Query 032471
Match_columns 140
No_of_seqs 118 out of 241
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 14:31:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032471.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032471hhsearch_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 2.7E-28 5.9E-33 165.1 4.0 51 49-99 7-57 (58)
2 PF09889 DUF2116: Uncharacteri 94.7 0.023 4.9E-07 38.8 2.0 27 59-94 4-30 (59)
3 COG4068 Uncharacterized protei 93.0 0.1 2.3E-06 36.5 2.9 29 59-98 9-37 (64)
4 PF12855 Ecl1: Life-span regul 93.0 0.041 8.8E-07 35.5 0.7 30 56-91 4-33 (43)
5 PF06467 zf-FCS: MYM-type Zinc 92.8 0.071 1.5E-06 32.2 1.6 34 58-91 6-42 (43)
6 COG2075 RPL24A Ribosomal prote 90.7 0.23 4.9E-06 35.0 2.5 32 59-90 4-38 (66)
7 PF04640 PLATZ: PLATZ transcri 88.0 0.36 7.7E-06 34.2 1.8 44 22-88 26-70 (72)
8 PRK00418 DNA gyrase inhibitor; 84.2 0.75 1.6E-05 31.9 1.9 34 58-97 6-39 (62)
9 PF04945 YHS: YHS domain; Int 84.2 0.57 1.2E-05 29.2 1.2 28 63-91 5-35 (47)
10 PF03884 DUF329: Domain of unk 83.5 0.33 7.1E-06 33.0 -0.1 31 60-96 4-34 (57)
11 smart00746 TRASH metallochaper 80.1 2.5 5.4E-05 22.1 2.7 31 61-91 1-34 (39)
12 PRK01343 zinc-binding protein; 78.3 1.7 3.7E-05 29.7 1.9 29 59-97 10-38 (57)
13 PRK00807 50S ribosomal protein 74.9 3.4 7.5E-05 27.2 2.7 33 59-91 2-37 (52)
14 cd00153 RalGDS_RA Ubiquitin do 72.8 2.1 4.6E-05 31.6 1.4 24 5-35 20-43 (87)
15 PF02069 Metallothio_Pro: Prok 68.5 4 8.7E-05 27.4 1.9 32 59-92 8-39 (52)
16 PF00412 LIM: LIM domain; Int 65.5 3.8 8.3E-05 25.3 1.3 25 60-86 28-52 (58)
17 COG3024 Uncharacterized protei 64.9 3.4 7.3E-05 29.2 1.0 34 59-98 8-41 (65)
18 PRK14891 50S ribosomal protein 63.8 7.2 0.00016 30.7 2.7 34 59-92 5-41 (131)
19 cd00472 Ribosomal_L24e_L24 Rib 55.0 13 0.00028 24.9 2.4 34 59-92 4-40 (54)
20 PHA03073 late transcription fa 52.1 9.5 0.00021 30.7 1.7 36 57-93 48-87 (150)
21 PF06906 DUF1272: Protein of u 47.8 15 0.00033 25.3 1.9 29 60-89 7-36 (57)
22 smart00132 LIM Zinc-binding do 39.6 32 0.0007 18.9 2.2 23 60-83 1-23 (39)
23 KOG4357 Uncharacterized conser 36.8 15 0.00032 29.6 0.6 16 68-83 111-127 (164)
24 PF04181 RPAP2_Rtr1: Rtr1/RPAP 36.6 54 0.0012 22.4 3.3 14 82-95 60-73 (79)
25 PF12156 ATPase-cat_bd: Putati 36.1 72 0.0016 22.6 4.0 41 60-100 2-45 (88)
26 PF15279 SOBP: Sine oculis-bin 34.6 35 0.00076 29.9 2.6 37 61-99 2-45 (306)
27 PF13216 DUF4024: Protein of u 34.3 19 0.00041 22.5 0.7 7 1-7 1-7 (35)
28 PF08394 Arc_trans_TRASH: Arch 32.3 49 0.0011 20.8 2.3 31 61-91 1-32 (37)
29 PF10367 Vps39_2: Vacuolar sor 28.8 46 0.00099 22.6 1.9 24 59-83 79-102 (109)
30 PF01753 zf-MYND: MYND finger; 28.5 39 0.00084 19.9 1.4 15 79-93 16-30 (37)
31 PF01246 Ribosomal_L24e: Ribos 28.2 58 0.0013 22.9 2.4 33 59-91 4-39 (71)
32 cd01224 PH_Collybistin Collybi 26.1 31 0.00067 26.1 0.8 20 60-80 29-48 (109)
33 PF10013 DUF2256: Uncharacteri 25.8 21 0.00047 23.2 -0.1 31 59-90 9-40 (42)
34 PTZ00033 60S ribosomal protein 22.7 89 0.0019 24.5 2.7 33 59-91 4-43 (125)
35 COG3350 Uncharacterized conser 22.2 44 0.00096 22.7 0.9 28 64-91 8-38 (53)
36 COG1445 FrwB Phosphotransferas 20.0 1.1E+02 0.0023 23.9 2.6 31 2-32 31-62 (122)
No 1
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=99.94 E-value=2.7e-28 Score=165.09 Aligned_cols=51 Identities=65% Similarity=1.260 Sum_probs=47.7
Q ss_pred CCCCCchhhhccCccCCCCCCCCCceEEEcCCCcccChhhHHHHHHhhHHH
Q 032471 49 HSTFPVPTFLQHCFLCKQTLLPGKDIYMYKGDRAFCSVECRCRQIFMDEEE 99 (140)
Q Consensus 49 ~~~~~~~~FL~~C~~CkK~L~~gkDIyMYRGe~AFCS~ECR~~qI~~DE~~ 99 (140)
..++++.+||++|++|+|+|.+|+||||||||+||||.|||++||++||++
T Consensus 7 ~~~~~~~~FL~~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~~qi~~de~~ 57 (58)
T PF04570_consen 7 GSPFPSEHFLSFCYLCKKKLDPGKDIYMYRGDKAFCSEECRSQQILMDEEK 57 (58)
T ss_pred CCCCCcHHHHHHHHccCCCCCCCCCeeeeccccccccHHHHHHHHHHHHhc
Confidence 346788999999999999999999999999999999999999999999953
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=94.69 E-value=0.023 Score=38.83 Aligned_cols=27 Identities=37% Similarity=0.859 Sum_probs=21.7
Q ss_pred ccCccCCCCCCCCCceEEEcCCCcccChhhHHHHHH
Q 032471 59 QHCFLCKQTLLPGKDIYMYKGDRAFCSVECRCRQIF 94 (140)
Q Consensus 59 ~~C~~CkK~L~~gkDIyMYRGe~AFCS~ECR~~qI~ 94 (140)
+.|-.|.+.+.+ |..|||.+||+....
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 459999999964 689999999965443
No 3
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=93.03 E-value=0.1 Score=36.50 Aligned_cols=29 Identities=34% Similarity=0.894 Sum_probs=23.4
Q ss_pred ccCccCCCCCCCCCceEEEcCCCcccChhhHHHHHHhhHH
Q 032471 59 QHCFLCKQTLLPGKDIYMYKGDRAFCSVECRCRQIFMDEE 98 (140)
Q Consensus 59 ~~C~~CkK~L~~gkDIyMYRGe~AFCS~ECR~~qI~~DE~ 98 (140)
+.|--|.+.+.+| .-|||+||+ +|+..|.
T Consensus 9 ~HC~VCg~aIp~d---------e~~CSe~C~--eil~ker 37 (64)
T COG4068 9 RHCVVCGKAIPPD---------EQVCSEECG--EILNKER 37 (64)
T ss_pred ccccccCCcCCCc---------cchHHHHHH--HHHHHHH
Confidence 3599999999654 469999999 7888774
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=92.99 E-value=0.041 Score=35.49 Aligned_cols=30 Identities=30% Similarity=0.812 Sum_probs=23.6
Q ss_pred hhhccCccCCCCCCCCCceEEEcCCCcccChhhHHH
Q 032471 56 TFLQHCFLCKQTLLPGKDIYMYKGDRAFCSVECRCR 91 (140)
Q Consensus 56 ~FL~~C~~CkK~L~~gkDIyMYRGe~AFCS~ECR~~ 91 (140)
.|+++|-.|.|.+.... .+..+||++||..
T Consensus 4 ~F~~yC~~Cdk~~~~~~------~~~lYCSe~Cr~~ 33 (43)
T PF12855_consen 4 AFNDYCIVCDKQIDPPD------DGSLYCSEECRLK 33 (43)
T ss_pred hhhhHHHHhhccccCCC------CCccccCHHHHhH
Confidence 79999999999985432 2466799999953
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=92.84 E-value=0.071 Score=32.23 Aligned_cols=34 Identities=26% Similarity=0.619 Sum_probs=21.3
Q ss_pred hccCccCCCCCCCCCc--eEEEcC-CCcccChhhHHH
Q 032471 58 LQHCFLCKQTLLPGKD--IYMYKG-DRAFCSVECRCR 91 (140)
Q Consensus 58 L~~C~~CkK~L~~gkD--IyMYRG-e~AFCS~ECR~~ 91 (140)
...|..|++.+....+ +..|.| ..-|||..|+..
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 4569999999955555 677776 468999999864
No 6
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=90.72 E-value=0.23 Score=35.03 Aligned_cols=32 Identities=31% Similarity=0.786 Sum_probs=28.2
Q ss_pred ccCccCCCCCCCCCceEEEcCCCc---ccChhhHH
Q 032471 59 QHCFLCKQTLLPGKDIYMYKGDRA---FCSVECRC 90 (140)
Q Consensus 59 ~~C~~CkK~L~~gkDIyMYRGe~A---FCS~ECR~ 90 (140)
..|.+|.++|.||.-|+.-|+|.. |||..|+.
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 469999999999999988888764 99999997
No 7
>PF04640 PLATZ: PLATZ transcription factor; InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=87.99 E-value=0.36 Score=34.18 Aligned_cols=44 Identities=36% Similarity=0.693 Sum_probs=28.4
Q ss_pred hhhhccee-eeeCCCCCCCCCCccccCCCCCCCchhhhccCccCCCCCCCCCceEEEcCCCcccChhh
Q 032471 22 QVINKATM-IINNKPSFSSASSSDAANSHSTFPVPTFLQHCFLCKQTLLPGKDIYMYKGDRAFCSVEC 88 (140)
Q Consensus 22 qvI~K~t~-~~~~~~~~~~~s~~~~~~~~~~~~~~~FL~~C~~CkK~L~~gkDIyMYRGe~AFCS~EC 88 (140)
=|||.+.+ .+++.|... +....-..|..|.+.|. |- | -|||..|
T Consensus 26 Y~iNs~kVVfLn~Rpq~~--------------~~~~~~~~C~~C~R~L~---d~--~----~fCSl~C 70 (72)
T PF04640_consen 26 YVINSAKVVFLNPRPQSR--------------PSKGSGNICETCHRSLQ---DP--Y----RFCSLSC 70 (72)
T ss_pred EEeCCceEEEEccCCcCC--------------CCCCCCCccCCCCCCCC---CC--C----eEEeeeE
Confidence 38888864 455555111 11236678999999995 32 3 4999988
No 8
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=84.20 E-value=0.75 Score=31.90 Aligned_cols=34 Identities=29% Similarity=0.589 Sum_probs=23.3
Q ss_pred hccCccCCCCCCCCCceEEEcCCCcccChhhHHHHHHhhH
Q 032471 58 LQHCFLCKQTLLPGKDIYMYKGDRAFCSVECRCRQIFMDE 97 (140)
Q Consensus 58 L~~C~~CkK~L~~gkDIyMYRGe~AFCS~ECR~~qI~~DE 97 (140)
.-.|-.|+|... +.+-.-| .+|||+.|+ .|++-+
T Consensus 6 ~v~CP~C~k~~~-w~~~~~~---rPFCS~RCk--~IDLg~ 39 (62)
T PRK00418 6 TVNCPTCGKPVE-WGEISPF---RPFCSKRCQ--LIDLGE 39 (62)
T ss_pred cccCCCCCCccc-ccCCCCc---CCcccHHHH--hhhHHH
Confidence 346999999873 3322333 489999998 666654
No 9
>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=84.16 E-value=0.57 Score=29.25 Aligned_cols=28 Identities=32% Similarity=0.757 Sum_probs=18.5
Q ss_pred cCCCCCCCC--CceEEEcCCC-cccChhhHHH
Q 032471 63 LCKQTLLPG--KDIYMYKGDR-AFCSVECRCR 91 (140)
Q Consensus 63 ~CkK~L~~g--kDIyMYRGe~-AFCS~ECR~~ 91 (140)
-|...| ++ ...+.|+|.. -|||.+|++.
T Consensus 5 vcg~~v-~~~~~~~~~y~G~~Y~FCS~~C~~~ 35 (47)
T PF04945_consen 5 VCGMKV-PGNAAYSVEYNGRTYYFCSEGCKEK 35 (47)
T ss_dssp GGG-BE------EEEEETTEEEEESSHHHHHH
T ss_pred CCCCEE-ccCccEEEEECCEEEEEcCHHHHHH
Confidence 477777 44 4566888854 7999999953
No 10
>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=83.54 E-value=0.33 Score=33.01 Aligned_cols=31 Identities=26% Similarity=0.490 Sum_probs=16.9
Q ss_pred cCccCCCCCCCCCceEEEcCCCcccChhhHHHHHHhh
Q 032471 60 HCFLCKQTLLPGKDIYMYKGDRAFCSVECRCRQIFMD 96 (140)
Q Consensus 60 ~C~~CkK~L~~gkDIyMYRGe~AFCS~ECR~~qI~~D 96 (140)
.|-.|+|.... .+-. ...+|||+.|| .|.+-
T Consensus 4 ~CP~C~k~~~~-~~~n---~~rPFCS~RCk--~iDLg 34 (57)
T PF03884_consen 4 KCPICGKPVEW-SPEN---PFRPFCSERCK--LIDLG 34 (57)
T ss_dssp E-TTT--EEE--SSSS---S--SSSSHHHH--HHHHS
T ss_pred cCCCCCCeecc-cCCC---CcCCcccHhhc--ccCHH
Confidence 58889998743 2222 23699999999 56553
No 11
>smart00746 TRASH metallochaperone-like domain.
Probab=80.11 E-value=2.5 Score=22.08 Aligned_cols=31 Identities=29% Similarity=0.787 Sum_probs=19.4
Q ss_pred CccCCCCCC-CCCc-eEEEcC-CCcccChhhHHH
Q 032471 61 CFLCKQTLL-PGKD-IYMYKG-DRAFCSVECRCR 91 (140)
Q Consensus 61 C~~CkK~L~-~gkD-IyMYRG-e~AFCS~ECR~~ 91 (140)
|..|+..+. ++.. .+.+.| ..-|||.+|...
T Consensus 1 c~~C~~~~~~~~~~~~~~~~g~~~~FCs~~c~~~ 34 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVVNDGKVFYFCSSKCLSK 34 (39)
T ss_pred CCCCCCCccCCCCceEEEECCEEEEEeCHHHHHH
Confidence 677888885 3322 223444 336999999864
No 12
>PRK01343 zinc-binding protein; Provisional
Probab=78.33 E-value=1.7 Score=29.73 Aligned_cols=29 Identities=28% Similarity=0.592 Sum_probs=21.1
Q ss_pred ccCccCCCCCCCCCceEEEcCCCcccChhhHHHHHHhhH
Q 032471 59 QHCFLCKQTLLPGKDIYMYKGDRAFCSVECRCRQIFMDE 97 (140)
Q Consensus 59 ~~C~~CkK~L~~gkDIyMYRGe~AFCS~ECR~~qI~~DE 97 (140)
..|--|+|... + -..+|||+-|| .|++-.
T Consensus 10 ~~CP~C~k~~~-~-------~~rPFCS~RC~--~iDLg~ 38 (57)
T PRK01343 10 RPCPECGKPST-R-------EAYPFCSERCR--DIDLNR 38 (57)
T ss_pred CcCCCCCCcCc-C-------CCCcccCHHHh--hhhHHH
Confidence 56999999863 1 24599999999 565543
No 13
>PRK00807 50S ribosomal protein L24e; Validated
Probab=74.89 E-value=3.4 Score=27.16 Aligned_cols=33 Identities=30% Similarity=0.691 Sum_probs=25.7
Q ss_pred ccCccCCCCCCCCCceEEEcCCC---cccChhhHHH
Q 032471 59 QHCFLCKQTLLPGKDIYMYKGDR---AFCSVECRCR 91 (140)
Q Consensus 59 ~~C~~CkK~L~~gkDIyMYRGe~---AFCS~ECR~~ 91 (140)
..|..|..++.||.-+..++.|. -|||..|...
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 35999999999888776565443 5999999753
No 14
>cd00153 RalGDS_RA Ubiquitin domain of RalGDS-like factor (RLF) and related proteins. This CD represents the C-terminal Ras-associating (RA) domain of three closely related guanine-nucleotide exchange factors (GEF's), Ral guanine nucleotide dissociation stimulator (RalGDS), RalGDS-like (RGL), and RalGDS-like factor (RLF). The RalGDS proteins are downstream effectors of the Ras-related protein Ral, providing a mechanism for Ral activation by extracellular signals. The RA domain is structurally similar to ubiquitin and exists in a number of other signalling proteins including AF6, rasfadin, SNX27, CYR1, and STE50.
Probab=72.83 E-value=2.1 Score=31.62 Aligned_cols=24 Identities=50% Similarity=0.630 Sum_probs=16.0
Q ss_pred eEEEeeccCCCCCCcchhhhhcceeeeeCCC
Q 032471 5 SIVLENQKHGGFNKKSPQVINKATMIINNKP 35 (140)
Q Consensus 5 si~le~~~~~~~~~~~~qvI~K~t~~~~~~~ 35 (140)
||+|+.| -+|||||.+| |-=|+..
T Consensus 20 SIlltsq------DktP~VI~ra-l~Khnl~ 43 (87)
T cd00153 20 SILLTSQ------DKAPQVIRRA-MEKHNLE 43 (87)
T ss_pred EEEEecC------CcCHHHHHHH-HHHhCCC
Confidence 5555555 4899999996 5444433
No 15
>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=68.47 E-value=4 Score=27.45 Aligned_cols=32 Identities=22% Similarity=0.452 Sum_probs=18.2
Q ss_pred ccCccCCCCCCCCCceEEEcCCCcccChhhHHHH
Q 032471 59 QHCFLCKQTLLPGKDIYMYKGDRAFCSVECRCRQ 92 (140)
Q Consensus 59 ~~C~~CkK~L~~gkDIyMYRGe~AFCS~ECR~~q 92 (140)
-.|..|.=-+.....|- ++.+.|||++|-..+
T Consensus 8 CaC~~C~C~V~~~~Ai~--~dGk~YCS~aCA~gH 39 (52)
T PF02069_consen 8 CACPSCSCVVSEEEAIQ--KDGKYYCSEACANGH 39 (52)
T ss_dssp -SSTT----B-TTTSEE--SSS-EESSHHHHHTS
T ss_pred ecCCCCEeEECchHhHH--hCCEeeecHHHhccC
Confidence 45778887775544443 778999999997654
No 16
>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=65.52 E-value=3.8 Score=25.31 Aligned_cols=25 Identities=24% Similarity=0.654 Sum_probs=17.6
Q ss_pred cCccCCCCCCCCCceEEEcCCCcccCh
Q 032471 60 HCFLCKQTLLPGKDIYMYKGDRAFCSV 86 (140)
Q Consensus 60 ~C~~CkK~L~~gkDIyMYRGe~AFCS~ 86 (140)
.|..|++.|.++. |....++.||..
T Consensus 28 ~C~~C~~~l~~~~--~~~~~~~~~C~~ 52 (58)
T PF00412_consen 28 KCSKCGKPLNDGD--FYEKDGKPYCKD 52 (58)
T ss_dssp BETTTTCBTTTSS--EEEETTEEEEHH
T ss_pred ccCCCCCccCCCe--eEeECCEEECHH
Confidence 4888999996544 444555899864
No 17
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.93 E-value=3.4 Score=29.16 Aligned_cols=34 Identities=26% Similarity=0.493 Sum_probs=24.1
Q ss_pred ccCccCCCCCCCCCceEEEcCCCcccChhhHHHHHHhhHH
Q 032471 59 QHCFLCKQTLLPGKDIYMYKGDRAFCSVECRCRQIFMDEE 98 (140)
Q Consensus 59 ~~C~~CkK~L~~gkDIyMYRGe~AFCS~ECR~~qI~~DE~ 98 (140)
-.|-.|.|.. .+.+.--| .+|||..|. .|++.+=
T Consensus 8 v~CP~Cgkpv-~w~~~s~f---rPFCSkRCk--lIDLg~W 41 (65)
T COG3024 8 VPCPTCGKPV-VWGEESPF---RPFCSKRCK--LIDLGEW 41 (65)
T ss_pred ccCCCCCCcc-cccccCCc---CcchhHhhh--hcchhhh
Confidence 3599999987 44444334 499999887 7777663
No 18
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=63.76 E-value=7.2 Score=30.74 Aligned_cols=34 Identities=18% Similarity=0.415 Sum_probs=25.8
Q ss_pred ccCccCCCCCCCCCceEEEcCCC---cccChhhHHHH
Q 032471 59 QHCFLCKQTLLPGKDIYMYKGDR---AFCSVECRCRQ 92 (140)
Q Consensus 59 ~~C~~CkK~L~~gkDIyMYRGe~---AFCS~ECR~~q 92 (140)
..|.+|..+|-||.-+-.-|.|. -|||.-|....
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~k~f 41 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCEKNY 41 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEEEecHHHHHHH
Confidence 46999999999998665556553 49999996433
No 19
>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=55.04 E-value=13 Score=24.91 Aligned_cols=34 Identities=26% Similarity=0.684 Sum_probs=26.9
Q ss_pred ccCccCCCCCCCCCceEEEcCCC---cccChhhHHHH
Q 032471 59 QHCFLCKQTLLPGKDIYMYKGDR---AFCSVECRCRQ 92 (140)
Q Consensus 59 ~~C~~CkK~L~~gkDIyMYRGe~---AFCS~ECR~~q 92 (140)
..|..|..++-||.-+-.-|.|. -|||.-|+...
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~F~s~Kc~~~~ 40 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFRFCSSKCEKNF 40 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEEEECHHHHHHH
Confidence 46999999999998766667665 49999997543
No 20
>PHA03073 late transcription factor VLTF-2; Provisional
Probab=52.12 E-value=9.5 Score=30.68 Aligned_cols=36 Identities=31% Similarity=0.576 Sum_probs=25.6
Q ss_pred hhccCccCCCCCCCCCceEE---EcC-CCcccChhhHHHHH
Q 032471 57 FLQHCFLCKQTLLPGKDIYM---YKG-DRAFCSVECRCRQI 93 (140)
Q Consensus 57 FL~~C~~CkK~L~~gkDIyM---YRG-e~AFCS~ECR~~qI 93 (140)
=-+.|-+|+..|.. .++++ |.| -..|||.=||+---
T Consensus 48 ~~~~CwfC~q~~~~-~~~~iETl~g~~vg~FCS~ICRDSfa 87 (150)
T PHA03073 48 DNDYCWFCKQDLII-APLFIETLKGGAVGYFCSKICRDSFA 87 (150)
T ss_pred CCCcEEeecccccc-CceEEEeecCchhhhHhHHHHHHHHH
Confidence 34679999999954 44664 442 45799999998543
No 21
>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=47.77 E-value=15 Score=25.34 Aligned_cols=29 Identities=28% Similarity=0.818 Sum_probs=24.2
Q ss_pred cCccCCCCCCCCC-ceEEEcCCCcccChhhH
Q 032471 60 HCFLCKQTLLPGK-DIYMYKGDRAFCSVECR 89 (140)
Q Consensus 60 ~C~~CkK~L~~gk-DIyMYRGe~AFCS~ECR 89 (140)
.|-.|.+.|.++. |-||.-.|=-||. +|-
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~-~C~ 36 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCA-DCA 36 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccH-HHH
Confidence 5889999998887 9999888888885 454
No 22
>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=39.63 E-value=32 Score=18.95 Aligned_cols=23 Identities=13% Similarity=0.437 Sum_probs=15.2
Q ss_pred cCccCCCCCCCCCceEEEcCCCcc
Q 032471 60 HCFLCKQTLLPGKDIYMYKGDRAF 83 (140)
Q Consensus 60 ~C~~CkK~L~~gkDIyMYRGe~AF 83 (140)
.|..|++.|.++ +.++..++..|
T Consensus 1 ~C~~C~~~i~~~-~~~~~~~~~~~ 23 (39)
T smart00132 1 KCAGCGKPIRGG-ELVLRALGKVW 23 (39)
T ss_pred CccccCCcccCC-cEEEEeCCccc
Confidence 488999999655 44444455555
No 23
>KOG4357 consensus Uncharacterized conserved protein (involved in mesoderm differentiation in humans) [General function prediction only]
Probab=36.77 E-value=15 Score=29.59 Aligned_cols=16 Identities=38% Similarity=0.885 Sum_probs=13.8
Q ss_pred CCCCCceEEEc-CCCcc
Q 032471 68 LLPGKDIYMYK-GDRAF 83 (140)
Q Consensus 68 L~~gkDIyMYR-Ge~AF 83 (140)
++.++-|||++ |+.||
T Consensus 111 i~ddraifm~kdge~a~ 127 (164)
T KOG4357|consen 111 IDDDRAIFMFKDGEQAF 127 (164)
T ss_pred ecCCeEEEEEeChhHHH
Confidence 57789999999 88887
No 24
>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=36.56 E-value=54 Score=22.42 Aligned_cols=14 Identities=36% Similarity=0.759 Sum_probs=10.9
Q ss_pred cccChhhHHHHHHh
Q 032471 82 AFCSVECRCRQIFM 95 (140)
Q Consensus 82 AFCS~ECR~~qI~~ 95 (140)
-|||..|...-..+
T Consensus 60 ~fCS~~C~~~s~~~ 73 (79)
T PF04181_consen 60 KFCSKDCYKASEFY 73 (79)
T ss_pred CcCCHHHHHHHHHH
Confidence 89999998765443
No 25
>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=36.14 E-value=72 Score=22.56 Aligned_cols=41 Identities=22% Similarity=0.558 Sum_probs=30.0
Q ss_pred cCccCCCCCCCCCceEEEc--CCCcccChhhHHH-HHHhhHHHH
Q 032471 60 HCFLCKQTLLPGKDIYMYK--GDRAFCSVECRCR-QIFMDEEES 100 (140)
Q Consensus 60 ~C~~CkK~L~~gkDIyMYR--Ge~AFCS~ECR~~-qI~~DE~~~ 100 (140)
.|+.|...+.++..|-+.- .++.||-.-|..- +|+.+..++
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~~i~~~gL~ 45 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQLIHENGLE 45 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHHHHHHcchH
Confidence 5999999997677666553 3599999999975 444455544
No 26
>PF15279 SOBP: Sine oculis-binding protein
Probab=34.64 E-value=35 Score=29.89 Aligned_cols=37 Identities=35% Similarity=0.648 Sum_probs=24.1
Q ss_pred CccCCCCCCCCCceEEEcCCC----cccChhhHHHH---HHhhHHH
Q 032471 61 CFLCKQTLLPGKDIYMYKGDR----AFCSVECRCRQ---IFMDEEE 99 (140)
Q Consensus 61 C~~CkK~L~~gkDIyMYRGe~----AFCS~ECR~~q---I~~DE~~ 99 (140)
|-+||- +++.++ |+=-||. -|||..|..|. |++-|..
T Consensus 2 cdwckh-~rh~~~-y~d~~~g~~~lqfcs~kclnqykm~if~~etq 45 (306)
T PF15279_consen 2 CDWCKH-VRHTKS-YVDFQDGERQLQFCSDKCLNQYKMDIFYKETQ 45 (306)
T ss_pred ccchhc-ccchhh-eeccccchHHhhhccHHHHhHHHHHHHHHHHH
Confidence 888874 655554 5444444 49999999873 5555543
No 27
>PF13216 DUF4024: Protein of unknown function (DUF4024)
Probab=34.28 E-value=19 Score=22.50 Aligned_cols=7 Identities=71% Similarity=1.122 Sum_probs=5.7
Q ss_pred CcceeEE
Q 032471 1 MVGLSIV 7 (140)
Q Consensus 1 mvGLsi~ 7 (140)
||||||.
T Consensus 1 mvglsvt 7 (35)
T PF13216_consen 1 MVGLSVT 7 (35)
T ss_pred CcceEEE
Confidence 8898885
No 28
>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=32.31 E-value=49 Score=20.77 Aligned_cols=31 Identities=16% Similarity=0.370 Sum_probs=22.0
Q ss_pred CccCCCCCCCCCceEEEcCC-CcccChhhHHH
Q 032471 61 CFLCKQTLLPGKDIYMYKGD-RAFCSVECRCR 91 (140)
Q Consensus 61 C~~CkK~L~~gkDIyMYRGe-~AFCS~ECR~~ 91 (140)
|.+|.+.+...--+|=+.|. --||+..|..+
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 78899999655555555443 35899999864
No 29
>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=28.75 E-value=46 Score=22.57 Aligned_cols=24 Identities=13% Similarity=0.333 Sum_probs=16.4
Q ss_pred ccCccCCCCCCCCCceEEEcCCCcc
Q 032471 59 QHCFLCKQTLLPGKDIYMYKGDRAF 83 (140)
Q Consensus 59 ~~C~~CkK~L~~gkDIyMYRGe~AF 83 (140)
..|..|+|+|+. ..+.+|--...|
T Consensus 79 ~~C~vC~k~l~~-~~f~~~p~~~v~ 102 (109)
T PF10367_consen 79 TKCSVCGKPLGN-SVFVVFPCGHVV 102 (109)
T ss_pred CCccCcCCcCCC-ceEEEeCCCeEE
Confidence 449999999954 666677532433
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=28.53 E-value=39 Score=19.88 Aligned_cols=15 Identities=27% Similarity=0.556 Sum_probs=11.8
Q ss_pred CCCcccChhhHHHHH
Q 032471 79 GDRAFCSVECRCRQI 93 (140)
Q Consensus 79 Ge~AFCS~ECR~~qI 93 (140)
....|||.+|+....
T Consensus 16 ~~~~YCs~~Cq~~~w 30 (37)
T PF01753_consen 16 KSVYYCSEECQRADW 30 (37)
T ss_dssp SSSEESSHHHHHHHH
T ss_pred CCEEecCHHHHHHHH
Confidence 467899999997654
No 31
>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=28.23 E-value=58 Score=22.87 Aligned_cols=33 Identities=24% Similarity=0.575 Sum_probs=21.9
Q ss_pred ccCccCCCCCCCCCceEEEcCCC---cccChhhHHH
Q 032471 59 QHCFLCKQTLLPGKDIYMYKGDR---AFCSVECRCR 91 (140)
Q Consensus 59 ~~C~~CkK~L~~gkDIyMYRGe~---AFCS~ECR~~ 91 (140)
..|.+|..+|-||.-+-.-+-|. -|||.-|+..
T Consensus 4 ~~C~Fsg~~I~PG~G~~~Vr~DG~v~~F~s~Kc~~~ 39 (71)
T PF01246_consen 4 EKCSFSGYKIYPGHGKMYVRNDGKVFYFCSSKCEKL 39 (71)
T ss_dssp EE-TTT-SEE-SSSSEEEE-TTS-EEEESSHHHHHH
T ss_pred EEecccCCccCCCCCeEEEecCCCeEEEeCHHHHHH
Confidence 46999999999997665444443 4999999854
No 32
>cd01224 PH_Collybistin Collybistin pleckstrin homology (PH) domain. Collybistin pleckstrin homology (PH) domain. Collybistin is GEF which induces submembrane clustering of the receptor-associated peripheral membrane protein gephyrin. It consists of an SH3 domain, followed by a RhoGEF(dbH) and PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=26.10 E-value=31 Score=26.07 Aligned_cols=20 Identities=40% Similarity=0.811 Sum_probs=15.0
Q ss_pred cCccCCCCCCCCCceEEEcCC
Q 032471 60 HCFLCKQTLLPGKDIYMYKGD 80 (140)
Q Consensus 60 ~C~~CkK~L~~gkDIyMYRGe 80 (140)
.--+|||++. -+|.|.|+|-
T Consensus 29 ~LI~CKkd~~-r~~~~~yKgr 48 (109)
T cd01224 29 QMVLCKKDLI-RRDHLYYKGR 48 (109)
T ss_pred eEEEEecccc-cCCcEEEEEE
Confidence 3445999985 4789999973
No 33
>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=25.76 E-value=21 Score=23.19 Aligned_cols=31 Identities=19% Similarity=0.514 Sum_probs=19.0
Q ss_pred ccCccCCCCCCCCCceE-EEcCCCcccChhhHH
Q 032471 59 QHCFLCKQTLLPGKDIY-MYKGDRAFCSVECRC 90 (140)
Q Consensus 59 ~~C~~CkK~L~~gkDIy-MYRGe~AFCS~ECR~ 90 (140)
..|-.|.+... ++--+ -=-.++-|||+-||.
T Consensus 9 K~C~~C~rpf~-WRKKW~~~Wd~VkYCS~rCR~ 40 (42)
T PF10013_consen 9 KICPVCGRPFT-WRKKWARCWDEVKYCSDRCRR 40 (42)
T ss_pred CcCcccCCcch-HHHHHHHhchhhccHHHHhcc
Confidence 34888887763 22111 002478899999995
No 34
>PTZ00033 60S ribosomal protein L24; Provisional
Probab=22.70 E-value=89 Score=24.46 Aligned_cols=33 Identities=15% Similarity=0.297 Sum_probs=25.4
Q ss_pred ccCccCCCCCCCCCceEEEc----CCC---cccChhhHHH
Q 032471 59 QHCFLCKQTLLPGKDIYMYK----GDR---AFCSVECRCR 91 (140)
Q Consensus 59 ~~C~~CkK~L~~gkDIyMYR----Ge~---AFCS~ECR~~ 91 (140)
..|.+|..++-||.-+-.-+ .|. -|||.-|...
T Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr~~~~~Dgkv~~F~~sKc~~~ 43 (125)
T PTZ00033 4 IACEFSHFAVHPGHGRRYVPFAFLSTKPVLTFLRPKCFAL 43 (125)
T ss_pred eEecCcCCcccCCCCcEeeecccCCCCCEEEEecHHHHHH
Confidence 46999999999997665556 554 5999999643
No 35
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=22.23 E-value=44 Score=22.70 Aligned_cols=28 Identities=29% Similarity=0.552 Sum_probs=19.6
Q ss_pred CCCCCCCC--CceEEEcCCC-cccChhhHHH
Q 032471 64 CKQTLLPG--KDIYMYKGDR-AFCSVECRCR 91 (140)
Q Consensus 64 CkK~L~~g--kDIyMYRGe~-AFCS~ECR~~ 91 (140)
|+..+... .-.|-|+|-. =|||++|-..
T Consensus 8 cgm~v~~~~a~~k~~Y~GktYYFcse~~~~~ 38 (53)
T COG3350 8 CGMKVDNENAEYKSSYGGKTYYFCSEECKEK 38 (53)
T ss_pred cCccccccccceeEEeCCEEEEEeCHHHHHH
Confidence 77777533 3567788754 5999999754
No 36
>COG1445 FrwB Phosphotransferase system fructose-specific component IIB [Carbohydrate transport and metabolism]
Probab=20.03 E-value=1.1e+02 Score=23.93 Aligned_cols=31 Identities=26% Similarity=0.261 Sum_probs=25.9
Q ss_pred cceeEEEeeccCC-CCCCcchhhhhcceeeee
Q 032471 2 VGLSIVLENQKHG-GFNKKSPQVINKATMIIN 32 (140)
Q Consensus 2 vGLsi~le~~~~~-~~~~~~~qvI~K~t~~~~ 32 (140)
.|..|-+|+|-.. -.|.-|++=|+.|+++|-
T Consensus 31 ~g~~IKVETqGs~G~eN~LT~edI~~Ad~VI~ 62 (122)
T COG1445 31 LGVEIKVETQGAVGIENRLTAEDIAAADVVIL 62 (122)
T ss_pred cCCeEEEEcCCcccccCcCCHHHHHhCCEEEE
Confidence 4889999999744 478999999999987775
Done!