Query 039386
Match_columns 582
No_of_seqs 164 out of 393
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 09:09:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039386.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039386hhsearch_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 1.9E-15 4.1E-20 127.5 10.4 98 331-444 1-100 (100)
2 PF03754 DUF313: Domain of unk 98.0 2.1E-05 4.6E-10 71.6 7.4 80 325-404 18-114 (114)
3 PF09217 EcoRII-N: Restriction 97.8 4.9E-05 1.1E-09 72.6 7.6 85 328-412 7-106 (156)
4 PF00320 GATA: GATA zinc finge 91.3 0.069 1.5E-06 39.5 0.4 29 10-42 3-31 (36)
5 cd00202 ZnF_GATA Zinc finger D 90.6 0.15 3.2E-06 41.1 1.7 33 9-45 3-35 (54)
6 smart00249 PHD PHD zinc finger 89.4 0.23 5.1E-06 35.8 1.8 38 53-91 10-47 (47)
7 smart00401 ZnF_GATA zinc finge 88.6 0.2 4.2E-06 40.0 0.9 35 4-44 4-38 (52)
8 PF00628 PHD: PHD-finger; Int 55.8 4.7 0.0001 30.8 0.5 43 51-93 8-50 (51)
9 PF13248 zf-ribbon_3: zinc-rib 50.3 6.5 0.00014 27.2 0.5 14 54-67 13-26 (26)
10 smart00109 C1 Protein kinase C 46.9 11 0.00024 27.7 1.3 38 29-76 9-46 (49)
11 PF10844 DUF2577: Protein of u 46.0 84 0.0018 28.0 6.9 82 326-441 16-99 (100)
12 cd00029 C1 Protein kinase C co 45.4 14 0.00031 27.5 1.7 37 31-76 11-47 (50)
13 KOG4443 Putative transcription 42.4 7.8 0.00017 45.1 -0.2 59 32-95 137-203 (694)
14 PF12760 Zn_Tnp_IS1595: Transp 37.0 20 0.00042 27.7 1.3 26 34-66 21-46 (46)
15 PRK14559 putative protein seri 36.8 18 0.00039 42.1 1.6 36 31-67 15-51 (645)
16 KOG1601 GATA-4/5/6 transcripti 35.4 22 0.00047 33.6 1.6 32 10-45 204-235 (340)
17 PF00130 C1_1: Phorbol esters/ 33.8 32 0.00069 26.4 2.0 38 30-76 10-47 (53)
18 KOG4718 Non-SMC (structural ma 33.1 11 0.00023 38.8 -0.8 28 47-74 184-211 (235)
19 PF12773 DZR: Double zinc ribb 32.4 28 0.00062 26.6 1.5 34 31-64 12-50 (50)
20 PF04014 Antitoxin-MazE: Antid 28.2 77 0.0017 24.3 3.3 31 399-442 13-43 (47)
21 PRK00085 recO DNA repair prote 25.5 37 0.00079 33.6 1.4 34 52-92 140-177 (247)
22 TIGR01643 YD_repeat_2x YD repe 25.0 96 0.0021 22.6 3.2 23 363-385 3-25 (42)
23 PRK07757 acetyltransferase; Pr 22.9 33 0.00073 30.5 0.5 19 54-74 127-145 (152)
24 PF03120 DNA_ligase_OB: NAD-de 21.6 1E+02 0.0022 27.2 3.2 41 398-450 41-81 (82)
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=1.9e-15 Score=127.51 Aligned_cols=98 Identities=24% Similarity=0.432 Sum_probs=69.9
Q ss_pred EEEeccccCCCCCCceEeehhhhhhcCCCCCCCCCceEEEEECCCCeEEEEEEEcCCCCCcceEe-cCchhhhhccCCcc
Q 039386 331 FEKILSASDAGRIGRLVLPKACAEAYFPHISQSEGVPLRVQDVKGKEWVFQFRFWPNNNSRMYVL-EGVTPCIQSMQLRA 409 (582)
Q Consensus 331 F~KvLT~SDVg~~gRLVIPK~~AEa~FP~Ld~~eGv~L~v~D~~Gk~W~FRf~yw~Nn~SR~YvL-tGWs~FVrsK~LqA 409 (582)
|.|+|+++|+....+|+||++.|+.| .+....+..|.+.|..|++|.+++.++. ++.+ |+| .||..||++++|++
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 FFKVLKPSDVSSSCRLIIPKEFAKKH--GGNKRKSREVTLKDPDGRSWPVKLKYRK-NSGR-YYLTGGWKKFVRDNGLKE 76 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTT--S--SS--CEEEEEETTTEEEEEEEEEEC-CTTE-EEEETTHHHHHHHCT--T
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHh--CCCcCCCeEEEEEeCCCCEEEEEEEEEc-cCCe-EEECCCHHHHHHHcCCCC
Confidence 89999999999888999999999998 2222356899999999999999999883 3344 555 59999999999999
Q ss_pred ccccccccccccCceEEEEeeC-CCCeEEEeEEeCC
Q 039386 410 GDTSMIHSILTRDDKITFSRID-PGGKLVMGFRKAP 444 (582)
Q Consensus 410 GD~i~iy~~~~~~~kVvFsR~~-~~GkL~IG~RRa~ 444 (582)
||. ++|.... ...++.|.+.|++
T Consensus 77 GD~------------~~F~~~~~~~~~~~v~i~~~~ 100 (100)
T PF02362_consen 77 GDV------------CVFELIGNSNFTLKVHIFRKS 100 (100)
T ss_dssp T-E------------EEEEE-SSSCE-EEEEEE---
T ss_pred CCE------------EEEEEecCCCceEEEEEEECc
Confidence 999 9999875 3456799988763
No 2
>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=97.97 E-value=2.1e-05 Score=71.63 Aligned_cols=80 Identities=23% Similarity=0.425 Sum_probs=63.6
Q ss_pred CcccccEEEeccccCCCC-CCceEeehhhhhh--cCCC-----C-------CCCCCceEEEEECCCCeEEEEEEEcCC-C
Q 039386 325 STIVPLFEKILSASDAGR-IGRLVLPKACAEA--YFPH-----I-------SQSEGVPLRVQDVKGKEWVFQFRFWPN-N 388 (582)
Q Consensus 325 ~~~~~LF~KvLT~SDVg~-~gRLVIPK~~AEa--~FP~-----L-------d~~eGv~L~v~D~~Gk~W~FRf~yw~N-n 388 (582)
.....+|+|+|++|||.. .+||.||-..... +|-+ | ....|+.+.+.|..++.|..+++.|.- +
T Consensus 18 ~d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~ 97 (114)
T PF03754_consen 18 EDPKLIIEKTLFKTDVDPHQSRLSMPFNQIIDNDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGN 97 (114)
T ss_pred CCCeEEEeeeecccCCCCCCceeeccHHHhcccccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccC
Confidence 556789999999999994 7899999887633 2221 2 224689999999999999999999964 4
Q ss_pred CCcceEec-Cchhhhhc
Q 039386 389 NSRMYVLE-GVTPCIQS 404 (582)
Q Consensus 389 ~SR~YvLt-GWs~FVrs 404 (582)
..-.|+|. ||.+.|.+
T Consensus 98 ~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 98 GTSNYVLNSGWNKVVED 114 (114)
T ss_pred CceEEEEEcChHhhccC
Confidence 56789996 99999863
No 3
>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=97.84 E-value=4.9e-05 Score=72.62 Aligned_cols=85 Identities=21% Similarity=0.339 Sum_probs=54.5
Q ss_pred cccEEEeccccCCCCC----CceEeehhhhhhcCCCCCCCCC----ceEEEEECCC--CeEEEEEEEcCC----CCCcce
Q 039386 328 VPLFEKILSASDAGRI----GRLVLPKACAEAYFPHISQSEG----VPLRVQDVKG--KEWVFQFRFWPN----NNSRMY 393 (582)
Q Consensus 328 ~~LF~KvLT~SDVg~~----gRLVIPK~~AEa~FP~Ld~~eG----v~L~v~D~~G--k~W~FRf~yw~N----n~SR~Y 393 (582)
...|.|.|++.|++.+ .++.|||..++..||.+....+ +.|.+.+..+ ..|+|||+|..| ..+..|
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 4589999999999963 4899999999999998776443 6799999877 678899999943 247889
Q ss_pred EecCchhhhhccC-Cccccc
Q 039386 394 VLEGVTPCIQSMQ-LRAGDT 412 (582)
Q Consensus 394 vLtGWs~FVrsK~-LqAGD~ 412 (582)
-++.|+....--+ =.+||.
T Consensus 87 RIT~~G~~~~~~~~~~tGaL 106 (156)
T PF09217_consen 87 RITRFGRGFPLQNPENTGAL 106 (156)
T ss_dssp EEE---TTSGGG-GGGTT-E
T ss_pred EEeeecCCCccCCccccccE
Confidence 9999987665222 356777
No 4
>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=91.34 E-value=0.069 Score=39.52 Aligned_cols=29 Identities=38% Similarity=0.918 Sum_probs=20.6
Q ss_pred CCCCCCCcccccCeeeccCCchhhchhhhhhcc
Q 039386 10 KCRTANTHEWKKGWLLRSGVCADLCYDCGSAYE 42 (582)
Q Consensus 10 ~C~~~~~~~wrkGW~lrsG~~a~LC~~CgsayE 42 (582)
.|+++.+..||+|. .|... ||..||..|.
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 44433 9999999875
No 5
>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=90.65 E-value=0.15 Score=41.14 Aligned_cols=33 Identities=33% Similarity=0.728 Sum_probs=27.1
Q ss_pred CCCCCCCCcccccCeeeccCCchhhchhhhhhccccc
Q 039386 9 PKCRTANTHEWKKGWLLRSGVCADLCYDCGSAYENFI 45 (582)
Q Consensus 9 ~~C~~~~~~~wrkGW~lrsG~~a~LC~~CgsayE~~~ 45 (582)
+.|+++.|..||+|. .| -..||..||.-|-...
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 3589999999987665
No 6
>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 smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=88.56 E-value=0.2 Score=39.96 Aligned_cols=35 Identities=34% Similarity=0.750 Sum_probs=27.6
Q ss_pred ccccCCCCCCCCCcccccCeeeccCCchhhchhhhhhcccc
Q 039386 4 RICMNPKCRTANTHEWKKGWLLRSGVCADLCYDCGSAYENF 44 (582)
Q Consensus 4 k~C~N~~C~~~~~~~wrkGW~lrsG~~a~LC~~CgsayE~~ 44 (582)
+.|. .|++..+..||+|..-. ..||+.||.-|...
T Consensus 4 ~~C~--~C~~~~T~~WR~g~~g~----~~LCnaCgl~~~k~ 38 (52)
T smart00401 4 RSCS--NCGTTETPLWRRGPSGN----KTLCNACGLYYKKH 38 (52)
T ss_pred CCcC--CCCCCCCCccccCCCCC----CcEeecccHHHHHc
Confidence 4564 48999999999986433 69999999988754
No 8
>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=55.83 E-value=4.7 Score=30.75 Aligned_cols=43 Identities=19% Similarity=0.400 Sum_probs=31.0
Q ss_pred cCCCCCcccccccCCccccccccccccceeecCCCcccccccC
Q 039386 51 HLEEPGWRECNFCSKRLHCGCRASNSFLELLDYGGVGCRSCAM 93 (582)
Q Consensus 51 H~~~sGWR~C~~C~KrlHcgCi~s~~~f~lLD~GGv~C~~C~~ 93 (582)
...+.-|-.|..|+++.|-.|+.-...-+-...+.=.|..|.+
T Consensus 8 ~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 8 SDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp SCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred cCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 4567789999999999999999775543333334667777754
No 9
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=50.26 E-value=6.5 Score=27.19 Aligned_cols=14 Identities=29% Similarity=0.745 Sum_probs=11.6
Q ss_pred CCCcccccccCCcc
Q 039386 54 EPGWRECNFCSKRL 67 (582)
Q Consensus 54 ~sGWR~C~~C~Krl 67 (582)
+.+++-|..||.+|
T Consensus 13 ~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 13 DPDAKFCPNCGAKL 26 (26)
T ss_pred CcccccChhhCCCC
Confidence 67789999999875
No 10
>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=46.92 E-value=11 Score=27.72 Aligned_cols=38 Identities=18% Similarity=0.411 Sum_probs=26.2
Q ss_pred CchhhchhhhhhcccccccccccCCCCCcccccccCCccccccccccc
Q 039386 29 VCADLCYDCGSAYENFIFCNTFHLEEPGWRECNFCSKRLHCGCRASNS 76 (582)
Q Consensus 29 ~~a~LC~~CgsayE~~~FCe~FH~~~sGWR~C~~C~KrlHcgCi~s~~ 76 (582)
.....|+-|+..+-.. . .|+ .|..|+..+|-+|.....
T Consensus 9 ~~~~~C~~C~~~i~~~--------~-~~~-~C~~C~~~~H~~C~~~v~ 46 (49)
T smart00109 9 KKPTKCCVCRKSIWGS--------F-QGL-RCSWCKVKCHKKCAEKVP 46 (49)
T ss_pred CCCCCccccccccCcC--------C-CCc-CCCCCCchHHHHHHhhcC
Confidence 3355677777765321 1 465 499999999999987644
No 11
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=45.96 E-value=84 Score=28.01 Aligned_cols=82 Identities=13% Similarity=0.189 Sum_probs=46.4
Q ss_pred cccccEEEeccccCCC--CCCceEeehhhhhhcCCCCCCCCCceEEEEECCCCeEEEEEEEcCCCCCcceEecCchhhhh
Q 039386 326 TIVPLFEKILSASDAG--RIGRLVLPKACAEAYFPHISQSEGVPLRVQDVKGKEWVFQFRFWPNNNSRMYVLEGVTPCIQ 403 (582)
Q Consensus 326 ~~~~LF~KvLT~SDVg--~~gRLVIPK~~AEa~FP~Ld~~eGv~L~v~D~~Gk~W~FRf~yw~Nn~SR~YvLtGWs~FVr 403 (582)
.....|-++++.+-+. -.+++.|+++. -++|..-......+.+...... +-. .|.-
T Consensus 16 p~~i~~G~V~s~~PL~I~i~~~liL~~~~--L~i~~~l~~~~~~~~~~~~~~~----------------~~~----~i~~ 73 (100)
T PF10844_consen 16 PVDIVIGTVVSVPPLKIKIDQKLILDKDF--LIIPELLKDYTRDITIEHNSET----------------DNI----TITF 73 (100)
T ss_pred CceeEEEEEEecccEEEEECCeEEEchHH--EEeehhccceEEEEEEeccccc----------------cce----eEEE
Confidence 3334899999999744 23459998875 2344321111222333322110 000 0666
Q ss_pred ccCCccccccccccccccCceEEEEeeCCCCeEEEeEE
Q 039386 404 SMQLRAGDTSMIHSILTRDDKITFSRIDPGGKLVMGFR 441 (582)
Q Consensus 404 sK~LqAGD~i~iy~~~~~~~kVvFsR~~~~GkL~IG~R 441 (582)
...|++||. |...|.+.+.+|+|=-|
T Consensus 74 ~~~Lk~GD~------------V~ll~~~~gQ~yiVlDk 99 (100)
T PF10844_consen 74 TDGLKVGDK------------VLLLRVQGGQKYIVLDK 99 (100)
T ss_pred ecCCcCCCE------------EEEEEecCCCEEEEEEe
Confidence 778999999 88888764556666433
No 12
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=45.37 E-value=14 Score=27.48 Aligned_cols=37 Identities=24% Similarity=0.586 Sum_probs=27.4
Q ss_pred hhhchhhhhhcccccccccccCCCCCcccccccCCccccccccccc
Q 039386 31 ADLCYDCGSAYENFIFCNTFHLEEPGWRECNFCSKRLHCGCRASNS 76 (582)
Q Consensus 31 a~LC~~CgsayE~~~FCe~FH~~~sGWR~C~~C~KrlHcgCi~s~~ 76 (582)
...|+-|+..+-. ....|++ |..|+-.+|-+|.....
T Consensus 11 ~~~C~~C~~~i~~--------~~~~~~~-C~~C~~~~H~~C~~~v~ 47 (50)
T cd00029 11 PTFCDVCRKSIWG--------LFKQGLR-CSWCKVKCHKKCADKVP 47 (50)
T ss_pred CCChhhcchhhhc--------cccceeE-cCCCCCchhhhhhccCC
Confidence 4567777776532 2467777 99999999999988754
No 13
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=42.43 E-value=7.8 Score=45.07 Aligned_cols=59 Identities=20% Similarity=0.473 Sum_probs=39.7
Q ss_pred hhchhhhhhcccccccc---cccCCCCCc--ccccccCCcccccccccccc-ce--eecCCCcccccccCCC
Q 039386 32 DLCYDCGSAYENFIFCN---TFHLEEPGW--RECNFCSKRLHCGCRASNSF-LE--LLDYGGVGCRSCAMSP 95 (582)
Q Consensus 32 ~LC~~CgsayE~~~FCe---~FH~~~sGW--R~C~~C~KrlHcgCi~s~~~-f~--lLD~GGv~C~~C~~~~ 95 (582)
..|+-|++ +.||- .|-+..--= -.|..|.+|.||+|+...-. ++ -.| =+..|.+|.--+
T Consensus 137 ~~~~~c~s----~~~cPvc~~~Y~~~e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD-~~~~CS~CR~es 203 (694)
T KOG4443|consen 137 LQCAPCAS----LSYCPVCLIVYQDSESLPMVCCSICQRWSHGGCDGISDDKYMQAQVD-LQYKCSTCRGES 203 (694)
T ss_pred cccccccc----cccCchHHHhhhhccchhhHHHHHhcccccCCCCccchHHHHHHhhh-hhcccceeehhh
Confidence 46888888 45554 444433333 78999999999999987432 11 234 478899998554
No 14
>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=37.01 E-value=20 Score=27.67 Aligned_cols=26 Identities=35% Similarity=0.893 Sum_probs=18.9
Q ss_pred chhhhhhcccccccccccCCCCCcccccccCCc
Q 039386 34 CYDCGSAYENFIFCNTFHLEEPGWRECNFCSKR 66 (582)
Q Consensus 34 C~~CgsayE~~~FCe~FH~~~sGWR~C~~C~Kr 66 (582)
|.+||+. +.+.....+-..|..|++.
T Consensus 21 CP~Cg~~-------~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 21 CPHCGST-------KHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCe-------eeEEeCCCCeEECCCCCCc
Confidence 9999986 2333444788899999874
No 15
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=36.82 E-value=18 Score=42.08 Aligned_cols=36 Identities=17% Similarity=0.407 Sum_probs=20.5
Q ss_pred hhhchhhhhhcccccccccc-cCCCCCcccccccCCcc
Q 039386 31 ADLCYDCGSAYENFIFCNTF-HLEEPGWRECNFCSKRL 67 (582)
Q Consensus 31 a~LC~~CgsayE~~~FCe~F-H~~~sGWR~C~~C~Krl 67 (582)
|..|.+||..... .+|--. +....|++.|..||.++
T Consensus 15 akFC~~CG~~l~~-~~Cp~CG~~~~~~~~fC~~CG~~~ 51 (645)
T PRK14559 15 NRFCQKCGTSLTH-KPCPQCGTEVPVDEAHCPNCGAET 51 (645)
T ss_pred CccccccCCCCCC-CcCCCCCCCCCcccccccccCCcc
Confidence 4567777776653 234322 23456677777766654
No 16
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=35.41 E-value=22 Score=33.65 Aligned_cols=32 Identities=34% Similarity=0.752 Sum_probs=25.0
Q ss_pred CCCCCCCcccccCeeeccCCchhhchhhhhhccccc
Q 039386 10 KCRTANTHEWKKGWLLRSGVCADLCYDCGSAYENFI 45 (582)
Q Consensus 10 ~C~~~~~~~wrkGW~lrsG~~a~LC~~CgsayE~~~ 45 (582)
.|++..+..||+| -.| --.+|+.||..|-...
T Consensus 204 ~~~~~~t~~~r~~---~~g-~~~~cnacgl~~k~~~ 235 (340)
T KOG1601|consen 204 NCGTTKTPLWRRG---PEG-PKSLCNACGLRYKKGG 235 (340)
T ss_pred CCCCCCCcceecC---CCC-CccccccchhhhhhcC
Confidence 4688999999998 334 6688999888877765
No 17
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=33.79 E-value=32 Score=26.42 Aligned_cols=38 Identities=24% Similarity=0.607 Sum_probs=23.7
Q ss_pred chhhchhhhhhcccccccccccCCCCCcccccccCCccccccccccc
Q 039386 30 CADLCYDCGSAYENFIFCNTFHLEEPGWRECNFCSKRLHCGCRASNS 76 (582)
Q Consensus 30 ~a~LC~~CgsayE~~~FCe~FH~~~sGWR~C~~C~KrlHcgCi~s~~ 76 (582)
-...|+.|+... +-....|+ .|..|+-.+|-.|+....
T Consensus 10 ~~~~C~~C~~~i--------~g~~~~g~-~C~~C~~~~H~~C~~~~~ 47 (53)
T PF00130_consen 10 KPTYCDVCGKFI--------WGLGKQGY-RCSWCGLVCHKKCLSKVP 47 (53)
T ss_dssp STEB-TTSSSBE--------CSSSSCEE-EETTTT-EEETTGGCTSS
T ss_pred CCCCCcccCccc--------CCCCCCeE-EECCCCChHhhhhhhhcC
Confidence 345677776665 12233344 489999999999988754
No 18
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=33.09 E-value=11 Score=38.82 Aligned_cols=28 Identities=29% Similarity=0.537 Sum_probs=23.7
Q ss_pred cccccCCCCCcccccccCCccccccccc
Q 039386 47 CNTFHLEEPGWRECNFCSKRLHCGCRAS 74 (582)
Q Consensus 47 Ce~FH~~~sGWR~C~~C~KrlHcgCi~s 74 (582)
|...|.-.=-=+.|.+||-+.|||||+-
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 7788876665578999999999999985
No 19
>PF12773 DZR: Double zinc ribbon
Probab=32.36 E-value=28 Score=26.59 Aligned_cols=34 Identities=24% Similarity=0.589 Sum_probs=24.1
Q ss_pred hhhchhhhhhcc--c--cccccccc-CCCCCcccccccC
Q 039386 31 ADLCYDCGSAYE--N--FIFCNTFH-LEEPGWRECNFCS 64 (582)
Q Consensus 31 a~LC~~CgsayE--~--~~FCe~FH-~~~sGWR~C~~C~ 64 (582)
+..|..||.... . ..+|..-. ....+|+-|..||
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCccc
Confidence 778999998888 2 35665544 3566888888876
No 20
>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=28.22 E-value=77 Score=24.28 Aligned_cols=31 Identities=23% Similarity=0.351 Sum_probs=22.3
Q ss_pred hhhhhccCCccccccccccccccCceEEEEeeCCCCeEEEeEEe
Q 039386 399 TPCIQSMQLRAGDTSMIHSILTRDDKITFSRIDPGGKLVMGFRK 442 (582)
Q Consensus 399 s~FVrsK~LqAGD~i~iy~~~~~~~kVvFsR~~~~GkL~IG~RR 442 (582)
.+|.+..+|++||. |.|.-.+ +|+++|--.+
T Consensus 13 k~~~~~l~l~~Gd~------------v~i~~~~-~g~i~i~p~~ 43 (47)
T PF04014_consen 13 KEIREKLGLKPGDE------------VEIEVEG-DGKIVIRPVK 43 (47)
T ss_dssp HHHHHHTTSSTTTE------------EEEEEET-TSEEEEEEST
T ss_pred HHHHHHcCCCCCCE------------EEEEEeC-CCEEEEEECC
Confidence 36777889999999 7776653 5577775443
No 21
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=25.45 E-value=37 Score=33.62 Aligned_cols=34 Identities=26% Similarity=0.526 Sum_probs=25.1
Q ss_pred CCCCCc----ccccccCCccccccccccccceeecCCCccccccc
Q 039386 52 LEEPGW----RECNFCSKRLHCGCRASNSFLELLDYGGVGCRSCA 92 (582)
Q Consensus 52 ~~~sGW----R~C~~C~KrlHcgCi~s~~~f~lLD~GGv~C~~C~ 92 (582)
....|| ..|..||+.+. ..+-..-.||+-|..|.
T Consensus 140 L~~~G~~p~l~~C~~Cg~~~~-------~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 140 LAELGYGLDLDHCAVCGAPGD-------HRYFSPKEGGAVCSECG 177 (247)
T ss_pred HHHcCCccchhhHhcCCCCCC-------ceEEecccCCccccccc
Confidence 345566 58999999876 23334677999999997
No 22
>TIGR01643 YD_repeat_2x YD repeat (two copies). This model describes two tandem copies of a 21-residue extracellular repeat found in Gram-negative, Gram-positive, and animal proteins. The repeat is named for a YD dipeptide, the most strongly conserved motif of the repeat. These repeats appear in general to be involved in binding carbohydrate; the chicken teneurin-1 YD-repeat region has been shown to bind heparin.
Probab=25.04 E-value=96 Score=22.55 Aligned_cols=23 Identities=13% Similarity=0.154 Sum_probs=19.0
Q ss_pred CCCceEEEEECCCCeEEEEEEEc
Q 039386 363 SEGVPLRVQDVKGKEWVFQFRFW 385 (582)
Q Consensus 363 ~eGv~L~v~D~~Gk~W~FRf~yw 385 (582)
..|..+.+.|..|..|+|.|--.
T Consensus 3 ~~g~l~~~~~p~G~~~~~~YD~~ 25 (42)
T TIGR01643 3 AAGRLTGSTDADGTTTRYTYDAA 25 (42)
T ss_pred CCCCEEEEECCCCCEEEEEECCC
Confidence 35778899999999999997644
No 23
>PRK07757 acetyltransferase; Provisional
Probab=22.94 E-value=33 Score=30.53 Aligned_cols=19 Identities=26% Similarity=0.723 Sum_probs=14.7
Q ss_pred CCCcccccccCCccccccccc
Q 039386 54 EPGWRECNFCSKRLHCGCRAS 74 (582)
Q Consensus 54 ~sGWR~C~~C~KrlHcgCi~s 74 (582)
+.=|++|.-|++ ||.|-++
T Consensus 127 ~~~~~~~~~~~~--~~~~~~~ 145 (152)
T PRK07757 127 QKVWADCIKCPK--FPNCDEI 145 (152)
T ss_pred hhHHhcCccCCC--CCCcchh
Confidence 667999999999 5555554
No 24
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=21.57 E-value=1e+02 Score=27.22 Aligned_cols=41 Identities=27% Similarity=0.347 Sum_probs=23.5
Q ss_pred chhhhhccCCccccccccccccccCceEEEEeeCCCCeEEEeEEeCCCCCCCc
Q 039386 398 VTPCIQSMQLRAGDTSMIHSILTRDDKITFSRIDPGGKLVMGFRKAPIPGDMQ 450 (582)
Q Consensus 398 Ws~FVrsK~LqAGD~i~iy~~~~~~~kVvFsR~~~~GkL~IG~RRa~~~~~~~ 450 (582)
=.+|+++++|..||. |..+|...-=-.++++-+..++++++
T Consensus 41 N~~~i~~~~i~~Gd~------------V~V~raGdVIP~I~~vv~~~r~~~~~ 81 (82)
T PF03120_consen 41 NYDYIKELDIRIGDT------------VLVTRAGDVIPKIVGVVKEKRTGDEQ 81 (82)
T ss_dssp SHHHHHHTT-BBT-E------------EEEEEETTTEEEEEEE-GGG--SS-B
T ss_pred CHHHHHHcCCCCCCE------------EEEEECCCccceEeEeehhcCCCCCC
Confidence 358999999999999 88888631224455555555555443
Done!