Query 030577
Match_columns 175
No_of_seqs 130 out of 555
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 15:50:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030577.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030577hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00021 BBOX B-Box-type zinc f 97.9 9.6E-06 2.1E-10 49.6 3.0 38 22-63 2-39 (39)
2 PF00643 zf-B_box: B-box zinc 97.6 5.7E-05 1.2E-09 47.5 2.8 41 19-63 2-42 (42)
3 smart00336 BBOX B-Box-type zin 97.3 0.00025 5.4E-09 43.8 3.0 39 21-63 4-42 (42)
4 KOG4367 Predicted Zn-finger pr 72.5 1.2 2.6E-05 43.1 0.0 48 21-68 163-214 (699)
5 KOG0129 Predicted RNA-binding 62.1 3.5 7.5E-05 39.9 0.9 47 9-55 443-497 (520)
6 KOG1280 Uncharacterized conser 51.4 7.3 0.00016 36.4 1.1 35 5-48 2-40 (381)
7 PF07975 C1_4: TFIIH C1-like d 50.4 7 0.00015 26.8 0.6 23 31-53 20-42 (51)
8 PF07649 C1_3: C1-like domain; 46.1 7.9 0.00017 22.9 0.3 26 22-52 2-27 (30)
9 cd02342 ZZ_UBA_plant Zinc fing 34.7 25 0.00055 23.5 1.4 29 22-50 2-34 (43)
10 TIGR00622 ssl1 transcription f 32.1 38 0.00082 26.7 2.2 33 21-53 56-102 (112)
11 PF03107 C1_2: C1 domain; Int 31.1 27 0.00059 20.8 1.0 26 22-52 2-27 (30)
12 PF01412 ArfGap: Putative GTPa 29.9 37 0.00081 25.7 1.8 35 18-53 11-45 (116)
13 PF04438 zf-HIT: HIT zinc fing 28.8 26 0.00057 21.3 0.6 22 22-44 4-25 (30)
14 cd02335 ZZ_ADA2 Zinc finger, Z 26.5 97 0.0021 20.2 3.1 31 22-52 2-36 (49)
15 cd02249 ZZ Zinc finger, ZZ typ 25.9 1E+02 0.0022 19.7 3.1 30 22-51 2-34 (46)
16 PF10080 DUF2318: Predicted me 25.5 32 0.0007 26.4 0.8 31 20-53 35-65 (102)
17 smart00109 C1 Protein kinase C 24.2 36 0.00077 20.7 0.7 30 20-53 11-40 (49)
18 PF08271 TF_Zn_Ribbon: TFIIB z 23.0 68 0.0015 20.2 1.8 30 22-52 2-31 (43)
19 KOG1428 Inhibitor of type V ad 22.5 20 0.00044 40.0 -1.1 50 19-69 3321-3373(3738)
20 KOG2177 Predicted E3 ubiquitin 21.2 83 0.0018 24.4 2.3 40 22-66 88-128 (386)
21 KOG2807 RNA polymerase II tran 20.0 49 0.0011 31.0 0.9 34 20-53 330-366 (378)
No 1
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=97.93 E-value=9.6e-06 Score=49.62 Aligned_cols=38 Identities=39% Similarity=0.834 Sum_probs=34.1
Q ss_pred CcccccCCCceEEecCCCcccccccccCCcCCCCCCCceEec
Q 030577 22 RCDICENAPAFFYCEIDGSSLCLQCDMTVHVGGKRTHGRYLL 63 (175)
Q Consensus 22 lCD~C~~aPA~vyC~aD~A~LC~~CD~~vHsaN~~rH~RvpL 63 (175)
+|+.+...++.+||.+|.+.+|..|+...| +.|.++||
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H----~~H~~~~i 39 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLCVDCDLSVH----SGHRRVPL 39 (39)
T ss_pred CCCccCCcceEEEeCccChhhhhhcChhhc----CCCCEeeC
Confidence 599999889999999999999999998877 37888875
No 2
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=97.59 E-value=5.7e-05 Score=47.52 Aligned_cols=41 Identities=27% Similarity=0.614 Sum_probs=35.4
Q ss_pred CCCCcccccCCCceEEecCCCcccccccccCCcCCCCCCCceEec
Q 030577 19 DVPRCDICENAPAFFYCEIDGSSLCLQCDMTVHVGGKRTHGRYLL 63 (175)
Q Consensus 19 ~~plCD~C~~aPA~vyC~aD~A~LC~~CD~~vHsaN~~rH~RvpL 63 (175)
....|+.|...++.+||..+...+|..|....|.. |..++|
T Consensus 2 ~~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~----H~~~~i 42 (42)
T PF00643_consen 2 QEPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG----HKIVPI 42 (42)
T ss_dssp SSSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT----SEEEEC
T ss_pred cCccCccCCccceEEEecCCCCccCccCCCCCCCC----CEEeEC
Confidence 45789999998899999999999999999999854 888775
No 3
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.30 E-value=0.00025 Score=43.82 Aligned_cols=39 Identities=46% Similarity=0.883 Sum_probs=33.9
Q ss_pred CCcccccCCCceEEecCCCcccccccccCCcCCCCCCCceEec
Q 030577 21 PRCDICENAPAFFYCEIDGSSLCLQCDMTVHVGGKRTHGRYLL 63 (175)
Q Consensus 21 plCD~C~~aPA~vyC~aD~A~LC~~CD~~vHsaN~~rH~RvpL 63 (175)
..|..|...++.+||..|.+.+|..|....| +.|.+++|
T Consensus 4 ~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H----~~H~~~~l 42 (42)
T smart00336 4 PKCDSHGDEPAEFFCEECGALLCRTCDEAEH----RGHTVVLL 42 (42)
T ss_pred CcCCCCCCCceEEECCCCCcccccccChhhc----CCCceecC
Confidence 4799999889999999999999999998766 47877765
No 4
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=72.47 E-value=1.2 Score=43.09 Aligned_cols=48 Identities=29% Similarity=0.511 Sum_probs=39.6
Q ss_pred CCcccccCCC--ceEEecCCCcccccccccCCcCCCC--CCCceEecccccc
Q 030577 21 PRCDICENAP--AFFYCEIDGSSLCLQCDMTVHVGGK--RTHGRYLLLRQRV 68 (175)
Q Consensus 21 plCD~C~~aP--A~vyC~aD~A~LC~~CD~~vHsaN~--~rH~RvpL~~~~~ 68 (175)
..|..|+.+| |.|+|+.+..+.|.-|..+.|-+-. .+|.-+|-..-++
T Consensus 163 ~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grv 214 (699)
T KOG4367|consen 163 LKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRV 214 (699)
T ss_pred hhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCce
Confidence 4799999987 9999999999999999999998754 5787776654443
No 5
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=62.09 E-value=3.5 Score=39.88 Aligned_cols=47 Identities=26% Similarity=0.457 Sum_probs=38.3
Q ss_pred ceecccCCC-CCCCCcccccC-----CCceEEecCCC--cccccccccCCcCCCC
Q 030577 9 HVRVGLANP-SDVPRCDICEN-----APAFFYCEIDG--SSLCLQCDMTVHVGGK 55 (175)
Q Consensus 9 H~Rv~L~~~-~~~plCD~C~~-----aPA~vyC~aD~--A~LC~~CD~~vHsaN~ 55 (175)
+.||-+.+- -+..+||.|+. ..|-+||.+-. -+.|..|=..+|+.-.
T Consensus 443 ~KRVEIkPYv~eDq~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~~~ 497 (520)
T KOG0129|consen 443 DKRVEIKPYVMEDQLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSGPG 497 (520)
T ss_pred ceeeeecceeccccchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcCCc
Confidence 347777664 48899999999 88999997654 5899999999998743
No 6
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=51.37 E-value=7.3 Score=36.37 Aligned_cols=35 Identities=34% Similarity=0.535 Sum_probs=25.8
Q ss_pred cccCceecccCCCCCCCCcccccCCCceEEecC---C-Cccccccccc
Q 030577 5 LASRHVRVGLANPSDVPRCDICENAPAFFYCEI---D-GSSLCLQCDM 48 (175)
Q Consensus 5 LasRH~Rv~L~~~~~~plCD~C~~aPA~vyC~a---D-~A~LC~~CD~ 48 (175)
+++||.+|. ||.|.+..=+++|-- + .--||..|=.
T Consensus 2 ~~~rHe~v~---------CdgC~k~~~t~rrYkCL~C~DyDlC~sCye 40 (381)
T KOG1280|consen 2 LTSRHEGVS---------CDGCGKTAFTFRRYKCLRCSDYDLCFSCYE 40 (381)
T ss_pred CCCCcCCce---------eccccccceeeeeeEeeeecchhHHHHHhh
Confidence 689999995 999999877777632 2 2357877743
No 7
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=50.40 E-value=7 Score=26.79 Aligned_cols=23 Identities=22% Similarity=0.658 Sum_probs=15.7
Q ss_pred ceEEecCCCcccccccccCCcCC
Q 030577 31 AFFYCEIDGSSLCLQCDMTVHVG 53 (175)
Q Consensus 31 A~vyC~aD~A~LC~~CD~~vHsa 53 (175)
..+.|......+|.+||.-+|..
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTT
T ss_pred CeEECCCCCCccccCcChhhhcc
Confidence 56889999999999999999965
No 8
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=46.08 E-value=7.9 Score=22.88 Aligned_cols=26 Identities=31% Similarity=0.613 Sum_probs=8.8
Q ss_pred CcccccCCCceEEecCCCcccccccccCCcC
Q 030577 22 RCDICENAPAFFYCEIDGSSLCLQCDMTVHV 52 (175)
Q Consensus 22 lCD~C~~aPA~vyC~aD~A~LC~~CD~~vHs 52 (175)
.|+.|+..-.. +..+-|..||..+|.
T Consensus 2 ~C~~C~~~~~~-----~~~Y~C~~Cdf~lH~ 27 (30)
T PF07649_consen 2 RCDACGKPIDG-----GWFYRCSECDFDLHE 27 (30)
T ss_dssp --TTTS----S-------EEE-TTT-----H
T ss_pred cCCcCCCcCCC-----CceEECccCCCccCh
Confidence 48888876432 245678899988884
No 9
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=34.74 E-value=25 Score=23.51 Aligned_cols=29 Identities=24% Similarity=0.605 Sum_probs=21.1
Q ss_pred CcccccCCC---ceEEecCCCc-ccccccccCC
Q 030577 22 RCDICENAP---AFFYCEIDGS-SLCLQCDMTV 50 (175)
Q Consensus 22 lCD~C~~aP---A~vyC~aD~A-~LC~~CD~~v 50 (175)
.||.|+..| ..+.|....- -||..|-.+.
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 499999877 5677776554 4999986554
No 10
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.12 E-value=38 Score=26.72 Aligned_cols=33 Identities=24% Similarity=0.590 Sum_probs=26.9
Q ss_pred CCcccccCCC--------------ceEEecCCCcccccccccCCcCC
Q 030577 21 PRCDICENAP--------------AFFYCEIDGSSLCLQCDMTVHVG 53 (175)
Q Consensus 21 plCD~C~~aP--------------A~vyC~aD~A~LC~~CD~~vHsa 53 (175)
..|-.|+..- ....|....-.+|.+||.-+|..
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~ 102 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHES 102 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhh
Confidence 3599998731 34779999999999999999974
No 11
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=31.12 E-value=27 Score=20.75 Aligned_cols=26 Identities=38% Similarity=0.824 Sum_probs=18.4
Q ss_pred CcccccCCCceEEecCCCcccccccccCCcC
Q 030577 22 RCDICENAPAFFYCEIDGSSLCLQCDMTVHV 52 (175)
Q Consensus 22 lCD~C~~aPA~vyC~aD~A~LC~~CD~~vHs 52 (175)
.|++|+.....++ .+-|..|+..+|.
T Consensus 2 ~C~~C~~~~~~~~-----~Y~C~~c~f~lh~ 27 (30)
T PF03107_consen 2 WCDVCRRKIDGFY-----FYHCSECCFTLHV 27 (30)
T ss_pred CCCCCCCCcCCCE-----eEEeCCCCCeEcC
Confidence 5899988755543 5777777777774
No 12
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=29.86 E-value=37 Score=25.69 Aligned_cols=35 Identities=23% Similarity=0.429 Sum_probs=23.5
Q ss_pred CCCCCcccccCCCceEEecCCCcccccccccCCcCC
Q 030577 18 SDVPRCDICENAPAFFYCEIDGSSLCLQCDMTVHVG 53 (175)
Q Consensus 18 ~~~plCD~C~~aPA~vyC~aD~A~LC~~CD~~vHsa 53 (175)
+....|.-|+.....+-+..=+.+||..|= .+|..
T Consensus 11 ~~N~~CaDCg~~~p~w~s~~~GiflC~~Ca-g~HR~ 45 (116)
T PF01412_consen 11 PGNKVCADCGAPNPTWASLNYGIFLCLECA-GIHRS 45 (116)
T ss_dssp TTCTB-TTT-SBS--EEETTTTEEE-HHHH-HHHHH
T ss_pred cCcCcCCCCCCCCCCEEEeecChhhhHHHH-HHHHH
Confidence 455789999988888888888999999995 44544
No 13
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=28.75 E-value=26 Score=21.30 Aligned_cols=22 Identities=36% Similarity=0.904 Sum_probs=16.5
Q ss_pred CcccccCCCceEEecCCCccccc
Q 030577 22 RCDICENAPAFFYCEIDGSSLCL 44 (175)
Q Consensus 22 lCD~C~~aPA~vyC~aD~A~LC~ 44 (175)
+|.+|+. ++...|....+..|.
T Consensus 4 ~C~vC~~-~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 4 LCSVCGN-PAKYRCPRCGARYCS 25 (30)
T ss_dssp EETSSSS-EESEE-TTT--EESS
T ss_pred CCccCcC-CCEEECCCcCCceeC
Confidence 6999998 899999998888774
No 14
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=26.51 E-value=97 Score=20.22 Aligned_cols=31 Identities=26% Similarity=0.483 Sum_probs=23.5
Q ss_pred CcccccCCCce---EEecCC-CcccccccccCCcC
Q 030577 22 RCDICENAPAF---FYCEID-GSSLCLQCDMTVHV 52 (175)
Q Consensus 22 lCD~C~~aPA~---vyC~aD-~A~LC~~CD~~vHs 52 (175)
.||.|...+-. +.|... .--||..|=..--.
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~ 36 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAE 36 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCC
Confidence 59999987654 888887 56899999765433
No 15
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=25.86 E-value=1e+02 Score=19.71 Aligned_cols=30 Identities=23% Similarity=0.490 Sum_probs=21.9
Q ss_pred CcccccCC--CceEEecCCC-cccccccccCCc
Q 030577 22 RCDICENA--PAFFYCEIDG-SSLCLQCDMTVH 51 (175)
Q Consensus 22 lCD~C~~a--PA~vyC~aD~-A~LC~~CD~~vH 51 (175)
.|+.|... ...+.|.... --||..|=...+
T Consensus 2 ~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~ 34 (46)
T cd02249 2 SCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK 34 (46)
T ss_pred CCcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc
Confidence 48888872 2677887776 689999966554
No 16
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=25.49 E-value=32 Score=26.39 Aligned_cols=31 Identities=23% Similarity=0.713 Sum_probs=24.2
Q ss_pred CCCcccccCCCceEEecCCCcccccccccCCcCC
Q 030577 20 VPRCDICENAPAFFYCEIDGSSLCLQCDMTVHVG 53 (175)
Q Consensus 20 ~plCD~C~~aPA~vyC~aD~A~LC~~CD~~vHsa 53 (175)
...|++|+ +..+| ..+....|..|+.+.+..
T Consensus 35 ~daCeiC~--~~GY~-q~g~~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 35 FDACEICG--PKGYY-QEGDQLVCKNCGVRFNLP 65 (102)
T ss_pred EEeccccC--CCceE-EECCEEEEecCCCEEehh
Confidence 36799994 55566 888889999999887754
No 17
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=24.16 E-value=36 Score=20.73 Aligned_cols=30 Identities=17% Similarity=0.399 Sum_probs=22.5
Q ss_pred CCCcccccCCCceEEecCCCcccccccccCCcCC
Q 030577 20 VPRCDICENAPAFFYCEIDGSSLCLQCDMTVHVG 53 (175)
Q Consensus 20 ~plCD~C~~aPA~vyC~aD~A~LC~~CD~~vHsa 53 (175)
...|+.|...-..+. .+.-|..|...+|..
T Consensus 11 ~~~C~~C~~~i~~~~----~~~~C~~C~~~~H~~ 40 (49)
T smart00109 11 PTKCCVCRKSIWGSF----QGLRCSWCKVKCHKK 40 (49)
T ss_pred CCCccccccccCcCC----CCcCCCCCCchHHHH
Confidence 447999998654433 478899999999964
No 18
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=22.96 E-value=68 Score=20.24 Aligned_cols=30 Identities=17% Similarity=0.578 Sum_probs=23.2
Q ss_pred CcccccCCCceEEecCCCcccccccccCCcC
Q 030577 22 RCDICENAPAFFYCEIDGSSLCLQCDMTVHV 52 (175)
Q Consensus 22 lCD~C~~aPA~vyC~aD~A~LC~~CD~~vHs 52 (175)
.|..|.... .++-.+..-..|..|..-+..
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-BBEE-
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCCEeec
Confidence 588999876 888888888999999876654
No 19
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=22.48 E-value=20 Score=39.96 Aligned_cols=50 Identities=28% Similarity=0.689 Sum_probs=38.4
Q ss_pred CCCCcccccC--CCceEEecCCCcccccccccCCcCCCC-CCCceEeccccccc
Q 030577 19 DVPRCDICEN--APAFFYCEIDGSSLCLQCDMTVHVGGK-RTHGRYLLLRQRVE 69 (175)
Q Consensus 19 ~~plCD~C~~--aPA~vyC~aD~A~LC~~CD~~vHsaN~-~rH~RvpL~~~~~~ 69 (175)
-.|+||.-.. -.|.|+|..+. .||.+||.-.|-.-. +.|+|.-+.+-.+.
T Consensus 3321 Q~PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLHrrtktH~~q~f~eeeea 3373 (3738)
T KOG1428|consen 3321 QMPMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLHRRTKTHQRQVFKEEEEA 3373 (3738)
T ss_pred cCCcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHHhhccchhhhhhhhhhhh
Confidence 3578887754 36899999888 999999998876655 78999887654443
No 20
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.21 E-value=83 Score=24.36 Aligned_cols=40 Identities=28% Similarity=0.494 Sum_probs=28.3
Q ss_pred CcccccCCCceEEecCCCcccccccc-cCCcCCCCCCCceEecccc
Q 030577 22 RCDICENAPAFFYCEIDGSSLCLQCD-MTVHVGGKRTHGRYLLLRQ 66 (175)
Q Consensus 22 lCD~C~~aPA~vyC~aD~A~LC~~CD-~~vHsaN~~rH~RvpL~~~ 66 (175)
+|...... ..+||..|...+|..|. ...| ..|.-+++..+
T Consensus 88 ~c~~~~~~-~~~~c~~~~~~~c~~c~~~~~h----~~h~~~~~~~~ 128 (386)
T KOG2177|consen 88 LCEKHGEE-LKLFCEEDEKLLCVLCRESGEH----RGHPVLPLEEA 128 (386)
T ss_pred hhhhcCCc-ceEEecccccccCCCCCCcccc----cCCccccHHHH
Confidence 56655554 68999999999999999 4444 34555555544
No 21
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=20.05 E-value=49 Score=31.01 Aligned_cols=34 Identities=26% Similarity=0.660 Sum_probs=27.3
Q ss_pred CCCcccccC---CCceEEecCCCcccccccccCCcCC
Q 030577 20 VPRCDICEN---APAFFYCEIDGSSLCLQCDMTVHVG 53 (175)
Q Consensus 20 ~plCD~C~~---aPA~vyC~aD~A~LC~~CD~~vHsa 53 (175)
...|-.|+. .-..+.|..+.-.+|.+||.-+|..
T Consensus 330 ~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 330 SRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred CcceeeeccccCCCCcEEchhccceeeccchHHHHhh
Confidence 345999932 3467899999999999999999965
Done!