RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5116
(422 letters)
>gnl|CDD|202398 pfam02791, DDT, DDT domain. This domain is approximately 60
residues in length, and is predicted to be a DNA binding
domain. The DDT domain is named after (DNA binding
homeobox and Different Transcription factors). It is
exclusively associated with nuclear domains, and is
thought to be arranged into three alpha helices.
Length = 61
Score = 71.1 bits (175), Expect = 7e-16
Identities = 19/58 (32%), Positives = 31/58 (53%)
Query: 185 VMQTLSIYEVLRHFKSLIRLSPFRFEDFCAVLNFEEQSNLLVEIHVSLLKTIFREEDT 242
L ++E L F ++ LSPF +DF L + LL E+H++LLK + +E+
Sbjct: 4 FGDLLMVWEFLNTFGEVLGLSPFTLDDFEEALLCTDSEELLGEVHIALLKLLVADEED 61
>gnl|CDD|214726 smart00571, DDT, domain in different transcription and chromosome
remodeling factors.
Length = 63
Score = 63.0 bits (154), Expect = 7e-13
Identities = 27/61 (44%), Positives = 36/61 (59%), Gaps = 2/61 (3%)
Query: 183 EYVMQTLSIYEVLRHFKSLIRLSPFR--FEDFCAVLNFEEQSNLLVEIHVSLLKTIFREE 240
E L +YE LR F ++ LSPFR EDF A L +Q+ LL E+HV LL+ I ++E
Sbjct: 2 EAFGDLLMVYEFLRSFGKVLGLSPFRATLEDFIAALKCRDQNGLLTEVHVVLLRAILKDE 61
Query: 241 D 241
Sbjct: 62 G 62
>gnl|CDD|201356 pfam00628, PHD, PHD-finger. PHD folds into an interleaved type of
Zn-finger chelating 2 Zn ions in a similar manner to
that of the RING and FYVE domains. Several PHD fingers
have been identified as binding modules of methylated
histone H3.
Length = 51
Score = 61.0 bits (148), Expect = 2e-12
Identities = 22/50 (44%), Positives = 28/50 (56%), Gaps = 5/50 (10%)
Query: 336 CRVCHRV---GELLCCETCPAVFHLECVDPPLRD--VPQEDWQCNLCKAH 380
C VC +V GELL C+ C FHL C+ PPL +P+ +W C CK
Sbjct: 2 CAVCGKVDDDGELLLCDGCDRWFHLACLGPPLEPEEIPEGEWYCPECKPK 51
>gnl|CDD|214584 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 RING finger and the FYVE finger. It is not yet known
if PHD fingers have a common molecular function. Several
reports suggest that it can function as a
protein-protein interacton domain and it was recently
demonstrated that the PHD finger of p300 can cooperate
with the adjacent BROMO domain in nucleosome binding in
vitro. Other reports suggesting that the PHD finger is a
ubiquitin ligase have been refuted as these domains were
RING fingers misidentified as PHD fingers.
Length = 47
Score = 52.6 bits (126), Expect = 2e-09
Identities = 18/46 (39%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 336 CRVCHRV---GELLCCETCPAVFHLECVDPPLRD-VPQEDWQCNLC 377
C VC + GELL C+ C +H C+ PPL + P W C C
Sbjct: 2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
>gnl|CDD|240069 cd04718, BAH_plant_2, BAH, or Bromo Adjacent Homology domain,
plant-specific sub-family with unknown function. BAH
domains are found in a variety of proteins playing roles
in transcriptional silencing and the remodeling of
chromatin. It is assumed that in most or all of these
instances the BAH domain mediates protein-protein
interactions.
Length = 148
Score = 44.9 bits (106), Expect = 9e-06
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 355 FHLECVDPPLRDVPQEDWQCNLCKAHKVTGVTDCLP 390
FHL C+ PPL++VP+ DW C C+ K +G +
Sbjct: 2 FHLCCLRPPLKEVPEGDWICPFCEVEK-SGQSAMPQ 36
>gnl|CDD|213034 cd11726, ADDz_ATRX, ADDz domain of ATRX (alpha-thalassemia/mental
retardation, X-linked). ADDz_ATRX is a PHD-like zinc
finger domain of ATRX, which belongs to the SNF2 family
of chromatin remodeling proteins. ATRX is a large
chromatin-associated nuclear protein with two domains,
ADDz_ATRX at the N-terminus, followed by a C-terminal
ATPase/helicase domain. The ADDz_ATRX domain recognizes
a specific methylated histone, and this interaction is
required for heterochromatin localization of the ATRX
protein. Missense mutations in either of the two ATRX
domains lead to the X-linked alpha-thalassemia and
mental retardation syndrome; however the mutations in
the ADDz_ATRX domain produce a more severe disease
phenotype that may also relate to disturbing unknown
functions or interaction sites of this domain. The ADDz
domain is also present in chromatin-associated proteins
cytosine-5-methyltransferase 3 (Dnmt3); it is a PHD-like
zinc finger motif that contains two parts, a C2-C2 and a
PHD-like zinc finger. PHD zinc finger domains have been
identified in more than 40 proteins that are mainly
involved in chromatin mediated transcriptional control;
the classical PHD zinc finger has a C4-H-C3 motif that
spans about 50-80 amino acids. In ADDz, the conserved
histidine residue of the PHD finger is replaced by a
cysteine, and an additional zinc finger C2-C2 like motif
is located about twenty residues upstream of the C4-C-C3
motif.
Length = 127
Score = 39.6 bits (93), Expect = 4e-04
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 6/52 (11%)
Query: 332 YDDHCRVCHRVGELLCCETCPAVFHLECV----DPP-LRDVPQED-WQCNLC 377
+++CR C GEL+CC++CP F +C+ L ++ ED W+C +C
Sbjct: 55 SEEYCRWCGEGGELICCDSCPNAFCKKCIKRNLGREELSEIEDEDKWKCFVC 106
>gnl|CDD|213032 cd11672, ADDz, ADDz for ATRX, Dnmt3 and Dnmt3l PHD-like zinc finger
domain. The ADDz zinc finger domain is present in the
chromatin-associated proteins
cytosine-5-methyltransferase 3 (Dnmt3) and ATRX, a SNF2
type transcription factor protein. The Dnmt3 family
includes two active DNA methyltransferases, Dnmt3a and
-3b, and one regulatory factor Dnmt3l. DNA methylation
is an important epigenetic mechanism involved in diverse
biological processes such as embryonic development, gene
expression, and genomic imprinting. The ADDz domain is a
PHD-like zinc finger motif that contains two parts, a
C2-C2 and a PHD-like zinc finger. PHD zinc finger
domains have been identified in more than 40 proteins
that are mainly involved in chromatin mediated
transcriptional control; the classical PHD zinc finger
has a C4-H-C3 motif that spans about 50-80 amino acids.
In ADDz, the conserved histidine residue of the PHD
finger is replaced by a cysteine, and an additional zinc
finger C2-C2 like motif is located about twenty residues
upstream of the C4-C-C3 motif.
Length = 120
Score = 36.9 bits (86), Expect = 0.004
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 8/62 (12%)
Query: 332 YDDHCRVCHRVGELLCC--ETCPAVFHLECVD-----PPLRDVPQED-WQCNLCKAHKVT 383
Y +C +C GE++ C E+C V+ C+D V ED W C LC
Sbjct: 46 YQSYCTICCGGGEVILCDNESCCRVYCTACLDFLVGPGTYDKVLDEDPWSCYLCLPESKQ 105
Query: 384 GV 385
G+
Sbjct: 106 GL 107
>gnl|CDD|213033 cd11725, ADDz_Dnmt3, ADDz domain of DNA (cytosine-5)
methyltransferases (C5-MTases) 3 (Dnmt3). Dnmt3 is a de
novo DNA methyltransferase family that includes two
active enzymes Dnmt3a and -3b and one regulatory factor
Dnmt3l. The ADDz domain of Dnmt3 is located in the
C-terminal region of Dnmt3, which is an active catalytic
domain in Dnmt3a and -b, but lacks some residues for
enzymatic activity in Dnmt3l. DNA methylation is an
important epigenetic mechanism involved in diverse
biological processes such as embryonic development, gene
expression, and genomic imprinting. The ADDz_Dnmt3
domain is a PHD-like zinc finger motif that contains two
parts, a C2-C2 and a PHD-like zinc finger. PHD zinc
finger domains have been identified in more than 40
proteins that are mainly involved in chromatin mediated
transcriptional control; the classical PHD zinc finger
has a C4-H-C3 motif that spans about 50-80 amino acids.
In ADDz, the conserved histidine residue of the PHD
finger is replaced by a cysteine, and an additional zinc
finger C2-C2 like motif is located about twenty residues
upstream of the C4-C-C3 motif.
Length = 126
Score = 33.8 bits (78), Expect = 0.050
Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 13/69 (18%)
Query: 330 FQYDD-----HCRVCHRVGELLCC--ETCPAVFHLECVD----PPLRD--VPQEDWQCNL 376
+ YD+ +C +C GE++ C E+C V+ C+D P D + ++ W C L
Sbjct: 39 YLYDNDGYQSYCTICCGGGEVILCDNESCCRVYCTACLDILVGPGTYDKVLLEDPWSCYL 98
Query: 377 CKAHKVTGV 385
C G+
Sbjct: 99 CLPESKQGL 107
>gnl|CDD|217476 pfam03286, Pox_Ag35, Pox virus Ag35 surface protein.
Length = 198
Score = 34.4 bits (79), Expect = 0.058
Identities = 20/87 (22%), Positives = 38/87 (43%), Gaps = 5/87 (5%)
Query: 51 SPQGSETSRRSTAKKGTKRKSNPPTRGGRGGNQKRKQTLETDYHYGSDFEDSTDHDDDLG 110
SP+ + R +T +K K + + + ++ E+D + E+ D++++ G
Sbjct: 47 SPKQPKKKRPTTPRKPATTKK--SKKKDKEKLTEEEKKPESDDDKTEENENDPDNNEESG 104
Query: 111 LSESET---EPEKDDPLDEMSDSDLSL 134
S+ D D+M DSDL L
Sbjct: 105 DSQESASANSLSDIDNEDDMDDSDLKL 131
>gnl|CDD|233041 TIGR00596, rad1, DNA repair protein (rad1). All proteins in this
family for which functions are known are components in a
multiprotein endonuclease complex (usually made up of
Rad1 and Rad10 homologs). This complex is used primarily
for nucleotide excision repair but also for some aspects
of recombinational repair in some species. Most Archaeal
species also have homologs of these genes, but the
function of these Archaeal genes is not known, so we
have set our cutoff to only pick up the eukaryotic
genes.This family is based on the phylogenomic analysis
of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA
metabolism, DNA replication, recombination, and repair].
Length = 814
Score = 34.4 bits (79), Expect = 0.11
Identities = 24/128 (18%), Positives = 44/128 (34%), Gaps = 10/128 (7%)
Query: 14 TPNTERPKFQVHLLKKPQYLQNLEA-RGLNSPITSRTSSPQGSETSRRSTAKKGTKRKSN 72
T N +R L K Y + E L + S+ + P+ + ++ T +K
Sbjct: 317 TSNKKRGSRAFLLNKLRWYRKWREETSKLAKEVQSQDTFPENASSNVNKTFRKEQVPTKR 376
Query: 73 PPTRGGRGGNQKRKQTLETDY--HYGSD--FEDSTDHDDDLGLSESETEP-----EKDDP 123
RGG ++ + T+ H+ D E+ D +D E E D
Sbjct: 377 RRVRGGSEVAVEKLRNANTNDMQHFEEDHELEEEGDDLEDGPAQEINAANDSKIFEIIDE 436
Query: 124 LDEMSDSD 131
+++
Sbjct: 437 ENDIDIYS 444
>gnl|CDD|224906 COG1995, PdxA, Pyridoxal phosphate biosynthesis protein [Coenzyme
metabolism].
Length = 332
Score = 34.2 bits (79), Expect = 0.13
Identities = 13/64 (20%), Positives = 25/64 (39%), Gaps = 14/64 (21%)
Query: 315 LITSPVREDLIHEGGFQYDDHCRV------CHRVGELLCCE---TCPAVFHLECVDPPLR 365
++T+P+ ++ +++ G Y H H +L H+ PL+
Sbjct: 117 IVTAPINKEALNDAGIPYPGHTEFLAELSGTHDPVMMLAVPELRVALVTTHI-----PLK 171
Query: 366 DVPQ 369
DVP
Sbjct: 172 DVPD 175
>gnl|CDD|233254 TIGR01059, gyrB, DNA gyrase, B subunit. This model describes the
common type II DNA topoisomerase (DNA gyrase). Two
apparently independently arising families, one in the
Proteobacteria and one in Gram-positive lineages, are
both designated toposisomerase IV. Proteins scoring
above the noise cutoff for this model and below the
trusted cutoff for topoisomerase IV models probably
should be designated GyrB [DNA metabolism, DNA
replication, recombination, and repair].
Length = 654
Score = 33.9 bits (78), Expect = 0.15
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 289 ILNTCEYPFTNIEKRLRVLQFLTDQILIT 317
I T E+ F + KRLR L FL + I+
Sbjct: 170 IFETTEFDFDILAKRLRELAFLNSGVKIS 198
>gnl|CDD|237860 PRK14939, gyrB, DNA gyrase subunit B; Provisional.
Length = 756
Score = 33.1 bits (77), Expect = 0.26
Identities = 20/65 (30%), Positives = 27/65 (41%), Gaps = 15/65 (23%)
Query: 277 ESDKT-----F--DEEVLNILNTCEYPFTNIEKRLRVLQFLTDQILIT-----SPVREDL 324
E+DKT F E I E+ + + KRLR L FL + I E+
Sbjct: 161 ETDKTGTEVRFWPSPE---IFENTEFDYDILAKRLRELAFLNSGVRIRLKDERDGKEEEF 217
Query: 325 IHEGG 329
+EGG
Sbjct: 218 HYEGG 222
>gnl|CDD|220102 pfam09073, BUD22, BUD22. BUD22 has been shown in yeast to be a
nuclear protein involved in bud-site selection. It plays
a role in positioning the proximal bud pole signal. More
recently it has been shown to be involved in ribosome
biogenesis.
Length = 424
Score = 32.5 bits (74), Expect = 0.47
Identities = 11/51 (21%), Positives = 22/51 (43%)
Query: 96 GSDFEDSTDHDDDLGLSESETEPEKDDPLDEMSDSDLSLSSFSTTSGTNKK 146
S E+ + + +E +E E D+ E+S+S S ++ + K
Sbjct: 213 DSSDEEEGEEAPSINYNEDTSESESDESDSEISESRSVSDSEESSPPSKKP 263
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 32.3 bits (74), Expect = 0.54
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 95 YGSDFEDSTDHDDDLGLSESETEPEKDDPLDEMSDSDL 132
G D ED D DDDL E + + ++ +E DSD
Sbjct: 328 DGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDD 365
>gnl|CDD|217937 pfam04166, PdxA, Pyridoxal phosphate biosynthetic protein PdxA. In
Escherichia coli the coenzyme pyridoxal 5'-phosphate is
synthesised de novo by a pathway that is thought to
involve the condensation of
4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose,
catalyzed by the enzymes PdxA and PdxJ, to form either
pyridoxine (vitamin B6) or pyridoxine 5'-phosphate.
Length = 299
Score = 30.8 bits (70), Expect = 1.2
Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 14/64 (21%)
Query: 315 LITSPVREDLIHEGGFQYDDHC-RVCHRVGE-----LLCCETCPAVF---HLECVDPPLR 365
++T P+ + + + GF Y H + R G +L H+ PL+
Sbjct: 93 IVTGPINKGALKDAGFPYSGHTEFLAERTGTHSVVMMLATGDLRVALVTTHI-----PLK 147
Query: 366 DVPQ 369
DVP
Sbjct: 148 DVPD 151
>gnl|CDD|188119 TIGR01206, lysW, lysine biosynthesis protein LysW. This very
small, poorly characterized protein has been shown
essential in Thermus thermophilus for an unusual pathway
of Lys biosynthesis from aspartate by way of
alpha-aminoadipate (AAA) rather than diaminopimelate. It
is found also in Deinococcus radiodurans and Pyrococcus
horikoshii, which appear to share the AAA pathway [Amino
acid biosynthesis, Aspartate family].
Length = 54
Score = 27.9 bits (62), Expect = 1.3
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 342 VGELLCCETCPAVFHLECVDPP-LRDVPQ--EDW 372
+GEL+ C+ C A + +DP L P+ EDW
Sbjct: 19 LGELVICDECGAELEVVSLDPLRLEQAPEEAEDW 52
>gnl|CDD|227862 COG5575, ORC2, Origin recognition complex, subunit 2 [DNA
replication, recombination, and repair].
Length = 535
Score = 30.4 bits (68), Expect = 1.8
Identities = 15/92 (16%), Positives = 32/92 (34%), Gaps = 2/92 (2%)
Query: 83 QKRKQTLETDYHYGSDFEDSTDHDDDLGLSESETEPEKDDPLDEMSDSDLSLSSFSTTSG 142
++R+ +E + H +F+D+ + L + E E P + D + + S
Sbjct: 84 KRRRGRIEIERHLLGEFDDNVGSNSLLDVPLYSLEAEPLSPSVMLEDESMEGINQSPQGI 143
Query: 143 TNKKFSYISRMSPEPLWLQTERQIQPLELPRS 174
+ +K S ++ E S
Sbjct: 144 SVEKLGKEDNRSRSSTPAS--PSLESHEFSES 173
>gnl|CDD|217738 pfam03801, Ndc80_HEC, HEC/Ndc80p family. Members of this family
are components of the mitotic spindle. It has been shown
that Ndc80/HEC from yeast is part of a complex called
the Ndc80p complex. This complex is thought to bind to
the microtubules of the spindle.
Length = 159
Score = 29.6 bits (67), Expect = 1.8
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 280 KTFDEEVLNILNTCEYPFTNIEKR 303
K +EEV +IL YP+ I K
Sbjct: 91 KKIEEEVPSILKDLGYPYLTITKS 114
>gnl|CDD|236504 PRK09418, PRK09418, bifunctional 2',3'-cyclic nucleotide
2'-phosphodiesterase/3'-nucleotidase precursor protein;
Reviewed.
Length = 780
Score = 30.4 bits (68), Expect = 1.8
Identities = 22/108 (20%), Positives = 40/108 (37%), Gaps = 5/108 (4%)
Query: 18 ERPKFQVHLLKKPQYLQNLEARGLNSPITSRTSSPQGSETSRRSTAKKGTKRK--SNPPT 75
E K+ + + KK + + G +P T T E +G + + PPT
Sbjct: 644 EFAKYAIDITKKND---DDKETGGENPTTPPTGEGDNGENPTTPPTGEGNNGENPTTPPT 700
Query: 76 RGGRGGNQKRKQTLETDYHYGSDFEDSTDHDDDLGLSESETEPEKDDP 123
G G + + + GS + + + + SE + E+D P
Sbjct: 701 GEGNNGGNPTTPSTDEGNNAGSGQTTTDNQNSKETTTVSENKEERDLP 748
>gnl|CDD|213036 cd11728, ADDz_Dnmt3b, ADDz domain of DNA (cytosine-5)
methyltransferases (C5-MTases) 3 b (Dnmt3b).
ADDz_Dnmt3b is an active catalytic domain of Dnmt3b.
Dnmt3b is a member of the Dnmt3 family and is a de novo
DNA methyltransferases that has an N-terminal variable
region followed by a conserved PWWP region and the
cysteine-rich ADDz domain. DNA methylation is an
important epigenetic mechanism involved in diverse
biological processes such as embryonic development, gene
expression, and genomic imprinting. The
methyltransferase activity of Dnmt3a is not only
responsible for the establishment of DNA methylation
pattern, but is also essential for the inheritance of
these patterns during mitosis. Dnmt3b is ubiquitously
expressed in most adult tissues. The ADDz_Dnmt3 domain
is a PHD-like zinc finger motif that contains two parts,
a C2-C2 and a PHD-like zinc finger. PHD zinc finger
domains have been identified in more than 40 proteins
that are mainly involved in chromatin mediated
transcriptional control; the classical PHD zinc finger
has a C4-H-C3 motif that spans about 50-80 amino acids.
In ADDz, the conserved histidine residue of the PHD
finger is replaced by a cysteine, and an additional zinc
finger C2-C2 like motif is located about twenty residues
upstream of the C4-C-C3 motif. A knockout of Dnmt3b has
been shown to be lethal in the mouse model.
Length = 150
Score = 29.4 bits (66), Expect = 2.0
Identities = 25/77 (32%), Positives = 33/77 (42%), Gaps = 13/77 (16%)
Query: 322 EDLIHEGGFQYDD-----HCRVCHRVGELLCCE--TCPAVFHLEC----VDPPLRDVP-- 368
+D E + YDD +C VC ELL C +C F +EC V P
Sbjct: 44 KDRFLELFYMYDDDGYQSYCTVCCEGRELLLCSNASCCRCFCVECLDVLVGPGTSANAKE 103
Query: 369 QEDWQCNLCKAHKVTGV 385
QE W C +C+ + GV
Sbjct: 104 QEPWSCYMCQPQRQYGV 120
>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 843
Score = 30.3 bits (69), Expect = 2.2
Identities = 22/109 (20%), Positives = 39/109 (35%), Gaps = 31/109 (28%)
Query: 240 EDTQQT---HFGPLDQKDSANSVLYFIDAMTWPEALRSYIE-----SDKTFDEEVLNILN 291
+DTQ+T H + + D + + +DA T R+ E + +L+
Sbjct: 238 KDTQKTFLPHIQIIQRYDLEDYM--VLDAAT----RRNL-ELFSNLRGNGKKGSLFWLLD 290
Query: 292 TC-------------EYPFTN---IEKRLRVLQFLTDQILITSPVREDL 324
P + IE+RL ++ L D + +RE L
Sbjct: 291 RTVTPMGSRLLKRWLLQPLLDKEEIEERLDAVEELKDNPELREKLREML 339
>gnl|CDD|233023 TIGR00557, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase.
This model represents PdxA, an NAD+-dependent
4-hydroxythreonine 4-phosphate dehydrogenase (EC
1.1.1.262) active in pyridoxal phosphate biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Pyridoxine].
Length = 320
Score = 29.8 bits (68), Expect = 2.4
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 16/65 (24%)
Query: 315 LITSPVREDLIHEGGFQYDDH-------CRVCHRVGELLCCE---TCPAVFHLECVDPPL 364
L+T+P+ + I++ GF + H V +L A H+ PL
Sbjct: 111 LVTAPIHKGAINQAGFPFPGHTEFLAELTG-VKDVVMMLAGPGLRVALATTHI-----PL 164
Query: 365 RDVPQ 369
+DVP
Sbjct: 165 KDVPA 169
>gnl|CDD|213035 cd11727, ADDz_Dnmt3l, ADDz domain of DNA (cytosine-5)
methyltransferases (C5-MTases) 3 like (Dnmt3l). Dnmt3l
is a regulator of DNA methylation, which acts by
recognizing unmethylated histone H3 tails and
interacting with Dnmt3a to stimulate its de novo DNA
methylation activity. The ADDz_Dnmt3l domain is located
in the C-terminal region of Dnmt3l that otherwise lacks
some residues required for DNA methyltransferase
activity. DNA methylation is an important epigenetic
mechanism involved in diverse biological processes such
as embryonic development, gene expression, and genomic
imprinting. Dnmt3l is also associating with HDAC1 and
acts as a transcriptional repressor. The ADDz_Dnmt3l
domain is a PHD-like zinc finger motif that contains two
parts, a C2-C2 and a PHD-like zinc finger. PHD zinc
finger domains have been identified in more than 40
proteins that are mainly involved in chromatin mediated
transcriptional control; the classical PHD zinc finger
has a C4-H-C3 motif that spans about 50-80 amino acids.
In ADDz, the conserved histidine residue of the PHD
finger is replaced by a cysteine, and an additional zinc
finger C2-C2 like motif is located about twenty residues
upstream of the C4-C-C3 motif.
Length = 149
Score = 29.0 bits (65), Expect = 2.8
Identities = 20/61 (32%), Positives = 24/61 (39%), Gaps = 13/61 (21%)
Query: 330 FQYDD-----HCRVCHRVGELLCCET--CPAVFHLECVD----PPLRDVPQ--EDWQCNL 376
F YDD +C +C LL CE C + ECVD P +W C L
Sbjct: 52 FLYDDDGYQSYCSICCSGETLLICENPDCTRCYCFECVDALVGPGTSGKVHAMSNWVCFL 111
Query: 377 C 377
C
Sbjct: 112 C 112
>gnl|CDD|202139 pfam02178, AT_hook, AT hook motif. At hooks are DNA binding
motifs with a preference for A/T rich regions.
Length = 13
Score = 26.0 bits (59), Expect = 3.6
Identities = 6/12 (50%), Positives = 8/12 (66%)
Query: 6 KRRGRPPKTPNT 17
++RGRP K P
Sbjct: 2 RKRGRPRKAPKD 13
>gnl|CDD|219734 pfam08164, TRAUB, Apoptosis-antagonizing transcription factor,
C-terminal. This C terminal domain is found in traube
proteins. This is the domain of the AATF proteins that
interacts with BLOS2 or Ceap, that functions as an
adaptor in processes such as protein and vesicle
processing and transport, and perhaps transcription.
Length = 80
Score = 27.6 bits (62), Expect = 3.6
Identities = 12/46 (26%), Positives = 17/46 (36%), Gaps = 4/46 (8%)
Query: 41 LNSPITSRTSSPQGSETSRRSTAKKGTKRKSNPPTRGGRGGNQKRK 86
L I ++SS K K+K N T+ +G RK
Sbjct: 5 LKELIERKSSSSSNGGAQWLELQKLQKKKKKNVDTKASKG----RK 46
>gnl|CDD|222892 PHA02586, 68, prohead core protein; Provisional.
Length = 140
Score = 28.5 bits (64), Expect = 3.7
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 55 SETSRRSTAKKGTK-RKSNPPTRGGRGGNQKRKQTL 89
S+ RR A+K K +++NP R +KRK+ L
Sbjct: 99 SKAKRRQIARKAAKTKRANP--SIQRKAQRKRKKAL 132
>gnl|CDD|163175 TIGR03178, allantoinase, allantoinase. This enzyme carries out the
first step in the degradation of allantoin, a
ring-opening hydrolysis. The seed members of this model
are all in the vicinity of other genes involved in the
processes of xanthine/urate/allantoin catabolism.
Although not included in the seed, many eukaryotic
homologs of this family are included above the trusted
cutoff. Below the noise cutoff are related
hydantoinases.
Length = 443
Score = 29.3 bits (66), Expect = 3.8
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 17/65 (26%)
Query: 348 CETCPAVFHL--ECVD---------PPLRDVPQED--WQCNLCKAHKVTGVTD---CLPD 391
ETCP L E V PP+RD+ ++ W+ L V+D C PD
Sbjct: 258 VETCPHYLTLTAEEVPDGGTLAKCAPPIRDLANQEGLWEA-LLNGLIDCVVSDHSPCTPD 316
Query: 392 VEKSG 396
++++G
Sbjct: 317 LKRAG 321
>gnl|CDD|197691 smart00384, AT_hook, DNA binding domain with preference for A/T
rich regions. Small DNA-binding motif first described
in the high mobility group non-histone chromosomal
protein HMG-I(Y).
Length = 13
Score = 25.7 bits (58), Expect = 3.9
Identities = 6/11 (54%), Positives = 8/11 (72%)
Query: 6 KRRGRPPKTPN 16
++RGRP K P
Sbjct: 2 RKRGRPRKAPK 12
>gnl|CDD|235542 PRK05644, gyrB, DNA gyrase subunit B; Validated.
Length = 638
Score = 29.3 bits (67), Expect = 4.6
Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 7/48 (14%)
Query: 289 ILNTCEYPFTNIEKRLRVLQFLTDQILIT-------SPVREDLIHEGG 329
I T E+ + + RLR L FL + IT E +EGG
Sbjct: 177 IFETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEEKEETFHYEGG 224
>gnl|CDD|117316 pfam08746, zf-RING-like, RING-like domain. This is a zinc finger
domain that is related to the C3HC4 RING finger domain
(pfam00097).
Length = 43
Score = 26.2 bits (58), Expect = 4.9
Identities = 8/29 (27%), Positives = 14/29 (48%), Gaps = 3/29 (10%)
Query: 336 CRVCHRVG-ELLCCET--CPAVFHLECVD 361
C VCH + + C C +H++C+
Sbjct: 1 CEVCHEIVTQGQRCGNRDCNIRWHVDCLA 29
>gnl|CDD|222918 PHA02687, PHA02687, ORF061 late transcription factor VLTF-4;
Provisional.
Length = 231
Score = 28.4 bits (63), Expect = 5.6
Identities = 26/92 (28%), Positives = 38/92 (41%), Gaps = 9/92 (9%)
Query: 52 PQGSETSRRSTAKKGTKRKSNPPTRGGRGGNQKRKQTLETDYHYGS-DFEDSTDHDDDLG 110
P +T +R T KK K + +K + D + + +++ G
Sbjct: 80 PAPVKTPKRRTKKKAKADKPEKSPKAV----EKLCPPDDRDDKNEEKEPTEEAQRNEESG 135
Query: 111 LSE---SETEPEKDDPLDEMSDSDLSLSSFST 139
+E S P DD LDEM DSDL L +FS
Sbjct: 136 DAEGGASGRSPSDDDNLDEMDDSDLML-AFSA 166
>gnl|CDD|180536 PRK06347, PRK06347, autolysin; Reviewed.
Length = 592
Score = 28.9 bits (64), Expect = 5.8
Identities = 8/49 (16%), Positives = 16/49 (32%)
Query: 43 SPITSRTSSPQGSETSRRSTAKKGTKRKSNPPTRGGRGGNQKRKQTLET 91
+ T++P+ + + TK ++ P Q K E
Sbjct: 70 TKEAPATATPENTTEPTVEPKQTETKEQTKTPEEKQPAAKQVEKAPAEP 118
>gnl|CDD|222406 pfam13831, PHD_2, PHD-finger. PHD folds into an interleaved type
of Zn-finger chelating 2 Zn ions in a similar manner to
that of the RING and FYVE domains. Several PHD fingers
have been identified as binding modules of methylated
histone H3.
Length = 33
Score = 25.7 bits (57), Expect = 6.0
Identities = 9/35 (25%), Positives = 12/35 (34%), Gaps = 2/35 (5%)
Query: 343 GELLCCETCPAVFHLECVDPPLRDVPQEDWQCNLC 377
LL C C H C + ++ W C C
Sbjct: 1 NPLLVCSKCSVAVHASCY--GVPELSDGPWLCRRC 33
>gnl|CDD|227931 COG5644, COG5644, Uncharacterized conserved protein [Function
unknown].
Length = 869
Score = 28.9 bits (64), Expect = 6.5
Identities = 16/36 (44%), Positives = 18/36 (50%)
Query: 97 SDFEDSTDHDDDLGLSESETEPEKDDPLDEMSDSDL 132
SD S D + + SESE E D DE SDS L
Sbjct: 156 SDASSSNDSESEESDSESEIESSDSDHDDENSDSKL 191
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 28.6 bits (64), Expect = 7.0
Identities = 17/53 (32%), Positives = 23/53 (43%)
Query: 336 CRVCHRVGELLCCETCPAVFHLECVDPPLRDVPQEDWQCNLCKAHKVTGVTDC 388
C VC R GE +C ET + LEC LR V + K ++ +C
Sbjct: 31 CVVCGRYGEYICDETDDDICSLECKQALLRRVAKSRVAVGAPKPKRLPATDEC 83
>gnl|CDD|234368 TIGR03835, termin_org_DnaJ, terminal organelle assembly protein
TopJ. This model describes TopJ (MG_200, CbpA), a DnaJ
homolog and probable assembly protein of the Mycoplasma
terminal organelle. The terminal organelle is involved
in both cytadherence and gliding motility [Cellular
processes, Chemotaxis and motility].
Length = 871
Score = 28.6 bits (63), Expect = 8.9
Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 2/67 (2%)
Query: 106 DDDLGLSESETEPEKDDPLDEMSDSDLSLSSFSTTSGTNKKFSYISRMSPEPLWLQTERQ 165
+D + E EP+ D D + +SS T + PEP+ +T +
Sbjct: 230 EDGNWVWTRELEPQDDSEDDYVIPDAEIISS--PTLEVTAPKEVEQPLQPEPVDEETVAE 287
Query: 166 IQPLELP 172
+ E P
Sbjct: 288 TKAEEEP 294
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.136 0.411
Gapped
Lambda K H
0.267 0.0762 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,299,865
Number of extensions: 2012835
Number of successful extensions: 1745
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1733
Number of HSP's successfully gapped: 62
Length of query: 422
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 323
Effective length of database: 6,546,556
Effective search space: 2114537588
Effective search space used: 2114537588
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.8 bits)