RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12304
(620 letters)
>gnl|CDD|238192 cd00315, Cyt_C5_DNA_methylase, Cytosine-C5 specific DNA methylases;
Methyl transfer reactions play an important role in many
aspects of biology. Cytosine-specific DNA methylases are
found both in prokaryotes and eukaryotes. DNA
methylation, or the covalent addition of a methyl group
to cytosine within the context of the CpG dinucleotide,
has profound effects on the mammalian genome. These
effects include transcriptional repression via
inhibition of transcription factor binding or the
recruitment of methyl-binding proteins and their
associated chromatin remodeling factors, X chromosome
inactivation, imprinting and the suppression of
parasitic DNA sequences. DNA methylation is also
essential for proper embryonic development and is an
important player in both DNA repair and genome
stability.
Length = 275
Score = 128 bits (324), Expect = 2e-33
Identities = 56/198 (28%), Positives = 90/198 (45%), Gaps = 27/198 (13%)
Query: 118 LKCLDLFSGCGGLMEGLCQAGVAKPCWSVELERSEAASYDANFQECSVIQDDCNLVLKSL 177
L+ +DLF+G GG GL +AG + + E+++S A +Y+ANF + D + K
Sbjct: 1 LRVIDLFAGIGGFRLGLEKAG-FEIVAANEIDKSAAETYEANFPNKLIEGDITKIDEKDF 59
Query: 178 LKGHTQHKGVSLPQKHEVDLIVAGPPCQGFSQ--LNRARELEKSKLKNGLVFTFLSFCDL 235
++DL+ G PCQ FS + E + L F +
Sbjct: 60 --------------IPDIDLLTGGFPCQPFSIAGKRKGFEDTRGTL-------FFEIIRI 98
Query: 236 ---FQPKYIILENVTGLVHFNKNEILQCIFHCLLKMNYQVTFDVLQSGNYGVAQSRNRVV 292
+PKY +LENV GL+ + L+ I + L ++ Y V + +L + +YGV Q+R RV
Sbjct: 99 LKEKKPKYFLLENVKGLLTHDNGNTLKVILNTLEELGYNVYWKLLNASDYGVPQNRERVF 158
Query: 293 ILASKPGYKLPSFPQPLH 310
I+ + L F
Sbjct: 159 IIGIRKDLILNFFSPFPK 176
Score = 81.1 bits (201), Expect = 6e-17
Identities = 31/89 (34%), Positives = 41/89 (46%), Gaps = 7/89 (7%)
Query: 517 VLGRLAWDESFDTIVTTPNPLNKQ------GKILHPEQDRVLTVREYARAQGFPDSYVFR 570
+L DE T+ + I R LT RE AR QGFPD + F
Sbjct: 187 ILRIRDPDEPSPTLTASYGKGTGSVHPTAPDMIGKESNIRRLTPRECARLQGFPDDFEFP 246
Query: 571 GG-ICDMYKQIGNAVPPPLAKAIGYEIIK 598
G + Y+QIGN+VP P+A+AI I +
Sbjct: 247 GKSVTQAYRQIGNSVPVPVAEAIAKAIKE 275
>gnl|CDD|215747 pfam00145, DNA_methylase, C-5 cytosine-specific DNA methylase.
Length = 320
Score = 128 bits (325), Expect = 5e-33
Identities = 59/205 (28%), Positives = 89/205 (43%), Gaps = 35/205 (17%)
Query: 118 LKCLDLFSGCGGLMEGLCQAGVAKPCWSVELERSEAASYDANFQECSVIQDDCNLVLKSL 177
K +DLF+G GG GL QAG + + E+++S A +Y+ANF V D L+
Sbjct: 1 FKFIDLFAGIGGFRLGLEQAGF-ECVAANEIDKSAAKTYEANF--PKVPIGDITLIDIKD 57
Query: 178 LKGHTQHKGVSLPQKHEVDLIVAGPPCQGFSQ--LNRARELEKSKLKNGLVFTFLSFCDL 235
+ D++ G PCQ FS + E + L F +
Sbjct: 58 IPDI--------------DILTGGFPCQDFSIAGKQKGFEDTRGTL-------FFEIIRI 96
Query: 236 ---FQPKYIILENVTGLVHFNKNEILQCIFHCLLKMNYQVTFDVLQSGNYGVAQSRNRVV 292
+PK +LENV GL+ + L I L ++ Y V++ VL + +YGV Q+R RV
Sbjct: 97 IKEKKPKAFLLENVKGLLSHDNGNTLNVILETLEELGYSVSWKVLNASDYGVPQNRERVF 156
Query: 293 ILASKPGY------KLPSFPQPLHA 311
I+ + FP+P A
Sbjct: 157 IVGIRNDLILNFPVPEFDFPKPSTA 181
Score = 93.9 bits (234), Expect = 5e-21
Identities = 33/69 (47%), Positives = 40/69 (57%)
Query: 530 IVTTPNPLNKQGKILHPEQDRVLTVREYARAQGFPDSYVFRGGICDMYKQIGNAVPPPLA 589
L K G+ P+ R LT RE AR QGFPD ++F G +YKQIGNAVP P+A
Sbjct: 252 EAPKTGILGKNGERFRPKNIRRLTPRECARLQGFPDDFIFPGSKTQLYKQIGNAVPVPVA 311
Query: 590 KAIGYEIIK 598
+AI I K
Sbjct: 312 EAIAKAIKK 320
>gnl|CDD|223348 COG0270, Dcm, Site-specific DNA methylase [DNA replication,
recombination, and repair].
Length = 328
Score = 122 bits (307), Expect = 2e-30
Identities = 57/190 (30%), Positives = 93/190 (48%), Gaps = 16/190 (8%)
Query: 117 PLKCLDLFSGCGGLMEGLCQAGVAKPCWSVELERSEAASYDANFQECSVIQDDCNLVLKS 176
+K +DLF+G GGL G +AG + ++ E++ A+Y ANF +I D +
Sbjct: 3 KMKVIDLFAGIGGLSLGFEEAG-FEIVFANEIDPPAVATYKANFPHGDIILGDIKELDGE 61
Query: 177 LLKGHTQHKGVSLPQKHEVDLIVAGPPCQGFSQLNRARELEKSKLKNGLVFTFLSFCDLF 236
L +K +VD+++ GPPCQ FS + R + + L F+ +
Sbjct: 62 AL------------RKSDVDVLIGGPPCQDFSIAGKRRGYDDP--RGSLFLEFIRLIEQL 107
Query: 237 QPKYIILENVTGLVHFNKNEILQCIFHCLLKMNYQVTFDVLQSGNYGVAQSRNRVVILAS 296
+PK+ +LENV GL+ +K + I L ++ Y V F++L + +YGV QSR RV I+
Sbjct: 108 RPKFFVLENVKGLLS-SKGQTFDEIKKELEELGYGVEFNILNAADYGVPQSRERVFIVGF 166
Query: 297 KPGYKLPSFP 306
+
Sbjct: 167 RRDNIDLDPN 176
Score = 91.7 bits (228), Expect = 4e-20
Identities = 40/89 (44%), Positives = 50/89 (56%), Gaps = 5/89 (5%)
Query: 516 GVLGRLAWDESFDTIVTTPNPLNKQGKILHPEQDRVLTVREYARAQGFPDSYVFRGGICD 575
G RL D+ T+ N +HP +DR LTVRE AR QGFPD +VF G D
Sbjct: 245 GSYIRLHPDKPAPTVRGGGNERF-----IHPLEDRELTVREAARLQGFPDDFVFPGSKTD 299
Query: 576 MYKQIGNAVPPPLAKAIGYEIIKCIGNAV 604
Y+QIGN+VPP LA+AI I+K +
Sbjct: 300 QYRQIGNSVPPLLAEAIAKAILKKLNEKN 328
>gnl|CDD|233085 TIGR00675, dcm, DNA-methyltransferase (dcm). All proteins in this
family for which functions are known are DNA-cytosine
methyltransferases. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 315
Score = 100 bits (251), Expect = 3e-23
Identities = 55/190 (28%), Positives = 93/190 (48%), Gaps = 20/190 (10%)
Query: 122 DLFSGCGGLMEGLCQAGVAKPCWSVELERSEAASYDANFQECSVIQDDCNLVLKSLLKGH 181
DLF+G GG+ G QAG K ++ E+++ +Y+ANF V D + S
Sbjct: 3 DLFAGIGGIRLGFEQAGF-KCVFASEIDKYAQKTYEANFGN-KVPFGDITKISPS----- 55
Query: 182 TQHKGVSLPQKHEVDLIVAGPPCQGFSQLNRARELEKSKLKNGLVFTFLSFCDLFQPKYI 241
+P + D+++ G PCQ FS + + E ++ L F + +PK+
Sbjct: 56 ------DIP---DFDILLGGFPCQPFSIAGKRKGFEDTR--GTLFFEIVRILKEKKPKFF 104
Query: 242 ILENVTGLVHFNKNEILQCIFHCLLKMNYQVTFDVLQSGNYGVAQSRNRVVILASKP--G 299
+LENV GLV +K + I L ++ Y+V + VL + ++GV Q+R R+ I+ +
Sbjct: 105 LLENVKGLVSHDKGRTFKVIIETLEELGYKVYYKVLNAKDFGVPQNRERIYIVGFRDFDD 164
Query: 300 YKLPSFPQPL 309
FP+P+
Sbjct: 165 KLNFEFPKPI 174
Score = 75.8 bits (187), Expect = 5e-15
Identities = 27/89 (30%), Positives = 39/89 (43%), Gaps = 1/89 (1%)
Query: 509 SRNNNWQGVLGRLAWDESFDTIVTTPNPLNKQGKIL-HPEQDRVLTVREYARAQGFPDSY 567
+ ++ L+ + + HP + R LT RE AR QGFPD +
Sbjct: 227 YNRESKSSIIRTLSARGYTFVKGGKSVLIVPHKSTVVHPGRIRRLTPRECARLQGFPDDF 286
Query: 568 VFRGGICDMYKQIGNAVPPPLAKAIGYEI 596
F +YKQ GNAV P+ +AI +I
Sbjct: 287 KFPVSDSQLYKQAGNAVVVPVIEAIAKQI 315
>gnl|CDD|214664 smart00439, BAH, Bromo adjacent homology domain.
Length = 121
Score = 41.1 bits (97), Expect = 2e-04
Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 2/66 (3%)
Query: 2 KAHVQWLVRPNDTILGDKIQFDNSTLFLTNACESIDLSVIKKTVCVDFVT--NDSSEEEI 59
V+W RP +T+L FD + +FL++ +++ LS I V + + E
Sbjct: 38 MVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGKCNVLYKSDYPGLRPEGS 97
Query: 60 LDNEHE 65
+
Sbjct: 98 IGEPDV 103
>gnl|CDD|216495 pfam01426, BAH, BAH domain. This domain has been called BAH (Bromo
adjacent homology) domain and has also been called ELM1
and BAM (Bromo adjacent motif) domain. The function of
this domain is unknown but may be involved in
protein-protein interaction.
Length = 120
Score = 39.2 bits (92), Expect = 7e-04
Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 5/88 (5%)
Query: 1 MKAHVQWLVRPNDTILGDKIQFDNSTLFLTNACESIDLSVIKKTVCVDFVTNDSSEEEIL 60
HV+W RP +T+ F+ +FL++ C+ + L I V S+ E L
Sbjct: 36 KMVHVRWFYRPEETVHRLGRAFNKDEVFLSDECDDVPLEDIIGKCNVIIK----SDPESL 91
Query: 61 DNEHEEKDETIYT-EYYRKTKDKHFVQP 87
+ ++ E + F +
Sbjct: 92 QPRKINGEPDVFFCELLYDPERGSFKKL 119
>gnl|CDD|239835 cd04370, BAH, BAH, or Bromo Adjacent Homology domain (also called
ELM1 and BAM for Bromo Adjacent Motif). BAH domains have
first been described as domains found in the polybromo
protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure
of Chromatin). They also occur in mammalian DNA
methyltransferases and the MTA1 subunits of histone
deacetylase complexes. A BAH domain is also found in
Yeast Sir3p and in the origin receptor complex protein 1
(Orc1p), where it was found to interact with the
N-terminal lobe of the silence information regulator 1
protein (Sir1p), confirming the initial hypothesis that
BAH plays a role in protein-protein interactions.
Length = 123
Score = 38.9 bits (91), Expect = 0.001
Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 3/75 (4%)
Query: 1 MKAHVQWLVRPNDTILGDKIQFDNSTLFLTNACESIDLSVIKKTVCVDFVTNDSSEEEIL 60
+ V+W RP +T G LFL++ + I + I V FV S E +
Sbjct: 39 KQVKVRWFYRPEETPKGLSPFALRRELFLSDHLDEIPVESIIGKCKVLFV---SEFEGLK 95
Query: 61 DNEHEEKDETIYTEY 75
++ + +
Sbjct: 96 QRPNKIDTDDFFCRL 110
>gnl|CDD|240063 cd04712, BAH_DCM_I, BAH, or Bromo Adjacent Homology domain, as
present in DNA (Cytosine-5)-methyltransferases (DCM) 1.
DNA methylation, or the covalent addition of a methyl
group to cytosine within the context of the CpG
dinucleotide, has profound effects on the genome. These
effects include transcriptional repression via
inhibition of transcription factor binding, the
recruitment of methyl-binding proteins and their
associated chromatin remodeling factors, X chromosome
inactivation, imprinting, and the suppression of
parasitic DNA sequences. DNA methylation is also
essential for proper embryonic development and is an
important player in both DNA repair and genome
stability. 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 = 130
Score = 38.9 bits (91), Expect = 0.001
Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 19/80 (23%)
Query: 4 HVQWLVRPNDTILGDKIQFDNSTLFLTNACESIDL----SVIKKTVCVDFVTNDSSEEEI 59
H +WL R DT+LG + LFLTN C ++L + IK VD+
Sbjct: 52 HGRWLYRGCDTVLG--NYANERELFLTNECTCLELDLLSTEIKGVHKVDW---------- 99
Query: 60 LDNEHEEKDETIYTEYYRKT 79
+ + + R++
Sbjct: 100 ---SGTPWGKGLPEFFVRQS 116
>gnl|CDD|236696 PRK10458, PRK10458, DNA cytosine methylase; Provisional.
Length = 467
Score = 37.4 bits (87), Expect = 0.022
Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 10/62 (16%)
Query: 535 NPLNKQGKILHPEQDRVLTVREYARAQGF--PDSYVFRGGICDM--YKQIGNAVPPPLAK 590
+P N+Q + R LT RE AR GF P FR + D Y+Q GN+V P+
Sbjct: 393 DPENQQ------HRPRRLTPRECARLMGFEAPGEAKFRIPVSDTQAYRQFGNSVVVPVFA 446
Query: 591 AI 592
A+
Sbjct: 447 AV 448
Score = 31.6 bits (72), Expect = 1.2
Identities = 45/167 (26%), Positives = 69/167 (41%), Gaps = 19/167 (11%)
Query: 121 LDLFSGCGGLMEGLCQAG---VAKPCWSVELERSEAASYDANFQECSVIQD--DCNLVLK 175
+DLF+G GG+ G G V W+ R+ A++ + +D D L K
Sbjct: 92 IDLFAGIGGIRRGFEAIGGQCVFTSEWNKHAVRTYKANWYCDPATHRFNEDIRDITLSHK 151
Query: 176 SLLKGHT--QHKGVSLPQKHEVDLIVAGPPCQGFS--------QLNRARELEKSKLKNGL 225
+ +H +P H D+++AG PCQ FS L RA E + + L
Sbjct: 152 EGVSDEEAAEHIRQHIPD-H--DVLLAGFPCQPFSLAGVSKKNSLGRAHGFE-CETQGTL 207
Query: 226 VFTFLSFCDLFQPKYIILENVTGLVHFNKNEILQCIFHCLLKMNYQV 272
F D +P +LENV L +K + + I L ++ Y V
Sbjct: 208 FFDVARIIDAKRPAIFVLENVKNLKSHDKGKTFRIIMQTLDELGYDV 254
>gnl|CDD|240107 cd04760, BAH_Dnmt1_I, BAH, or Bromo Adjacent Homology domain, first
copy present in DNA (Cytosine-5)-methyltransferases from
Bilateria, Dnmt1 and similar proteins. DNA methylation,
or the covalent addition of a methyl group to cytosine
within the context of the CpG dinucleotide, has profound
effects on the genome. These effects include
transcriptional repression via inhibition of
transcription factor binding, the recruitment of
methyl-binding proteins and their associated chromatin
remodeling factors, X chromosome inactivation,
imprinting, and the suppression of parasitic DNA
sequences. DNA methylation is also essential for proper
embryonic development and is an important player in both
DNA repair and genome stability. 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 = 124
Score = 34.7 bits (80), Expect = 0.031
Identities = 27/83 (32%), Positives = 39/83 (46%), Gaps = 4/83 (4%)
Query: 4 HVQWLVRPNDTILGDKIQFDNSTLFLTNACESIDLSVIKKTVCVDFVTN--DSSEEEILD 61
H W R +DT+LG+ D LFL + CE + LS I V V + + S E +D
Sbjct: 40 HAHWFCRGSDTVLGET--SDPLELFLVDECEDMALSSIHGKVNVIYKAPSENWSMEGGMD 97
Query: 62 NEHEEKDETIYTEYYRKTKDKHF 84
E E ++ T +Y+K D
Sbjct: 98 EEDEIFEDDGKTFFYQKWYDPEC 120
>gnl|CDD|188022 TIGR00095, TIGR00095, RNA methyltransferase, RsmD family. This
model represents a family of uncharacterized bacterial
proteins. Members are present in nearly every complete
bacterial genome, always in a single copy. PSI-BLAST
analysis shows homology to several families of
SAM-dependent methyltransferases, including ribosomal
RNA adenine dimethylases [Protein synthesis, tRNA and
rRNA base modification].
Length = 190
Score = 33.5 bits (77), Expect = 0.16
Identities = 22/79 (27%), Positives = 31/79 (39%), Gaps = 9/79 (11%)
Query: 118 LKCLDLFSGCGGL-MEGLCQAGVAKPCWSVELERSEAASYDANFQ------ECSVIQDDC 170
LDLF+G G L +E L + A VE +R A + N E + + +D
Sbjct: 52 AHFLDLFAGSGALGLEALSRG--AASAVFVEQDRKVAQTLKENLSTLKKSGEQATVLNDA 109
Query: 171 NLVLKSLLKGHTQHKGVSL 189
L L K T + L
Sbjct: 110 VRALLFLAKKQTPFDIIYL 128
>gnl|CDD|100107 cd02440, AdoMet_MTases, S-adenosylmethionine-dependent
methyltransferases (SAM or AdoMet-MTase), class I;
AdoMet-MTases are enzymes that use
S-adenosyl-L-methionine (SAM or AdoMet) as a substrate
for methyltransfer, creating the product
S-adenosyl-L-homocysteine (AdoHcy). There are at least
five structurally distinct families of AdoMet-MTases,
class I being the largest and most diverse. Within this
class enzymes can be classified by different substrate
specificities (small molecules, lipids, nucleic acids,
etc.) and different target atoms for methylation
(nitrogen, oxygen, carbon, sulfur, etc.).
Length = 107
Score = 31.6 bits (72), Expect = 0.31
Identities = 28/123 (22%), Positives = 44/123 (35%), Gaps = 25/123 (20%)
Query: 119 KCLDLFSGCGGLMEGLCQAGVAKPCWSVE-----LERSEAASYDANFQECSVIQDDCNLV 173
+ LDL G G L L +G V+ LE + A+ V++ D +
Sbjct: 1 RVLDLGCGTGALALAL-ASGPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEEL 59
Query: 174 LKSLLKGHTQHKGVSLPQKHEVDLIVAGPPCQGFSQLNRARELEKSK--LKNG--LVFTF 229
D+I++ PP + AR LE+++ LK G LV T
Sbjct: 60 P--------------PEADESFDVIISDPPLH-HLVEDLARFLEEARRLLKPGGVLVLTL 104
Query: 230 LSF 232
+
Sbjct: 105 VLA 107
>gnl|CDD|237019 PRK11907, PRK11907, bifunctional 2',3'-cyclic nucleotide
2'-phosphodiesterase/3'-nucleotidase precursor protein;
Reviewed.
Length = 814
Score = 33.3 bits (76), Expect = 0.41
Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 11/70 (15%)
Query: 488 ESFDMT-GQKNTIIPWS-----LVHTASRNNNWQGVLGRLAWDESFDTIVTTPNPLNKQG 541
E +M+ GQ N I P S LV+T R N+ V+ + + FD +T PN ++ G
Sbjct: 546 EWLEMSAGQFNQIDPNSKEPQNLVNTDYRTYNFD-VIDGVTYK--FD--ITQPNKYDRDG 600
Query: 542 KILHPEQDRV 551
K+++P RV
Sbjct: 601 KLVNPTASRV 610
>gnl|CDD|200467 cd11328, AmyAc_maltase, Alpha amylase catalytic domain found in
maltase (also known as alpha glucosidase) and related
proteins. Maltase (EC 3.2.1.20) hydrolyzes the
terminal, non-reducing (1->4)-linked alpha-D-glucose
residues in maltose, releasing alpha-D-glucose. In most
cases, maltase is equivalent to alpha-glucosidase, but
the term "maltase" emphasizes the disaccharide nature of
the substrate from which glucose is cleaved, and the
term "alpha-glucosidase" emphasizes the bond, whether
the substrate is a disaccharide or polysaccharide. The
Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 470
Score = 33.0 bits (76), Expect = 0.55
Identities = 21/69 (30%), Positives = 28/69 (40%), Gaps = 20/69 (28%)
Query: 13 DTILGDKIQFDNSTLFLTNACESIDLSVIKKTVCVDFVTNDSSEEEILDNEHE-----EK 67
D I G F+ L + + L VI +DFV N SS +EHE K
Sbjct: 71 DPIFGTMEDFEE----LIAEAKKLGLKVI-----LDFVPNHSS------DEHEWFQKSVK 115
Query: 68 DETIYTEYY 76
+ Y +YY
Sbjct: 116 RDEPYKDYY 124
>gnl|CDD|222295 pfam13659, Methyltransf_26, Methyltransferase domain. This family
contains methyltransferase domains.
Length = 117
Score = 29.7 bits (67), Expect = 1.9
Identities = 16/87 (18%), Positives = 29/87 (33%), Gaps = 8/87 (9%)
Query: 117 PLKCLDLFSGCGGLMEGLCQAGVAKPCWSVELERSEAASYDANFQECSVIQDDCNLVLKS 176
+ LD +G G + +AG VEL+ AA + + +V+
Sbjct: 1 GDRVLDPGAGSGAFLLAAARAGPDARVVGVELDPEAAALARRRLAL-AGLAPRVRVVVGD 59
Query: 177 LLKGHTQHKGVSLPQKHEVDLIVAGPP 203
+ + DL++ PP
Sbjct: 60 ARE-------LLELPDGSFDLVLGNPP 79
>gnl|CDD|225285 COG2429, COG2429, Archaeal GTP cyclohydrolase III [Nucleotide
transport and metabolism].
Length = 250
Score = 30.1 bits (68), Expect = 3.1
Identities = 18/79 (22%), Positives = 27/79 (34%), Gaps = 7/79 (8%)
Query: 280 GNYGVAQSRNRVVILASKPGYKLPSFPQPLHAFSNQLFTINGNLVANKTSHAPYRSIT-V 338
G AQ NR +L K + Q H F +N +PY + T +
Sbjct: 106 QEAGSAQDENRQEVLEIKREEGTDGYVQIAH------FDVNDATGTYTDIVSPYDTYTEI 159
Query: 339 RDAISDLPRVSQGANCYLF 357
+ + L R + LF
Sbjct: 160 QRVYATLMRFLEKIGALLF 178
>gnl|CDD|240062 cd04711, BAH_Dnmt1_II, BAH, or Bromo Adjacent Homology domain,
second copy present in DNA
(Cytosine-5)-methyltransferases from Bilateria, Dnmt1
and similar proteins. DNA methylation, or the covalent
addition of a methyl group to cytosine within the
context of the CpG dinucleotide, has profound effects on
the genome. These effects include transcriptional
repression via inhibition of transcription factor
binding, the recruitment of methyl-binding proteins and
their associated chromatin remodeling factors, X
chromosome inactivation, imprinting, and the suppression
of parasitic DNA sequences. DNA methylation is also
essential for proper embryonic development and is an
important player in both DNA repair and genome
stability. 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 = 137
Score = 29.0 bits (65), Expect = 3.5
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 5/55 (9%)
Query: 68 DETIYTEYYRKTKDKHFVQPN---ARPLELAYILKIIHSKEFLPKFPMPLDTPLK 119
DE +Y EYYRK+ D + N P + I +I +K P D L+
Sbjct: 1 DEDLYPEYYRKSSD-YIKGSNLDAPEPFRIGRIKEIFCAKRS-NGKPNESDIKLR 53
>gnl|CDD|234748 PRK00402, PRK00402, 3-isopropylmalate dehydratase large subunit;
Reviewed.
Length = 418
Score = 30.1 bits (69), Expect = 3.7
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 554 VREYARAQGFPDSYVFRGGIC 574
+RE+A+ QG P+ + GIC
Sbjct: 81 LREFAKEQGIPNFFDVGEGIC 101
>gnl|CDD|107337 cd06342, PBP1_ABC_LIVBP_like, Type I periplasmic ligand-binding
domain of ABC (Atpase Binding Cassette)-type active
transport systems that are involved in the transport of
all three branched chain aliphatic amino acids (leucine,
isoleucine and valine). This subgroup includes the type
I periplasmic ligand-binding domain of ABC (Atpase
Binding Cassette)-type active transport systems that are
involved in the transport of all three branched chain
aliphatic amino acids (leucine, isoleucine and valine).
This subgroup also includes a leucine-specific binding
protein (or LivK), which is very similar in sequence and
structure to leucine-isoleucine-valine binding protein
(LIVBP). ABC-type active transport systems are
transmembrane proteins that function in the transport of
diverse sets of substrates across extra- and
intracellular membranes, including carbohydrates, amino
acids, inorganic ions, dipeptides and oligopeptides,
metabolic products, lipids and sterols, and heme, to
name a few.
Length = 334
Score = 29.0 bits (66), Expect = 6.5
Identities = 8/30 (26%), Positives = 16/30 (53%)
Query: 473 RNNNWQGVLGRLAWDESFDMTGQKNTIIPW 502
R ++ GV G++++D D+ G T+
Sbjct: 305 RKVDFDGVTGKISFDAKGDLKGAAVTVYQV 334
>gnl|CDD|240059 cd04708, BAH_plantDCM_II, BAH, or Bromo Adjacent Homology domain,
second copy present in DNA
(Cytosine-5)-methyltransferases (DCM) from plants. DNA
methylation, or the covalent addition of a methyl group
to cytosine within the context of the CpG dinucleotide,
has profound effects on the genome. These effects
include transcriptional repression via inhibition of
transcription factor binding, the recruitment of
methyl-binding proteins and their associated chromatin
remodeling factors, X chromosome inactivation,
imprinting, and the suppression of parasitic DNA
sequences. DNA methylation is also essential for proper
embryonic development and is an important player in both
DNA repair and genome stability. 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 = 202
Score = 28.6 bits (64), Expect = 7.2
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 113 PLDTPLKCLDLFSGCGGL 130
P + L LD+F+GCGGL
Sbjct: 185 PKENRLATLDIFAGCGGL 202
>gnl|CDD|237799 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional.
Length = 1627
Score = 29.4 bits (66), Expect = 7.8
Identities = 13/62 (20%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 52 NDSSEEEILDNEHEEKDETIYTEYYRKTKDKHFVQPNARPLELAYILKIIHSKEFLPKFP 111
++ EE+ E +E+ E +Y + +K ++ N + +I ++I + P F
Sbjct: 287 DEEKSEEVKTEEVDEEFEEEEKGFYYELYEKVNIEANKK-----FIKEVIAGR---PVFA 338
Query: 112 MP 113
P
Sbjct: 339 HP 340
>gnl|CDD|215737 pfam00128, Alpha-amylase, Alpha amylase, catalytic domain. Alpha
amylase is classified as family 13 of the glycosyl
hydrolases. The structure is an 8 stranded alpha/beta
barrel containing the active site, interrupted by a ~70
a.a. calcium-binding domain protruding between beta
strand 3 and alpha helix 3, and a carboxyl-terminal
Greek key beta-barrel domain.
Length = 314
Score = 28.8 bits (65), Expect = 9.8
Identities = 15/64 (23%), Positives = 22/64 (34%), Gaps = 9/64 (14%)
Query: 13 DTILGDKIQFDNSTLFLTNACESIDLSVIKKTVCVDFVTNDSSEEEILDNEHEEKDETIY 72
D G F L + + VI +D V N +S+E E + Y
Sbjct: 45 DPHFGTMDDFKE----LIDKAHERGIKVI-----LDLVPNHTSDEHAWFQESRSSKDNPY 95
Query: 73 TEYY 76
+YY
Sbjct: 96 RDYY 99
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
0.320 0.136 0.425
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,254,065
Number of extensions: 2997411
Number of successful extensions: 2299
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2284
Number of HSP's successfully gapped: 28
Length of query: 620
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 517
Effective length of database: 6,369,140
Effective search space: 3292845380
Effective search space used: 3292845380
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 62 (27.6 bits)