCCCe-eEe-ECCEEECHH
Confidence 5788999999544 555 445999975
No 16
>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=63.09 E-value=8.3 Score=26.01 Aligned_cols=35 Identities=23% Similarity=0.568 Sum_probs=27.3
Q ss_pred hccccccCCCCCCCceEEEcCCc---cccChhhHHHHH
Q 032100 69 KSCYLCNKNLSLDKEVYMYRGDQ---GFCSIECRDRQI 103 (147)
Q Consensus 69 ~~C~lCkK~L~~~kDIyMYRGe~---AFCS~ECR~~qI 103 (147)
..|..|..+|.||.-+-.-+.|. -|||.-|+...+
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~F~s~Kc~~~~~ 41 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFRFCSSKCEKNFL 41 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEEEECHHHHHHHH
Confidence 46999999999997665556665 499999976543
No 17
>PHA03073 late transcription factor VLTF-2; Provisional
Probab=52.43 E-value=9.4 Score=30.98 Aligned_cols=35 Identities=29% Similarity=0.625 Sum_probs=26.0
Q ss_pred hhhhccccccCCCCCCCceEE---EcC-CccccChhhHHH
Q 032100 66 CYLKSCYLCNKNLSLDKEVYM---YRG-DQGFCSIECRDR 101 (147)
Q Consensus 66 ~FL~~C~lCkK~L~~~kDIyM---YRG-e~AFCS~ECR~~ 101 (147)
+=-..|-+|+..|. ..++++ |.| -..|||.=||+.
T Consensus 47 s~~~~CwfC~q~~~-~~~~~iETl~g~~vg~FCS~ICRDS 85 (150)
T PHA03073 47 SDNDYCWFCKQDLI-IAPLFIETLKGGAVGYFCSKICRDS 85 (150)
T ss_pred cCCCcEEeeccccc-cCceEEEeecCchhhhHhHHHHHHH
Confidence 34568999999998 455765 332 357999999986
No 18
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=48.81 E-value=14 Score=25.73 Aligned_cols=27 Identities=33% Similarity=0.747 Sum_probs=23.7
Q ss_pred hccccccCCCCCCC-ceEEEcCCccccC
Q 032100 69 KSCYLCNKNLSLDK-EVYMYRGDQGFCS 95 (147)
Q Consensus 69 ~~C~lCkK~L~~~k-DIyMYRGe~AFCS 95 (147)
..|-.|.+.|.++. |.||..-|=-||.
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~ 33 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCA 33 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccH
Confidence 46889999999997 9999888888885
No 19
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=46.68 E-value=39 Score=24.14 Aligned_cols=36 Identities=17% Similarity=0.503 Sum_probs=27.7
Q ss_pred ccccccCCCCCCCceEEEcC--CccccChhhHHHHHHH
Q 032100 70 SCYLCNKNLSLDKEVYMYRG--DQGFCSIECRDRQIFL 105 (147)
Q Consensus 70 ~C~lCkK~L~~~kDIyMYRG--e~AFCS~ECR~~qI~~ 105 (147)
.|+.|..++.++..+-+... +..||-.-|..-.-++
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~~i 39 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQLI 39 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHHHH
Confidence 59999999987776666543 5899999998754443
No 20
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.97 E-value=11 Score=26.89 Aligned_cols=40 Identities=30% Similarity=0.451 Sum_probs=26.8
Q ss_pred hccccccCCCCCCCceEEEcCCccccChhhHHHHHHHHHHHHHHHH
Q 032100 69 KSCYLCNKNLSLDKEVYMYRGDQGFCSIECRDRQIFLDEMKELEAS 114 (147)
Q Consensus 69 ~~C~lCkK~L~~~kDIyMYRGe~AFCS~ECR~~qI~~DE~~E~~~s 114 (147)
-.|--|.|+.. +.+.=-| .+|||..|. .|.+-+....+..
T Consensus 8 v~CP~Cgkpv~-w~~~s~f---rPFCSkRCk--lIDLg~Wa~eey~ 47 (65)
T COG3024 8 VPCPTCGKPVV-WGEESPF---RPFCSKRCK--LIDLGEWAAEEYA 47 (65)
T ss_pred ccCCCCCCccc-ccccCCc---CcchhHhhh--hcchhhhhccCcc
Confidence 46889999987 3333233 589999885 5777776554443
No 21
>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=38.85 E-value=32 Score=19.14 Aligned_cols=23 Identities=17% Similarity=0.287 Sum_probs=15.6
Q ss_pred ccccccCCCCCCCceEEEcCCccc
Q 032100 70 SCYLCNKNLSLDKEVYMYRGDQGF 93 (147)
Q Consensus 70 ~C~lCkK~L~~~kDIyMYRGe~AF 93 (147)
.|..|++.|.++ +.++..++..|
T Consensus 1 ~C~~C~~~i~~~-~~~~~~~~~~~ 23 (39)
T smart00132 1 KCAGCGKPIRGG-ELVLRALGKVW 23 (39)
T ss_pred CccccCCcccCC-cEEEEeCCccc
Confidence 488899999865 44554455555
No 22
>PF04181 RPAP2_Rtr1: Rtr1/RPAP2 family; InterPro: IPR007308 This entry represents a domain found in PAP2 (RNAP II associated polypeptide) protein and the yeast Rtr1 proteins. Its function is not known however it is thought to be a zinc finger.
Probab=38.64 E-value=37 Score=23.43 Aligned_cols=12 Identities=33% Similarity=0.758 Sum_probs=9.8
Q ss_pred cccChhhHHHHH
Q 032100 92 GFCSIECRDRQI 103 (147)
Q Consensus 92 AFCS~ECR~~qI 103 (147)
.|||..|...-.
T Consensus 60 ~fCS~~C~~~s~ 71 (79)
T PF04181_consen 60 KFCSKDCYKASE 71 (79)
T ss_pred CcCCHHHHHHHH
Confidence 899999987643
No 23
>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=36.11 E-value=39 Score=23.97 Aligned_cols=34 Identities=21% Similarity=0.392 Sum_probs=22.1
Q ss_pred hccccccCCCCCCCceEEEcCCc---cccChhhHHHH
Q 032100 69 KSCYLCNKNLSLDKEVYMYRGDQ---GFCSIECRDRQ 102 (147)
Q Consensus 69 ~~C~lCkK~L~~~kDIyMYRGe~---AFCS~ECR~~q 102 (147)
..|++|..+|.||.-+-.-+-|. -|||.-|+...
T Consensus 4 ~~C~Fsg~~I~PG~G~~~Vr~DG~v~~F~s~Kc~~~~ 40 (71)
T PF01246_consen 4 EKCSFSGYKIYPGHGKMYVRNDGKVFYFCSSKCEKLF 40 (71)
T ss_dssp EE-TTT-SEE-SSSSEEEE-TTS-EEEESSHHHHHHH
T ss_pred EEecccCCccCCCCCeEEEecCCCeEEEeCHHHHHHH
Confidence 46999999999997554334443 49999998763
No 24
>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=35.27 E-value=42 Score=21.25 Aligned_cols=31 Identities=19% Similarity=0.445 Sum_probs=22.2
Q ss_pred cccccCCCCCCCceEEEcCC-ccccChhhHHH
Q 032100 71 CYLCNKNLSLDKEVYMYRGD-QGFCSIECRDR 101 (147)
Q Consensus 71 C~lCkK~L~~~kDIyMYRGe-~AFCS~ECR~~ 101 (147)
|..|.+.|...--+|=+.|. --||+..|..+
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~~~ 32 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCLSQ 32 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHHHH
Confidence 78899999944445555443 25899999876
No 25
>PF04640 PLATZ: PLATZ transcription factor; InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=34.62 E-value=31 Score=24.57 Aligned_cols=23 Identities=30% Similarity=0.687 Sum_probs=18.2
Q ss_pred hhhccccccCCCCCCCceEEEcCCccccChhh
Q 032100 67 YLKSCYLCNKNLSLDKEVYMYRGDQGFCSIEC 98 (147)
Q Consensus 67 FL~~C~lCkK~L~~~kDIyMYRGe~AFCS~EC 98 (147)
.-..|..|.+.|.. - --|||..|
T Consensus 48 ~~~~C~~C~R~L~d---~------~~fCSl~C 70 (72)
T PF04640_consen 48 SGNICETCHRSLQD---P------YRFCSLSC 70 (72)
T ss_pred CCCccCCCCCCCCC---C------CeEEeeeE
Confidence 56789999999982 2 34899888
No 26
>KOG4357 consensus Uncharacterized conserved protein (involved in mesoderm differentiation in humans) [General function prediction only]
Probab=30.28 E-value=22 Score=28.88 Aligned_cols=16 Identities=31% Similarity=0.968 Sum_probs=13.5
Q ss_pred CCCCCceEEEc-CCccc
Q 032100 78 LSLDKEVYMYR-GDQGF 93 (147)
Q Consensus 78 L~~~kDIyMYR-Ge~AF 93 (147)
++.++-|||++ |+.||
T Consensus 111 i~ddraifm~kdge~a~ 127 (164)
T KOG4357|consen 111 IDDDRAIFMFKDGEQAF 127 (164)
T ss_pred ecCCeEEEEEeChhHHH
Confidence 56788999998 88887
No 27
>PTZ00033 60S ribosomal protein L24; Provisional
Probab=30.23 E-value=56 Score=25.78 Aligned_cols=35 Identities=9% Similarity=0.116 Sum_probs=26.1
Q ss_pred hccccccCCCCCCCceEEEc----CCc---cccChhhHHHHH
Q 032100 69 KSCYLCNKNLSLDKEVYMYR----GDQ---GFCSIECRDRQI 103 (147)
Q Consensus 69 ~~C~lCkK~L~~~kDIyMYR----Ge~---AFCS~ECR~~qI 103 (147)
..|++|..++.||.-+-+-+ .|. -|||.-|....+
T Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr~~~~~Dgkv~~F~~sKc~~~~~ 45 (125)
T PTZ00033 4 IACEFSHFAVHPGHGRRYVPFAFLSTKPVLTFLRPKCFALYM 45 (125)
T ss_pred eEecCcCCcccCCCCcEeeecccCCCCCEEEEecHHHHHHHH
Confidence 46999999999997654445 554 499999965533
No 28
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=29.36 E-value=45 Score=22.78 Aligned_cols=25 Identities=16% Similarity=0.393 Sum_probs=18.0
Q ss_pred hhccccccCCCCCCCceEEEcCCccc
Q 032100 68 LKSCYLCNKNLSLDKEVYMYRGDQGF 93 (147)
Q Consensus 68 L~~C~lCkK~L~~~kDIyMYRGe~AF 93 (147)
-..|..|+|+|. ++.+.+|--...|
T Consensus 78 ~~~C~vC~k~l~-~~~f~~~p~~~v~ 102 (109)
T PF10367_consen 78 STKCSVCGKPLG-NSVFVVFPCGHVV 102 (109)
T ss_pred CCCccCcCCcCC-CceEEEeCCCeEE
Confidence 356999999999 4777777633444
No 29
>PF11792 Baculo_LEF5_C: Baculoviridae late expression factor 5 C-terminal domain; InterPro: IPR021758 This C-terminal domain is likely to be a zinc-binding domain.
Probab=24.98 E-value=24 Score=23.27 Aligned_cols=17 Identities=29% Similarity=0.807 Sum_probs=15.1
Q ss_pred CCCchhhhhhccccccC
Q 032100 60 SGDQYYCYLKSCYLCNK 76 (147)
Q Consensus 60 ~g~~~~~FL~~C~lCkK 76 (147)
+|++..+|...|..|+.
T Consensus 26 AGDE~VSfI~~C~~C~~ 42 (43)
T PF11792_consen 26 AGDEAVSFIKYCQKCGQ 42 (43)
T ss_pred ccchHHHHHHHHHHhCC
Confidence 47899999999999985
No 30
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=22.75 E-value=55 Score=19.38 Aligned_cols=15 Identities=27% Similarity=0.552 Sum_probs=11.9
Q ss_pred CCccccChhhHHHHH
Q 032100 89 GDQGFCSIECRDRQI 103 (147)
Q Consensus 89 Ge~AFCS~ECR~~qI 103 (147)
+...|||.+|.....
T Consensus 16 ~~~~YCs~~Cq~~~w 30 (37)
T PF01753_consen 16 KSVYYCSEECQRADW 30 (37)
T ss_dssp SSSEESSHHHHHHHH
T ss_pred CCEEecCHHHHHHHH
Confidence 457899999988754
No 31
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.75 E-value=31 Score=22.66 Aligned_cols=29 Identities=28% Similarity=0.770 Sum_probs=20.2
Q ss_pred hccccccCCCCCCC----ceEEEcCCccccChhhHHH
Q 032100 69 KSCYLCNKNLSLDK----EVYMYRGDQGFCSIECRDR 101 (147)
Q Consensus 69 ~~C~lCkK~L~~~k----DIyMYRGe~AFCS~ECR~~ 101 (147)
+.|..|.++.. ++ .-| .+.-|||+-||..
T Consensus 9 K~C~~C~rpf~-WRKKW~~~W---d~VkYCS~rCR~~ 41 (42)
T PF10013_consen 9 KICPVCGRPFT-WRKKWARCW---DEVKYCSDRCRRR 41 (42)
T ss_pred CcCcccCCcch-HHHHHHHhc---hhhccHHHHhccC
Confidence 46888888776 32 222 4788999999963
No 32
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=20.55 E-value=40 Score=23.13 Aligned_cols=28 Identities=29% Similarity=0.689 Sum_probs=19.8
Q ss_pred ccCCCCCC--CceEEEcCCc-cccChhhHHH
Q 032100 74 CNKNLSLD--KEVYMYRGDQ-GFCSIECRDR 101 (147)
Q Consensus 74 CkK~L~~~--kDIyMYRGe~-AFCS~ECR~~ 101 (147)
|+.++... .-.|-|.|-. =|||++|-..
T Consensus 8 cgm~v~~~~a~~k~~Y~GktYYFcse~~~~~ 38 (53)
T COG3350 8 CGMKVDNENAEYKSSYGGKTYYFCSEECKEK 38 (53)
T ss_pred cCccccccccceeEEeCCEEEEEeCHHHHHH
Confidence 77777633 3567778744 5999999765
Done!