Query 002739
Match_columns 886
No_of_seqs 246 out of 507
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 06:08:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002739.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002739hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02362 B3: B3 DNA binding do 99.6 1.5E-15 3.2E-20 134.1 10.5 98 337-438 1-100 (100)
2 PF07496 zf-CW: CW-type Zinc F 99.6 1.2E-15 2.5E-20 124.6 2.0 45 569-614 1-50 (50)
3 PF03754 DUF313: Domain of unk 97.8 3.5E-05 7.7E-10 73.5 6.8 79 331-410 18-114 (114)
4 PF09217 EcoRII-N: Restriction 97.6 0.00015 3.2E-09 72.5 6.9 89 334-422 7-110 (156)
5 PF00320 GATA: GATA zinc finge 88.3 0.14 3E-06 39.9 -0.1 29 12-44 3-31 (36)
6 cd00202 ZnF_GATA Zinc finger D 88.2 0.3 6.6E-06 41.4 1.9 33 11-47 3-35 (54)
7 smart00401 ZnF_GATA zinc finge 83.6 0.44 9.6E-06 39.9 0.6 36 5-46 3-38 (52)
8 smart00249 PHD PHD zinc finger 74.5 1.7 3.7E-05 32.9 1.3 38 55-93 10-47 (47)
9 smart00249 PHD PHD zinc finger 73.1 3.4 7.4E-05 31.3 2.7 30 567-596 10-45 (47)
10 PF10844 DUF2577: Protein of u 59.9 30 0.00066 32.4 6.6 78 334-433 18-97 (100)
11 PF04014 Antitoxin-MazE: Antid 49.8 26 0.00057 28.3 3.9 30 405-435 13-42 (47)
12 PF00628 PHD: PHD-finger; Int 32.5 31 0.00067 27.7 1.8 16 565-580 8-23 (51)
13 PF12760 Zn_Tnp_IS1595: Transp 27.7 30 0.00064 28.2 1.0 26 36-68 21-46 (46)
14 TIGR01439 lp_hng_hel_AbrB loop 26.0 1.1E+02 0.0023 23.6 3.8 28 405-433 13-40 (43)
15 PHA02610 uvsY.-2 hypothetical 23.4 44 0.00094 29.1 1.2 21 682-702 3-30 (53)
16 PF02643 DUF192: Uncharacteriz 23.0 1.3E+02 0.0029 28.4 4.5 52 371-422 49-107 (108)
17 KOG1601 GATA-4/5/6 transcripti 22.4 42 0.00091 33.5 1.1 36 6-47 200-235 (340)
18 PF15396 FAM60A: Protein Famil 22.1 1.4E+02 0.003 32.4 4.8 15 702-716 51-65 (213)
19 PRK14559 putative protein seri 21.7 44 0.00094 41.0 1.3 14 675-688 480-493 (645)
20 PF12773 DZR: Double zinc ribb 20.9 64 0.0014 26.1 1.7 34 33-66 12-50 (50)
21 KOG4718 Non-SMC (structural ma 20.2 32 0.0007 37.2 -0.2 28 49-76 184-211 (235)
No 1
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=99.63 E-value=1.5e-15 Score=134.08 Aligned_cols=98 Identities=24% Similarity=0.437 Sum_probs=70.0
Q ss_pred EEEecccccCCCCCcEEeehhhhhhcCCCCCCCCCceEEEEeCCCCeEEEEEEEcCCCCCccccc-cCchhhhhccCCCC
Q 002739 337 FEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVL-EGVTPCIQNMQLQA 415 (886)
Q Consensus 337 F~KvLT~SDVgslgRLVIPKk~AEs~FPpL~~~eG~~L~v~D~~GK~W~FRfryw~Nn~SR~YVL-eGWs~FVRsK~Lqa 415 (886)
|.|+|+++|+....+|+||++.++.|. +....++.|.++|..|+.|.+++.++. +..+ |+| .||..||++++|++
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~--~~~~~~~~v~l~~~~g~~W~v~~~~~~-~~~~-~~l~~GW~~Fv~~n~L~~ 76 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHG--GNKRKSREVTLKDPDGRSWPVKLKYRK-NSGR-YYLTGGWKKFVRDNGLKE 76 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS----SS--CEEEEEETTTEEEEEEEEEEC-CTTE-EEEETTHHHHHHHCT--T
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhC--CCcCCCeEEEEEeCCCCEEEEEEEEEc-cCCe-EEECCCHHHHHHHcCCCC
Confidence 899999999998889999999999982 122357899999999999999999883 3334 555 69999999999999
Q ss_pred CCEEEEEEec-CCCeEEEEEEeCC
Q 002739 416 GDIVTFSRLE-PEGKLVMGFRKAS 438 (886)
Q Consensus 416 GDtVvF~R~e-~~GkL~IGVRRas 438 (886)
||+|+|+... ...++.|.+.|++
T Consensus 77 GD~~~F~~~~~~~~~~~v~i~~~~ 100 (100)
T PF02362_consen 77 GDVCVFELIGNSNFTLKVHIFRKS 100 (100)
T ss_dssp T-EEEEEE-SSSCE-EEEEEE---
T ss_pred CCEEEEEEecCCCceEEEEEEECc
Confidence 9999999975 3446699988763
No 2
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 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 CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=99.55 E-value=1.2e-15 Score=124.56 Aligned_cols=45 Identities=42% Similarity=1.032 Sum_probs=30.2
Q ss_pred CceEeccCcccccccCCCC-----CCCCCcEeecCCCCCCCCCCCcccccc
Q 002739 569 IQWVQCEDCSKWRKVPANA-----RLPSKWTCSGNLWDPERSVCSVAQELR 614 (886)
Q Consensus 569 ~~WVQCD~C~KWRrLP~~~-----~lP~kW~CsmN~WDp~~~sCsaPEE~~ 614 (886)
+.|||||.|+|||+||.++ .+|+.|+|+||+ |+.+++|++|||.+
T Consensus 1 ~~WVQCd~C~KWR~lp~~~~~~~~~~~d~W~C~~n~-~~~~~sC~~pee~e 50 (50)
T PF07496_consen 1 DYWVQCDSCLKWRRLPEEVDPIREELPDPWYCSMNP-DPPFNSCDAPEEIE 50 (50)
T ss_dssp -EEEE-TTT--EEEE-CCHHCTSCCSSTT--GGGSS--CCC-STTS--SS-
T ss_pred CeEEECCCCCceeeCChhhCcccccCCCeEEcCCCC-CCCCCCCCCcccCC
Confidence 4799999999999999884 468999999999 89999999999963
No 3
>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function.
Probab=97.85 E-value=3.5e-05 Score=73.48 Aligned_cols=79 Identities=20% Similarity=0.371 Sum_probs=64.2
Q ss_pred ccccceEEEecccccCCC-CCcEEeehhhhhhcCCCCC---------------CCCCceEEEEeCCCCeEEEEEEEcCC-
Q 002739 331 SVITPLFEKMLSASDAGR-IGRLVLPKKCAEAYFPPIS---------------QPEGLPLKVQDSKGKEWIFQFRFWPN- 393 (886)
Q Consensus 331 s~~~~LF~KvLT~SDVgs-lgRLVIPKk~AEs~FPpL~---------------~~eG~~L~v~D~~GK~W~FRfryw~N- 393 (886)
..+..+|+|+|++|||.. ..||.||...... ..+|. ...|+.+.+.|..++.|..+++.|.-
T Consensus 18 ~d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg 96 (114)
T PF03754_consen 18 EDPKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMG 96 (114)
T ss_pred CCCeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEeccc
Confidence 556899999999999995 7899999887643 23332 35789999999999999999999964
Q ss_pred CCCcccccc-Cchhhhhc
Q 002739 394 NNSRMYVLE-GVTPCIQN 410 (886)
Q Consensus 394 n~SR~YVLe-GWs~FVRs 410 (886)
+..-.|+|. ||.++|.+
T Consensus 97 ~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 97 NGTSNYVLNSGWNKVVED 114 (114)
T ss_pred CCceEEEEEcChHhhccC
Confidence 446689994 99998863
No 4
>PF09217 EcoRII-N: Restriction endonuclease EcoRII, N-terminal; InterPro: IPR023372 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the N-terminal effector-binding domain of the type II restriction endonuclease EcoRII, which has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not []. The domain represented by this entry is only found in bacterial proteins.; PDB: 3HQF_A 1NA6_A.
Probab=97.58 E-value=0.00015 Score=72.45 Aligned_cols=89 Identities=21% Similarity=0.347 Sum_probs=58.0
Q ss_pred cceEEEecccccCCCC----CcEEeehhhhhhcCCCCCC----CCCceEEEEeCCC--CeEEEEEEEcCC----CCCccc
Q 002739 334 TPLFEKMLSASDAGRI----GRLVLPKKCAEAYFPPISQ----PEGLPLKVQDSKG--KEWIFQFRFWPN----NNSRMY 399 (886)
Q Consensus 334 ~~LF~KvLT~SDVgsl----gRLVIPKk~AEs~FPpL~~----~eG~~L~v~D~~G--K~W~FRfryw~N----n~SR~Y 399 (886)
...|.|.||+.|++.+ .+++|||..++.+||.+.. .+.+.|.+++..+ ..|+|||+|.-| .-+..|
T Consensus 7 ~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTRNE~ 86 (156)
T PF09217_consen 7 WAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTRNEY 86 (156)
T ss_dssp EEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS--EE
T ss_pred eEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEcccccCCCcCce
Confidence 4689999999999964 5899999999999998764 3558899999877 668899999932 236679
Q ss_pred cccCchhhhhccC-CCCCCEEEEE
Q 002739 400 VLEGVTPCIQNMQ-LQAGDIVTFS 422 (886)
Q Consensus 400 VLeGWs~FVRsK~-LqaGDtVvF~ 422 (886)
-++.|+.+..--+ =.+||.++|.
T Consensus 87 RIT~~G~~~~~~~~~~tGaL~vla 110 (156)
T PF09217_consen 87 RITRFGRGFPLQNPENTGALLVLA 110 (156)
T ss_dssp EEE---TTSGGG-GGGTT-EEEEE
T ss_pred EEeeecCCCccCCccccccEEEEE
Confidence 9999986665333 4689988876
No 5
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=88.28 E-value=0.14 Score=39.92 Aligned_cols=29 Identities=31% Similarity=0.739 Sum_probs=20.8
Q ss_pred ccCCcCCCCCcCCcccccCChhhhhhhhhhhcc
Q 002739 12 ECKELKSERPRKGWLLRGGEFAELCDRCGSIYE 44 (886)
Q Consensus 12 ~C~~~~s~~wrkGW~lRSG~~A~LCdrCgsayE 44 (886)
.|++++|..||+|. .|..- ||..||..|.
T Consensus 3 ~C~tt~t~~WR~~~---~g~~~-LCn~Cg~~~k 31 (36)
T PF00320_consen 3 NCGTTETPQWRRGP---NGNRT-LCNACGLYYK 31 (36)
T ss_dssp TT--ST-SSEEEET---TSEE--EEHHHHHHHH
T ss_pred CCcCCCCchhhcCC---CCCCH-HHHHHHHHHH
Confidence 59999999999998 45443 9999999874
No 6
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=88.22 E-value=0.3 Score=41.36 Aligned_cols=33 Identities=24% Similarity=0.528 Sum_probs=26.8
Q ss_pred cccCCcCCCCCcCCcccccCChhhhhhhhhhhccccc
Q 002739 11 KECKELKSERPRKGWLLRGGEFAELCDRCGSIYEEGR 47 (886)
Q Consensus 11 ~~C~~~~s~~wrkGW~lRSG~~A~LCdrCgsayEq~~ 47 (886)
+.|+++.+..||+|. .| -..||..||.-|-...
T Consensus 3 ~~C~~~~Tp~WR~g~---~~-~~~LCNaCgl~~~k~~ 35 (54)
T cd00202 3 SNCGTTTTPLWRRGP---SG-GSTLCNACGLYWKKHG 35 (54)
T ss_pred CCCCCCCCcccccCC---CC-cchHHHHHHHHHHhcC
Confidence 369999999999998 22 3579999999887654
No 7
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=83.57 E-value=0.44 Score=39.93 Aligned_cols=36 Identities=25% Similarity=0.541 Sum_probs=28.2
Q ss_pred CccccccccCCcCCCCCcCCcccccCChhhhhhhhhhhcccc
Q 002739 5 SKICFNKECKELKSERPRKGWLLRGGEFAELCDRCGSIYEEG 46 (886)
Q Consensus 5 ~k~C~N~~C~~~~s~~wrkGW~lRSG~~A~LCdrCgsayEq~ 46 (886)
.+.|. .|++..+..||+|..-. ..||+.||.-|..-
T Consensus 3 ~~~C~--~C~~~~T~~WR~g~~g~----~~LCnaCgl~~~k~ 38 (52)
T smart00401 3 GRSCS--NCGTTETPLWRRGPSGN----KTLCNACGLYYKKH 38 (52)
T ss_pred CCCcC--CCCCCCCCccccCCCCC----CcEeecccHHHHHc
Confidence 45565 48999999999986543 69999999988653
No 8
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=59.86 E-value=30 Score=32.44 Aligned_cols=78 Identities=14% Similarity=0.141 Sum_probs=45.4
Q ss_pred cceEEEecccccCC--CCCcEEeehhhhhhcCCCCCCCCCceEEEEeCCCCeEEEEEEEcCCCCCccccccCchhhhhcc
Q 002739 334 TPLFEKMLSASDAG--RIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNM 411 (886)
Q Consensus 334 ~~LF~KvLT~SDVg--slgRLVIPKk~AEs~FPpL~~~eG~~L~v~D~~GK~W~FRfryw~Nn~SR~YVLeGWs~FVRsK 411 (886)
...|-++++.+-+. -.++|+||++.. ++|.+-......+.+...... +- ..|.-..
T Consensus 18 ~i~~G~V~s~~PL~I~i~~~liL~~~~L--~i~~~l~~~~~~~~~~~~~~~----------------~~----~~i~~~~ 75 (100)
T PF10844_consen 18 DIVIGTVVSVPPLKIKIDQKLILDKDFL--IIPELLKDYTRDITIEHNSET----------------DN----ITITFTD 75 (100)
T ss_pred eeEEEEEEecccEEEEECCeEEEchHHE--EeehhccceEEEEEEeccccc----------------cc----eeEEEec
Confidence 34799999999743 234599988742 344422222233333322110 00 0055667
Q ss_pred CCCCCCEEEEEEecCCCeEEEE
Q 002739 412 QLQAGDIVTFSRLEPEGKLVMG 433 (886)
Q Consensus 412 ~LqaGDtVvF~R~e~~GkL~IG 433 (886)
.|++||.|...+.+.+.+|+|=
T Consensus 76 ~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 76 GLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred CCcCCCEEEEEEecCCCEEEEE
Confidence 8999999999998644466653
No 11
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=49.80 E-value=26 Score=28.35 Aligned_cols=30 Identities=23% Similarity=0.314 Sum_probs=23.7
Q ss_pred hhhhhccCCCCCCEEEEEEecCCCeEEEEEE
Q 002739 405 TPCIQNMQLQAGDIVTFSRLEPEGKLVMGFR 435 (886)
Q Consensus 405 s~FVRsK~LqaGDtVvF~R~e~~GkL~IGVR 435 (886)
.+|.+..+|++||.|.|.-.+ +|+++|--.
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~~-~g~i~i~p~ 42 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVEG-DGKIVIRPV 42 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEET-TSEEEEEES
T ss_pred HHHHHHcCCCCCCEEEEEEeC-CCEEEEEEC
Confidence 367888899999999999874 667776543
No 12
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=32.45 E-value=31 Score=27.74 Aligned_cols=16 Identities=25% Similarity=0.989 Sum_probs=0.0
Q ss_pred CCCcCceEeccCcccc
Q 002739 565 VGEKIQWVQCEDCSKW 580 (886)
Q Consensus 565 ~ge~~~WVQCD~C~KW 580 (886)
......|||||.|..|
T Consensus 8 ~~~~~~~i~C~~C~~~ 23 (51)
T PF00628_consen 8 SDDDGDMIQCDSCNRW 23 (51)
T ss_dssp SCTTSSEEEBSTTSCE
T ss_pred cCCCCCeEEcCCCChh
No 13
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=27.70 E-value=30 Score=28.19 Aligned_cols=26 Identities=31% Similarity=0.897 Sum_probs=18.8
Q ss_pred hhhhhhhccccccccccccCCCCccccccCCCc
Q 002739 36 CDRCGSIYEEGRFCDTFHVNASGWRCCESCGKR 68 (886)
Q Consensus 36 CdrCgsayEq~~FCe~FH~~~sGWR~C~~C~Kr 68 (886)
|.+||+. ..+.....+-..|..|+++
T Consensus 21 CP~Cg~~-------~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 21 CPHCGST-------KHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCe-------eeEEeCCCCeEECCCCCCc
Confidence 9999985 2333444788889999874
No 14
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=25.96 E-value=1.1e+02 Score=23.60 Aligned_cols=28 Identities=21% Similarity=0.514 Sum_probs=22.8
Q ss_pred hhhhhccCCCCCCEEEEEEecCCCeEEEE
Q 002739 405 TPCIQNMQLQAGDIVTFSRLEPEGKLVMG 433 (886)
Q Consensus 405 s~FVRsK~LqaGDtVvF~R~e~~GkL~IG 433 (886)
..|.+..++..||.|.|.... +|.+.|-
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~-~~~l~l~ 40 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVE-DGEIILR 40 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeC-CCEEEEE
Confidence 478999999999999999763 6777653
No 15
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=23.36 E-value=44 Score=29.09 Aligned_cols=21 Identities=48% Similarity=0.991 Sum_probs=17.3
Q ss_pred ceeeeccCCC-------CCCCCCCCccc
Q 002739 682 SCIVCIQPPS-------GKGPKHKQTCT 702 (886)
Q Consensus 682 ~civciqpps-------gkgpkhk~tct 702 (886)
-|+||-||=. .+||-|-.-|-
T Consensus 3 iCvvCK~Pi~~al~v~T~~Gpvh~g~C~ 30 (53)
T PHA02610 3 ICVVCKQPIEKALVVETEKGPVHPGPCY 30 (53)
T ss_pred eeeeeCCchhhceEEecCCCCCCChhHH
Confidence 4999999954 58999998874
No 16
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=23.05 E-value=1.3e+02 Score=28.42 Aligned_cols=52 Identities=23% Similarity=0.273 Sum_probs=29.6
Q ss_pred CceEEEEeCCCCeEEEEEEEcCCC-------CCccccccCchhhhhccCCCCCCEEEEE
Q 002739 371 GLPLKVQDSKGKEWIFQFRFWPNN-------NSRMYVLEGVTPCIQNMQLQAGDIVTFS 422 (886)
Q Consensus 371 G~~L~v~D~~GK~W~FRfryw~Nn-------~SR~YVLeGWs~FVRsK~LqaGDtVvF~ 422 (886)
-+.|.+.|..|++=....-.-|.. ..-.|||+-=..++.+++|++||.|.|-
T Consensus 49 pLDi~fld~~g~Vv~i~~~~~P~~~~~~~~~~~a~~vLE~~aG~~~~~~i~~Gd~v~~~ 107 (108)
T PF02643_consen 49 PLDIAFLDSDGRVVKIERMVPPWRTYPCPSYKPARYVLELPAGWFEKLGIKVGDRVRIE 107 (108)
T ss_dssp -EEEEEE-TTSBEEEEEEEE-TT--S-EEECCEECEEEEEETTHHHHHT--TT-EEE--
T ss_pred eEEEEEECCCCeEEEEEccCCCCccCCCCCCCccCEEEEcCCCchhhcCCCCCCEEEec
Confidence 356777777776555544332211 1236899866778899999999999873
No 17
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=22.41 E-value=42 Score=33.52 Aligned_cols=36 Identities=33% Similarity=0.720 Sum_probs=27.1
Q ss_pred ccccccccCCcCCCCCcCCcccccCChhhhhhhhhhhccccc
Q 002739 6 KICFNKECKELKSERPRKGWLLRGGEFAELCDRCGSIYEEGR 47 (886)
Q Consensus 6 k~C~N~~C~~~~s~~wrkGW~lRSG~~A~LCdrCgsayEq~~ 47 (886)
..|+ .|++..+..||+| -.| .-.||..||..|-...
T Consensus 200 ~~c~--~~~~~~t~~~r~~---~~g-~~~~cnacgl~~k~~~ 235 (340)
T KOG1601|consen 200 RQCS--NCGTTKTPLWRRG---PEG-PKSLCNACGLRYKKGG 235 (340)
T ss_pred cccC--CCCCCCCcceecC---CCC-CccccccchhhhhhcC
Confidence 3454 4689999999998 334 6788999888887765
No 18
>PF15396 FAM60A: Protein Family FAM60A
Probab=22.06 E-value=1.4e+02 Score=32.44 Aligned_cols=15 Identities=33% Similarity=0.946 Sum_probs=11.2
Q ss_pred ccchhhhhhhhhhhh
Q 002739 702 TCNVCLTVKRRFHTL 716 (886)
Q Consensus 702 tcnvc~tvkrrf~tl 716 (886)
.||.|.-.=.|||.|
T Consensus 51 ICNACVLLVKRwKKL 65 (213)
T PF15396_consen 51 ICNACVLLVKRWKKL 65 (213)
T ss_pred hhHHHHHHHHHHhhC
Confidence 699998776777654
No 19
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=21.67 E-value=44 Score=40.98 Aligned_cols=14 Identities=14% Similarity=0.280 Sum_probs=8.9
Q ss_pred CCCCCCCceeeecc
Q 002739 675 PRHRPGCSCIVCIQ 688 (886)
Q Consensus 675 PRhRpGC~civciq 688 (886)
.+.|+|||..+++-
T Consensus 480 ~~~~MGTTlv~alI 493 (645)
T PRK14559 480 GSGRMGTTLVMALV 493 (645)
T ss_pred cCCCCCceeeeEEE
Confidence 34567888766654
No 20
>PF12773 DZR: Double zinc ribbon
Probab=20.93 E-value=64 Score=26.06 Aligned_cols=34 Identities=26% Similarity=0.776 Sum_probs=23.6
Q ss_pred hhhhhhhhhhcc--c--cccccccc-cCCCCccccccCC
Q 002739 33 AELCDRCGSIYE--E--GRFCDTFH-VNASGWRCCESCG 66 (886)
Q Consensus 33 A~LCdrCgsayE--q--~~FCe~FH-~~~sGWR~C~~C~ 66 (886)
+..|..||.... . ..||-.=. ....+|+-|..||
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCccc
Confidence 678889998888 2 35664433 3566888888876
No 21
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=20.16 E-value=32 Score=37.19 Aligned_cols=28 Identities=32% Similarity=0.641 Sum_probs=23.0
Q ss_pred ccccccCCCCccccccCCCceeeccccc
Q 002739 49 CDTFHVNASGWRCCESCGKRVHCGCITS 76 (886)
Q Consensus 49 Ce~FH~~~sGWR~C~~C~KrlHCGCIaS 76 (886)
|..-|.-.=-=+.|.+||-|.|||||.-
T Consensus 184 Cn~Ch~LvIqg~rCg~c~i~~h~~c~qt 211 (235)
T KOG4718|consen 184 CNLCHCLVIQGIRCGSCNIQYHRGCIQT 211 (235)
T ss_pred HhHhHHHhheeeccCcccchhhhHHHHH
Confidence 7777776655578999999999999984
Done!