RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13720
(487 letters)
>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 = 170 bits (433), Expect = 2e-51
Identities = 72/136 (52%), Positives = 88/136 (64%), Gaps = 1/136 (0%)
Query: 45 DEELYPEAYRKLSDYMKGSNAYTPAPFGIGYIVAIF-KKKGKKNVSASDVFLTVKKFYRP 103
DE+LYPE YRK SDY+KGSN P PF IG I IF K+ + SD+ L + KFYRP
Sbjct: 1 DEDLYPEYYRKSSDYIKGSNLDAPEPFRIGRIKEIFCAKRSNGKPNESDIKLRINKFYRP 60
Query: 104 ENTHRSVEFTYQLDLNKLYWSDEEEQVSLSDVQGKCFVVCEDNLQISTDRWSSRGPHRFY 163
ENTH+ + TY D+N LYWSDEE V S VQG+C V ++L S +S GP RFY
Sbjct: 61 ENTHKGFKATYHADINMLYWSDEEATVDFSAVQGRCTVEYGEDLPESVQEYSGGGPDRFY 120
Query: 164 FNEAYNSKTEEFTNLP 179
F EAYN+KT+ F + P
Sbjct: 121 FLEAYNAKTKSFEDPP 136
>gnl|CDD|223348 COG0270, Dcm, Site-specific DNA methylase [DNA replication,
recombination, and repair].
Length = 328
Score = 109 bits (273), Expect = 2e-26
Identities = 54/180 (30%), Positives = 87/180 (48%), Gaps = 17/180 (9%)
Query: 217 PLRCLEVFAGAGGLSRGLDKSGVARSTWAIEFDSAAATAFKMNNPGCTVFVDDCNKILQR 276
++ +++FAG GGLS G +++G +A E D A +K N P I+
Sbjct: 3 KMKVIDLFAGIGGLSLGFEEAG-FEIVFANEIDPPAVATYKANFP--------HGDIILG 53
Query: 277 VIDNEVCDDKKQKLPRKGEVEMLCGGPPCQGFSGMNRFNQRQYSAFKNSLIVSYLSYCDY 336
I + RK +V++L GGPPCQ FS +R Y + SL + ++ +
Sbjct: 54 DIKELDGEAL-----RKSDVDVLIGGPPCQDFSIAG--KRRGYDDPRGSLFLEFIRLIEQ 106
Query: 337 YRPRFFLLENVRNFVAFKNSMVLKMTMRCLTQIGYQCTFGTLQAGHFGVSQTRRRAIVLA 396
RP+FF+LENV+ ++ K + L ++GY F L A +GV Q+R R ++
Sbjct: 107 LRPKFFVLENVKGLLSSKGQ-TFDEIKKELEELGYGVEFNILNAADYGVPQSRERVFIVG 165
>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 = 106 bits (267), Expect = 5e-26
Identities = 61/230 (26%), Positives = 103/230 (44%), Gaps = 31/230 (13%)
Query: 218 LRCLEVFAGAGGLSRGLDKSGVARSTWAIEFDSAAATAFKMNNPGCTVFVDDCNKILQRV 277
LR +++FAG GG GL+K+G A E D +AA ++ N P + D KI
Sbjct: 1 LRVIDLFAGIGGFRLGLEKAG-FEIVAANEIDKSAAETYEANFPNKLIE-GDITKI---- 54
Query: 278 IDNEVCDDKKQKLPRKGEVEMLCGGPPCQGFS--GMNRFNQRQYSAFKNSLIVSYLSYCD 335
D+K +P ++++L GG PCQ FS G ++ + + +L +
Sbjct: 55 -------DEKDFIP---DIDLLTGGFPCQPFSIAG----KRKGFEDTRGTLFFEIIRILK 100
Query: 336 YYRPRFFLLENVRNFVAFKNSMVLKMTMRCLTQIGYQCTFGTLQAGHFGVSQTRRRAIVL 395
+P++FLLENV+ + N LK+ + L ++GY + L A +GV Q R R ++
Sbjct: 101 EKKPKYFLLENVKGLLTHDNGNTLKVILNTLEELGYNVYWKLLNASDYGVPQNRERVFII 160
Query: 396 AAAPGEVLPKYPEPWTVFSPRTSQLNVTISKKTYVSTCKWTQSAPYRTIT 445
+ P+ S+ T+ K + + +P T+T
Sbjct: 161 GI-----RKDLILNFFSPFPKPSEKKKTL--KDILRIRDPDEPSP--TLT 201
>gnl|CDD|215747 pfam00145, DNA_methylase, C-5 cytosine-specific DNA methylase.
Length = 320
Score = 105 bits (263), Expect = 4e-25
Identities = 46/182 (25%), Positives = 82/182 (45%), Gaps = 26/182 (14%)
Query: 218 LRCLEVFAGAGGLSRGLDKSGVARSTWAIEFDSAAATAFKMNNPGCTVFVDDCNKILQRV 277
+ +++FAG GG GL+++G A E D +AA ++ N P +V
Sbjct: 1 FKFIDLFAGIGGFRLGLEQAGF-ECVAANEIDKSAAKTYEANFP--------------KV 45
Query: 278 IDNEVCDDKKQKLPRKGEVEMLCGGPPCQGFS---GMNRFNQRQYSAFKNSLIVSYLSYC 334
++ + +P ++++L GG PCQ FS F + +L +
Sbjct: 46 PIGDITLIDIKDIP---DIDILTGGFPCQDFSIAGKQKGFEDTR-----GTLFFEIIRII 97
Query: 335 DYYRPRFFLLENVRNFVAFKNSMVLKMTMRCLTQIGYQCTFGTLQAGHFGVSQTRRRAIV 394
+P+ FLLENV+ ++ N L + + L ++GY ++ L A +GV Q R R +
Sbjct: 98 KEKKPKAFLLENVKGLLSHDNGNTLNVILETLEELGYSVSWKVLNASDYGVPQNRERVFI 157
Query: 395 LA 396
+
Sbjct: 158 VG 159
>gnl|CDD|214664 smart00439, BAH, Bromo adjacent homology domain.
Length = 121
Score = 83.9 bits (208), Expect = 1e-19
Identities = 36/122 (29%), Positives = 53/122 (43%), Gaps = 6/122 (4%)
Query: 58 DYMKGSNAYTPAPFGIGYIVAIFKKKGKKNVSASDVFLTVKKFYRPENTHRSVEFTYQLD 117
D++ P+ IG I IF+ K + V+ FYRPE T D
Sbjct: 6 DFVLVEPDDADEPYYIGRIEEIFETKKNSE----SKMVRVRWFYRPEETVLEK--AALFD 59
Query: 118 LNKLYWSDEEEQVSLSDVQGKCFVVCEDNLQISTDRWSSRGPHRFYFNEAYNSKTEEFTN 177
N+++ SDE + V LSD+ GKC V+ + + S P F+ AY+ + F
Sbjct: 60 KNEVFLSDEYDTVPLSDIIGKCNVLYKSDYPGLRPEGSIGEPDVFFCESAYDPEKGSFKK 119
Query: 178 LP 179
LP
Sbjct: 120 LP 121
>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 = 88.5 bits (220), Expect = 2e-19
Identities = 55/223 (24%), Positives = 92/223 (41%), Gaps = 31/223 (13%)
Query: 222 EVFAGAGGLSRGLDKSGVARSTWAIEFDSAAATAFKMNNPGCTVFVDDCNKILQRVIDNE 281
++FAG GG+ G +++G +A E D A ++ N V D KI
Sbjct: 3 DLFAGIGGIRLGFEQAGFK-CVFASEIDKYAQKTYEANFGN-KVPFGDITKI-------- 52
Query: 282 VCDDKKQKLPRKGEVEMLCGGPPCQGFS---GMNRFNQRQYSAFKNSLIVSYLSYCDYYR 338
+P + ++L GG PCQ FS F + +L + +
Sbjct: 53 ----SPSDIP---DFDILLGGFPCQPFSIAGKRKGFEDTR-----GTLFFEIVRILKEKK 100
Query: 339 PRFFLLENVRNFVAFKNSMVLKMTMRCLTQIGYQCTFGTLQAGHFGVSQTRRRAIVLAAA 398
P+FFLLENV+ V+ K+ + L ++GY+ + L A FGV Q R R ++
Sbjct: 101 PKFFLLENVKGLVSHDKGRTFKVIIETLEELGYKVYYKVLNAKDFGVPQNRERIYIVGFR 160
Query: 399 PGEVLPKYPEPWTVFSPRT------SQLNVTISKKTYVSTCKW 435
+ + P ++ + L+V + +K Y+S K
Sbjct: 161 DFDDKLNFEFPKPIYVAKKKRIGDLLDLSVDLEEKYYLSEEKK 203
>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 = 77.8 bits (192), Expect = 2e-17
Identities = 35/123 (28%), Positives = 54/123 (43%), Gaps = 10/123 (8%)
Query: 58 DYMKGSNAYTPAPFGIGYIVAIFK-KKGKKNVSASDVFLTVKKFYRPENTHRSVEFTYQL 116
D++ P +G I IF+ K G K V V+ FYRPE T + +
Sbjct: 7 DFVLVEPDDAGEPPYVGRIEEIFEDKDGSKMVH-------VRWFYRPEETVHRLGRAFNK 59
Query: 117 DLNKLYWSDEEEQVSLSDVQGKCFVVCEDNLQISTDRWSSRGPHRFYFNEAYNSKTEEFT 176
D ++ SDE + V L D+ GKC V+ + + + R + P F+ Y+ + F
Sbjct: 60 DE--VFLSDECDDVPLEDIIGKCNVIIKSDPESLQPRKINGEPDVFFCELLYDPERGSFK 117
Query: 177 NLP 179
LP
Sbjct: 118 KLP 120
>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 = 67.1 bits (164), Expect = 7e-13
Identities = 60/237 (25%), Positives = 93/237 (39%), Gaps = 51/237 (21%)
Query: 8 YEGEQYKLKSCVYVNPDCFKFKSKPQSAVQNNKRPVEDEELYPEAYRKLSDYMKGSNAYT 67
Y+G Y + +YV+PD F EE A K G N
Sbjct: 3 YDGVTYSVGDFLYVSPDAF------------------AEEERERATFK-----AGRNVGL 39
Query: 68 PAPFGIGYIVAIFKKKGKKNVSASDVFLTVKKFYRPENTHRSVEFTYQLDLNKLYWSDEE 127
A F + ++ I +K K + + V++FYRPE+ S E Y D+ ++Y+S++
Sbjct: 40 KA-FVVCQVLEIVVEKESKQADVASTQVKVRRFYRPEDV--SPEKAYASDIREVYYSEDT 96
Query: 128 EQVSLSDVQGKCFVVCEDNLQISTDRWSSRGP----HRFYFNEAYNSKTEEFTNLPT--E 181
V + V+GKC V +D S P H F+ Y+ LP +
Sbjct: 97 LTVPVEAVEGKCEVR------KKSDLPDSDAPVIFEHVFFCELLYDPAKGSLKQLPPNIK 150
Query: 182 ALFLGSVS--------KGKGKGKNQTNKPEEKDEITEWPSIARPLRCLEVFAGAGGL 230
+ + KGKGKG ++++ E L L++FAG GGL
Sbjct: 151 EEAYSTGASDSALRKRKGKGKGDSESDSEAPVKAPKE-----NRLATLDIFAGCGGL 202
>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 = 62.8 bits (153), Expect = 4e-12
Identities = 26/127 (20%), Positives = 49/127 (38%), Gaps = 8/127 (6%)
Query: 49 YPEAYRKLSDYMKGSNAYTPAPFGIGYIVAIFKKKGKKNVSASDVFLTVKKFYRPENTHR 108
S Y++ ++ P I I +++ + V+ FYRPE T
Sbjct: 1 GITYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTN------GSKQVKVRWFYRPEETP- 53
Query: 109 SVEFTYQLDLNKLYWSDEEEQVSLSDVQGKCFVVCEDNLQISTDRWSSRGPHRFYFNEAY 168
+ +L+ SD +++ + + GKC V+ + R + F+ AY
Sbjct: 54 -KGLSPFALRRELFLSDHLDEIPVESIIGKCKVLFVSEFEGLKQRPNKIDTDDFFCRLAY 112
Query: 169 NSKTEEF 175
+ T+EF
Sbjct: 113 DPTTKEF 119
>gnl|CDD|240061 cd04710, BAH_fungalPHD, BAH, or Bromo Adjacent Homology domain, as
present in fungal proteins containing PHD domains. 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 = 135
Score = 40.0 bits (94), Expect = 4e-04
Identities = 27/105 (25%), Positives = 45/105 (42%), Gaps = 12/105 (11%)
Query: 70 PFGIGYIVAIFKKKGKKNV------SASDVFLTVKKFYRPENTHRSVEFTYQLDLNKLYW 123
P+ IG I+ K + AS + + +YRP + R V +L LY
Sbjct: 28 PYYIGRIMEFVPKHEFPSGIHARVFPASYFQVRLNWYYRPRDISRRVVADSRL----LYA 83
Query: 124 SDEEEQVSLSDVQGKCFVVCEDNLQISTDRWSSRGPHRFYFNEAY 168
S + + V+GKC V D + + + R P+ FYF++ +
Sbjct: 84 SMHSDICPIGSVRGKCTVRHRDQI-PDLEEYKKR-PNHFYFDQLF 126
>gnl|CDD|236696 PRK10458, PRK10458, DNA cytosine methylase; Provisional.
Length = 467
Score = 40.8 bits (96), Expect = 0.001
Identities = 49/179 (27%), Positives = 79/179 (44%), Gaps = 42/179 (23%)
Query: 219 RCLEVFAGAGGLSRGLDKSG---VARSTWAIEFDSAAATAFKMN---NPGCTVFVDDCNK 272
R +++FAG GG+ RG + G V S W + A +K N +P F +D
Sbjct: 90 RFIDLFAGIGGIRRGFEAIGGQCVFTSEW----NKHAVRTYKANWYCDPATHRFNEDIRD 145
Query: 273 I----LQRVIDNEVCDDKKQKLPRKGEVEMLCGGPPCQGFS--GMNRFNQRQYSAFKNSL 326
I + V D E + +Q +P + ++L G PCQ FS G+++ KNSL
Sbjct: 146 ITLSHKEGVSDEEAAEHIRQHIP---DHDVLLAGFPCQPFSLAGVSK---------KNSL 193
Query: 327 IVSYLSYCDYY--------------RPRFFLLENVRNFVAFKNSMVLKMTMRCLTQIGY 371
++ C+ RP F+LENV+N + ++ M+ L ++GY
Sbjct: 194 GRAHGFECETQGTLFFDVARIIDAKRPAIFVLENVKNLKSHDKGKTFRIIMQTLDELGY 252
>gnl|CDD|240068 cd04717, BAH_polybromo, BAH, or Bromo Adjacent Homology domain, as
present in polybromo and yeast RSC1/2. The human
polybromo protein (BAF180) is a component of the SWI/SNF
chromatin-remodeling complex PBAF. It is thought that
polybromo participates in transcriptional regulation.
Saccharomyces cerevisiae RSC1 and RSC2 are part of the
15-subunit nucleosome remodeling RSC complex. 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 = 121
Score = 36.0 bits (84), Expect = 0.008
Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 12/89 (13%)
Query: 55 KLSDYMKGSNAYTPAPFGIGYIVAIFK-KKGKKNVSASDVFLTVKKFYRPENT-HRSVEF 112
++ D + +N P+ I I ++K + G+K F FYRPE T H
Sbjct: 5 RVGDCVYVANPEDPSKPIIFRIERLWKDEDGEK-------FFFGCWFYRPEETFHEPTRK 57
Query: 113 TYQLDLNKLYWSDEEEQVSLSDVQGKCFV 141
Y+ N+++ S E V + ++ GKC V
Sbjct: 58 FYK---NEVFKSPLYETVPVEEIVGKCAV 83
>gnl|CDD|223813 COG0742, COG0742, N6-adenine-specific methylase [DNA replication,
recombination, and repair].
Length = 187
Score = 36.4 bits (85), Expect = 0.013
Identities = 21/77 (27%), Positives = 30/77 (38%), Gaps = 17/77 (22%)
Query: 219 RCLEVFAGAGGL-----SRGLDKSGVARSTWAIEFDSAAATAFKMN------NPGCTVFV 267
R L++FAG+G L SRG A +E D A K N V
Sbjct: 46 RVLDLFAGSGALGLEALSRG------AARVVFVEKDRKAVKILKENLKALGLEGEARVLR 99
Query: 268 DDCNKILQRVIDNEVCD 284
+D + L+++ E D
Sbjct: 100 NDALRALKQLGTREPFD 116
>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 = 35.1 bits (81), Expect = 0.014
Identities = 12/61 (19%), Positives = 20/61 (32%), Gaps = 6/61 (9%)
Query: 219 RCLEVFAGAGGLSRGLDKSGVARSTWAIEFDSAAATAFKMNN-----PGCTVFVDDCNKI 273
R L++ G G L+ L AR T ++ A + V D ++
Sbjct: 1 RVLDLGCGTGALALALASGPGARVT-GVDISPVALELARKAAAALLADNVEVLKGDAEEL 59
Query: 274 L 274
Sbjct: 60 P 60
>gnl|CDD|222295 pfam13659, Methyltransf_26, Methyltransferase domain. This family
contains methyltransferase domains.
Length = 117
Score = 34.3 bits (79), Expect = 0.034
Identities = 24/112 (21%), Positives = 38/112 (33%), Gaps = 21/112 (18%)
Query: 217 PLRCLEVFAGAGGLSRGLDKSGVARSTWAIEFDSAAA------TAFKMNNPGCTVFVDDC 270
R L+ AG+G ++G +E D AA A P V V D
Sbjct: 1 GDRVLDPGAGSGAFLLAAARAGPDARVVGVELDPEAAALARRRLALAGLAPRVRVVVGDA 60
Query: 271 NKILQRVIDNEVCDDKKQKLPRKGEVEMLCGGPPCQGFSGMNRFNQRQYSAF 322
++L+ G +++ G PP +G + N+ Y F
Sbjct: 61 RELLEL---------------PDGSFDLVLGNPPYGPRAGDPKDNRDLYDRF 97
>gnl|CDD|202698 pfam03602, Cons_hypoth95, Conserved hypothetical protein 95.
Length = 183
Score = 31.8 bits (73), Expect = 0.51
Identities = 17/49 (34%), Positives = 21/49 (42%), Gaps = 11/49 (22%)
Query: 216 RPLRCLEVFAGAGGL-----SRGLDKSGVARSTWAIEFDSAAATAFKMN 259
R L++FAG+G L SRG A S +E D A K N
Sbjct: 43 GGARVLDLFAGSGALGLEALSRG------AASVVFVEKDKKAVATLKEN 85
>gnl|CDD|240065 cd04714, BAH_BAHCC1, BAH, or Bromo Adjacent Homology domain, as
present in mammalian BAHCC1 and similar proteins. BAHCC1
stands for BAH domain and coiled-coil containing 1. 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 = 121
Score = 30.4 bits (69), Expect = 0.75
Identities = 16/73 (21%), Positives = 35/73 (47%), Gaps = 14/73 (19%)
Query: 73 IGYIVAIFKKKGKKNVSASDVFLTVKKFYRPENTH--RSVEFTYQLDL-NKLYWSDEEEQ 129
+ I ++++ ++ + VK +YRPE T R +L+ SD +++
Sbjct: 23 VARIESLWEDPE------GNMVVRVKWYYRPEETKGGRK-----PNHGEKELFASDHQDE 71
Query: 130 VSLSDVQGKCFVV 142
S+ ++ KC+V+
Sbjct: 72 NSVQTIEHKCYVL 84
>gnl|CDD|139564 PRK13425, PRK13425, F0F1 ATP synthase subunit gamma; Provisional.
Length = 291
Score = 31.7 bits (72), Expect = 0.80
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 10/61 (16%)
Query: 263 CTVFVDDCNKILQRVIDNEVCDDKKQKLPRKGEVEMLCGGPPCQGFSGMNRFNQRQYSAF 322
C F + K+ Q+VI + L KG V M+C G G + F +R Y+
Sbjct: 89 CGAFNTNIIKLAQKVIHEDYAA-----LHAKGGVSMICAGT-----RGFDFFRKRGYNIV 138
Query: 323 K 323
K
Sbjct: 139 K 139
>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 = 30.5 bits (69), Expect = 1.2
Identities = 19/56 (33%), Positives = 24/56 (42%), Gaps = 15/56 (26%)
Query: 213 SIARP----LRCLEVFAGAGG-----LSRGLDKSGVARSTWAIEFDSAAATAFKMN 259
+I RP L++FAG+G LSRG A S +E D A K N
Sbjct: 43 NILRPDIVGAHFLDLFAGSGALGLEALSRG------AASAVFVEQDRKVAQTLKEN 92
>gnl|CDD|204099 pfam08933, DUF1864, Domain of unknown function (DUF1864). This
domain has no known function. It is found in various
hypothetical and conserved domain proteins.
Length = 387
Score = 30.9 bits (70), Expect = 1.7
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 165 NEAYNSKTEEFTNLPTEALFLGSVSKG 191
N A N + FT+LP E LFL +KG
Sbjct: 129 NPAANGLYKRFTDLPDEKLFLDYNTKG 155
>gnl|CDD|132751 cd06953, NR_LBD_DHR4_like, The ligand binding domain of orphan
nuclear receptor Ecdysone-induced receptor DHR4. The
ligand binding domain of Ecdysone-induced receptor DHR4:
Ecdysone-induced orphan receptor DHR4 is a member of the
nuclear receptor family. DHR4 is expressed during the
early Drosophila larval development and is induced by
ecdysone. DHR4 coordinates growth and maturation in
Drosophila by mediating endocrine response to the
attainment of proper body size during larval
development. Mutations in DHR4 result in shorter larval
development which translates into smaller and lighter
flies. Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
DHR4 has a central well conserved DNA binding domain
(DBD), a variable N-terminal domain, a flexible hinge
and a C-terminal ligand binding domain (LBD). .
Length = 213
Score = 29.7 bits (67), Expect = 2.9
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 10/65 (15%)
Query: 415 PRTSQLNVTISKKTYVSTCK-WTQ-SAPYRTITVRDVMSDLPEIQNGC------KMEELP 466
SQL ++ K+ Y + +T+ + P + D++S LPEI+ K+ LP
Sbjct: 151 TNASQLE-SLQKR-YWYVLQDFTELNYPNQPNRFSDLLSCLPEIRAAAGKLLHSKLFYLP 208
Query: 467 YKENA 471
A
Sbjct: 209 LLFKA 213
>gnl|CDD|235170 PRK03881, PRK03881, hypothetical protein; Provisional.
Length = 467
Score = 29.5 bits (67), Expect = 4.6
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 69 APFGIGYIVAIFKKKGKKNVSASDVFLTVKK 99
PFG+GY VA F+ + S + ++
Sbjct: 259 GPFGVGYGVARFEPGEEAGRSLLEKLREKRE 289
>gnl|CDD|233186 TIGR00920, 2A060605, 3-hydroxy-3-methylglutaryl-coenzyme A
reductase. [Transport and binding proteins,
Carbohydrates, organic alcohols, and acids].
Length = 889
Score = 29.5 bits (66), Expect = 4.7
Identities = 31/130 (23%), Positives = 44/130 (33%), Gaps = 19/130 (14%)
Query: 121 LYWSDEEEQVSLSDVQGKCFV----VCEDNLQISTDRW---SSRGPHRFYFNEAYNSKTE 173
+++S E + ++S G V + L+ R S+ EA SK
Sbjct: 334 IFFSQGETESTVSLKNGDPVVNPVSTDKKQLEYCCRRELTVSADTIVVSILEEALASKFV 393
Query: 174 EF---TNLPTEALFLG-----SVSKGKGKGKNQTNKPEEKDEITEWPSIARP----LRCL 221
F LPTE K G Q + K+ E P+ RP L L
Sbjct: 394 FFEVIKPLPTETGSDSWVEASFPVGHKYSGTEQPSCSAPKEPEEELPAEPRPIDECLSIL 453
Query: 222 EVFAGAGGLS 231
+ GA LS
Sbjct: 454 KSDKGAQALS 463
>gnl|CDD|197791 smart00562, NDK, Enzymes that catalyze nonsubstrate specific
conversions of nucleoside diphosphates to nucleoside
triphosphates. These enzymes play important roles in
bacterial growth, signal transduction and pathogenicity.
Length = 135
Score = 28.3 bits (64), Expect = 5.0
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 6/43 (13%)
Query: 73 IGYIVAIFKKKGKKNVSASDVFLT---VKKFYRPENTHRSVEF 112
IG I++ F++KG K V+ + LT ++FY H F
Sbjct: 17 IGEIISRFERKGFKIVAMKMLQLTEEQAEEFYA---EHEGKPF 56
>gnl|CDD|224512 COG1596, Wza, Periplasmic protein involved in polysaccharide
export, contains SLBB domain of b-grasp fold [Cell
wall/membrane/envelope biogenesis].
Length = 239
Score = 28.6 bits (64), Expect = 6.6
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 209 TEWPSIARPLRCLEVFAGAGGLSRGLDKSGVAR 241
++P R L L+ A AGGL+ DK V
Sbjct: 137 GQYPLTPRGLTVLDAIALAGGLTPRADKVNVQL 169
>gnl|CDD|235970 PRK07217, PRK07217, replication factor A; Reviewed.
Length = 311
Score = 28.1 bits (63), Expect = 9.7
Identities = 20/71 (28%), Positives = 29/71 (40%), Gaps = 10/71 (14%)
Query: 76 IVAIFKKKGKKNVSASDVF----LTVKKFYRPEN-THRSVEFTY----QLDLNKLYWSDE 126
I F G VS DV V +F PE+ RSV Y +D ++L
Sbjct: 11 IHEQFSDLGVD-VSVEDVEERLDTLVTEFKVPEDEARRSVTNYYLKEAGIDRDELSGGGG 69
Query: 127 EEQVSLSDVQG 137
E V+++D+
Sbjct: 70 SELVNIADIDE 80
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 0.134 0.411
Gapped
Lambda K H
0.267 0.0806 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,400,055
Number of extensions: 2308352
Number of successful extensions: 1708
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1680
Number of HSP's successfully gapped: 30
Length of query: 487
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 386
Effective length of database: 6,457,848
Effective search space: 2492729328
Effective search space used: 2492729328
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 (21.7 bits)
S2: 61 (27.1 bits)