RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9745
(570 letters)
>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse
transcriptases. Ribonuclease H (RNase H) is classified
into two families, type 1 (prokaryotic RNase HI,
eukaryotic RNase H1 and viral RNase H) and type 2
(prokaryotic RNase HII and HIII, and eukaryotic RNase
H2). Ribonuclease HI (RNase HI) is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. RNase H is widely present
in various organisms, including bacteria, archaea and
eukaryotes. RNase HI has also been observed as an
adjunct domain to the reverse transcriptase gene in
retroviruses, long-term repeat (LTR)-bearing
retrotransposons and non-LTR retrotransposons. RNase HI
in LTR retrotransposons perform degradation of the
original RNA template, generation of a polypurine tract
(the primer for plus-strand DNA synthesis), and final
removal of RNA primers from newly synthesized minus and
plus strands. The catalytic residues for RNase H
enzymatic activity, three aspartatic acids and one
glutamatic acid residue (DEDD), are unvaried across all
RNase H domains. The position of the RNase domain of
non-LTR and LTR transposons is at the carboxyl terminal
of the reverse transcriptase (RT) domain and their RNase
domains group together, indicating a common evolutionary
origin. Many non-LTR transposons have lost the RNase
domain because their activity is at the nucleus and
cellular RNase may suffice; however LTR retotransposons
always encode their own RNase domain because it requires
RNase activity in RNA-protein particles in the
cytoplasm. RNase H inhibitors have been explored as an
anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 128
Score = 123 bits (312), Expect = 1e-33
Identities = 46/126 (36%), Positives = 67/126 (53%), Gaps = 6/126 (4%)
Query: 378 CFTDGSKTTDHTGAAFIIRDE---ICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLV 434
+TDGSK TGA F I + S KL P CS+F AEL+AI + L+
Sbjct: 2 IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALRE-GRRA- 59
Query: 435 TQNFIICSDSKSSLQALQNVYHVSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDN 494
+ I SDS+++L+AL++ SPLV I I+++ + G +V W+P H GI N+
Sbjct: 60 -RKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNER 118
Query: 495 VDHAAR 500
D A+
Sbjct: 119 ADRLAK 124
>gnl|CDD|197311 cd09077, R1-I-EN, Endonuclease domain encoded by various R1- and
I-clade non-long terminal repeat retrotransposons. This
family contains the endonuclease (EN) domain of various
non-long terminal repeat (non-LTR) retrotransposons,
long interspersed nuclear elements (LINEs) which belong
to the subtype 2, R1- and I-clade. LINES can be
classified into two subtypes. Subtype 2 has two ORFs:
the second (ORF2) encodes a modular protein consisting
of an N-terminal apurine/apyrimidine endonuclease domain
(EN), a central reverse transcriptase, and a
zinc-finger-like domain at the C-terminus. Most non-LTR
retrotransposons are inserted throughout the host
genome; however, many retrotransposons of the R1 clade
exhibit target-specific retrotransposition. This family
includes the endonucleases of SART1 and R1bm, from the
silkworm Bombyx mori, which belong to the R1-clade. It
also includes the endonuclease of snail (Biomphalaria
glabrata) Nimbus/Bgl and mosquito Aedes aegypti
(MosquI), both which belong to the I-clade. This family
belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 205
Score = 76.9 bits (190), Expect = 4e-16
Identities = 31/94 (32%), Positives = 43/94 (45%), Gaps = 3/94 (3%)
Query: 84 DEIYNIKRQLPRPYIICSDMNAHNTIWGGSKIDSNGVQVEKFLLENDDVCLLNTNEATHF 143
+ + I R L RP II D NA + WG + D G +E ++ + LLN + F
Sbjct: 104 ENLVRIVRGLSRPVIIGGDFNAWSPAWGSKRTDRRGRLLEDWIANL-GLVLLNDGNSPTF 162
Query: 144 NSSNGTFSAIDLTLASRSI-TPDLKWSVHDDLYL 176
GT S ID+T S S+ W V +D L
Sbjct: 163 VRPRGT-SIIDVTFCSPSLARRISNWRVLEDETL 195
>gnl|CDD|215695 pfam00075, RNase_H, RNase H. RNase H digests the RNA strand of an
RNA/DNA hybrid. Important enzyme in retroviral
replication cycle, and often found as a domain
associated with reverse transcriptases. Structure is a
mixed alpha+beta fold with three a/b/a layers.
Length = 126
Score = 64.2 bits (157), Expect = 1e-12
Identities = 34/130 (26%), Positives = 54/130 (41%), Gaps = 20/130 (15%)
Query: 378 CFTDGS--KTTDHTGAAFII-RDEICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLV 434
+TDGS GA ++ + S L P + AEL+A+ + LE L
Sbjct: 6 VYTDGSCNGNPGPGGAGYVTDGGKQRSKPL-PGTTNQRAELLALIEALE--------ALS 56
Query: 435 TQNFIICSDSKSSLQALQNVY---HVS-PLVCDIISTIQDIRDLGTRVSFLWIPSHLGIR 490
Q I +DS+ + + N + S P+ +I +Q +V W+P H GI
Sbjct: 57 GQKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIWELLQ----KKHKVYIQWVPGHSGIP 112
Query: 491 ENDNVDHAAR 500
N+ D A+
Sbjct: 113 GNELADKLAK 122
>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA
strand of an RNA/DNA hybrid in a sequence non-specific
manner. Ribonuclease H (RNase H) enzymes are divided
into two major families, Type 1 and Type 2, based on
amino acid sequence similarities and biochemical
properties. RNase H is an endonuclease that cleaves the
RNA strand of an RNA/DNA hybrid in a sequence
non-specific manner in the presence of divalent cations.
RNase H is widely present in various organisms,
including bacteria, archaea and eukaryotes. Most
prokaryotic and eukaryotic genomes contain multiple
RNase H genes. Despite the lack of amino acid sequence
homology, Type 1 and type 2 RNase H share a main-chain
fold and steric configurations of the four acidic
active-site residues and have the same catalytic
mechanism and functions in cells. RNase H is involved in
DNA replication, repair and transcription. One of the
important functions of RNase H is to remove Okazaki
fragments during DNA replication. RNase H inhibitors
have been explored as an anti-HIV drug target because
RNase H inactivation inhibits reverse transcription.
Length = 123
Score = 52.7 bits (127), Expect = 1e-08
Identities = 29/132 (21%), Positives = 50/132 (37%), Gaps = 20/132 (15%)
Query: 379 FTDGSKTTD--HTGAAFIIRDEICSMKL-----NPICSIFTAELIAIEKCLEKIKDV-VT 430
TDGS + GA ++RD + P + AEL+A+ + LE D+ +
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60
Query: 431 HDLVTQNFIICSDSKSSLQALQNVYHVSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGIR 490
II +DSK + + + ++ I + + F +P R
Sbjct: 61 K------LIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVP-----R 109
Query: 491 ENDNV-DHAARH 501
E + V D A+
Sbjct: 110 EGNEVADRLAKE 121
>gnl|CDD|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term
repeat retroelements. Ribonuclease H (RNase H) enzymes
are divided into two major families, Type 1 and Type 2,
based on amino acid sequence similarities and
biochemical properties. RNase H is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner in the presence of divalent
cations. RNase H is widely present in various organisms,
including bacteria, archaea and eukaryote. RNase HI has
also been observed as adjunct domains to the reverse
transcriptase gene in retroviruses, in long-term repeat
(LTR)-bearing retrotransposons and non-LTR
retrotransposons. RNase HI in LTR retrotransposons
perform degradation of the original RNA template,
generation of a polypurine tract (the primer for
plus-strand DNA synthesis), and final removal of RNA
primers from newly synthesized minus and plus strands.
The catalytic residues for RNase H enzymatic activity,
three aspartatic acids and one glutamatic acid residue
(DEDD), are unvaried across all RNase H domains.
Phylogenetic patterns of RNase HI of LTR retroelements
is classified into five major families, Ty3/Gypsy,
Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate
retroviruses. Bel/Pao family has been described only in
metazoan genomes. RNase H inhibitors have been explored
as an anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 135
Score = 51.1 bits (123), Expect = 7e-08
Identities = 34/141 (24%), Positives = 51/141 (36%), Gaps = 24/141 (17%)
Query: 377 LCFTDGSKTTDHTGAAFIIRDEICSMK-LNPICSIFTAELIAIEKCLEKIKDVVTHDLVT 435
FTDGS G A + ++ + L S AELIA+ + LE K
Sbjct: 1 TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALELAKG-------- 52
Query: 436 QNFIICSDSK---SSLQALQNVYHVSPLVC-------DIISTIQDIRDLGTRVSFLWIPS 485
+ I +DS L AL+ ++ + +I +Q V+ + I +
Sbjct: 53 KPVNIYTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKPVAVIHIRA 112
Query: 486 HLG-----IRENDNVDHAARH 501
H G N D AAR
Sbjct: 113 HSGLPGPLALGNARADQAARQ 133
>gnl|CDD|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and
more complex than their prokaryotic counterparts and
unlike prokaryote, RNase H are essential in higher
eukaryote. Ribonuclease H (RNase H) is classified into
two families, type 1 (prokaryotic RNase HI, eukaryotic
RNase H1 and viral RNase H) and type 2 (prokaryotic
RNase HII and HIII, and eukaryotic RNase H2). RNase H is
an endonuclease that cleaves the RNA strand of an
RNA/DNA hybrid in a sequence non-specific manner. RNase
H is involved in DNA replication, repair and
transcription. One of the important functions of RNase H
is to remove Okazaki fragments during DNA replication.
RNase H is widely present in various organisms,
including bacteria, archaea and eukaryote and most
prokaryotic and eukaryotic genomes contain multiple
RNase H genes. Despite the lack of amino acid sequence
homology, Type 1 and type 2 RNase H share a main-chain
fold and steric configurations of the four acidic
active-site (DEDD) residues and have the same catalytic
mechanism and functions in cells. Eukaryotic RNase H is
longer and more complex than in prokaryotes. Almost all
eukaryotic RNase HI have highly conserved regions at the
N-terminal called hybrid binding domain (HBD). It is
speculated that the HBD contributes to binding the
RNA/DNA hybrid. Prokaryotes and some single-cell
eukaryotes do not require RNase H for viability, but
RNase H is essential in higher eukaryotes. RNase H
knockout mice lack mitochondrial DNA replication and die
as embryos.
Length = 150
Score = 41.0 bits (97), Expect = 3e-04
Identities = 24/108 (22%), Positives = 40/108 (37%), Gaps = 27/108 (25%)
Query: 413 AELIAIEKCLEKIKDVVTHDLVTQNFIICSDSK--------------------SSLQALQ 452
AEL A+ L IK+ +I +DS+ S + +
Sbjct: 46 AELRAVIHALRLIKE---VGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVA 102
Query: 453 NVYHVSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAAR 500
N + L ++++ + G RV F +P H GI N+ D A+
Sbjct: 103 NKDLIKELD----KLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146
>gnl|CDD|238827 cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat)
retrotransposon and non-LTR retrovirus reverse
transcriptase (RT). This subfamily contains both non-LTR
retrotransposons and non-LTR retrovirus RTs. RTs
catalyze the conversion of single-stranded RNA into
double-stranded DNA for integration into host
chromosomes. RT is a multifunctional enzyme with
RNA-directed DNA polymerase, DNA directed DNA polymerase
and ribonuclease hybrid (RNase H) activities.
Length = 220
Score = 38.0 bits (89), Expect = 0.007
Identities = 24/97 (24%), Positives = 39/97 (40%), Gaps = 23/97 (23%)
Query: 184 IRQGSSLSGDLCNIATSDLPQYIPTV---------VSHGMFVDDLAIFMRGKDMDHIEET 234
+RQG LS L N+A DL + + ++H + DD+ +F GK ++E
Sbjct: 107 VRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEGKSRK-LQEL 165
Query: 235 LQNTIQFKENTRYLGLNLDSSLTWKFHIEQTKSKSLK 271
LQ ++ S I +KSK +
Sbjct: 166 LQRLQEW-------------SKESGLKINPSKSKVML 189
>gnl|CDD|215698 pfam00078, RVT_1, Reverse transcriptase (RNA-dependent DNA
polymerase). A reverse transcriptase gene is usually
indicative of a mobile element such as a retrotransposon
or retrovirus. Reverse transcriptases occur in a variety
of mobile elements, including retrotransposons,
retroviruses, group II introns, bacterial msDNAs,
hepadnaviruses, and caulimoviruses.
Length = 194
Score = 37.7 bits (88), Expect = 0.007
Identities = 17/87 (19%), Positives = 38/87 (43%), Gaps = 18/87 (20%)
Query: 184 IRQGSSLSGDLCNIATSDLPQYIPTV---VSHGMFVDDLAIFMRGKD-----MDHIEETL 235
+ QGS LS L N+ ++L + + +++ + DD+ IF + + ++ + E L
Sbjct: 108 LPQGSVLSPLLFNLFMNELLRPLRKRFPGLTYLRYADDILIFSKSPEELQEILEEVLEFL 167
Query: 236 QN----------TIQFKENTRYLGLNL 252
+ I + ++LG +
Sbjct: 168 KELGLKLNPEKTKITHSDEVKFLGYVI 194
>gnl|CDD|222802 PHA00497, pol, RNA-dependent RNA polymerase.
Length = 673
Score = 36.7 bits (85), Expect = 0.032
Identities = 21/105 (20%), Positives = 39/105 (37%), Gaps = 23/105 (21%)
Query: 8 TINSPLQVVAARVRSPVLSCPLTVCCLYIS----HDRKITKDEIYNIKRQLPRPYIICSD 63
TIN+P+Q A R+ + Y R+ +++Y K + +D
Sbjct: 302 TINAPIQCFAQGCRNAMYE-------RYAYTWHHTTREDKIEKVYEWK------FAEATD 348
Query: 64 MNAHNTIWGGSKIDSN-----GITKDEIYNIKRQLPR-PYIICSD 102
++ H+T + G ID + + R L R P + +
Sbjct: 349 VSDHDTFFSGWLIDLICDELPEMFAPWWMELARSLHRLPVYVRAP 393
>gnl|CDD|205634 pfam13456, RVT_3, Reverse transcriptase-like. This domain is found
in plants and appears to be part of a retrotransposon.
Length = 88
Score = 33.7 bits (78), Expect = 0.035
Identities = 23/94 (24%), Positives = 40/94 (42%), Gaps = 11/94 (11%)
Query: 409 SIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQALQNVYHVSPLVCDIISTI 468
S AE A LE ++ + +L + I+ SDS+ +Q +Q Y + ++ I
Sbjct: 1 SPLEAEAEA---LLEGLQ--LALELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREI 55
Query: 469 QDIRDLGTRVSFLWIPSHLGIRENDNV-DHAARH 501
+ + VS +P RE + V D A+
Sbjct: 56 RKLLKKFDSVSVSHVP-----RECNRVADALAKL 84
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 31.9 bits (73), Expect = 0.39
Identities = 21/104 (20%), Positives = 38/104 (36%), Gaps = 25/104 (24%)
Query: 413 AELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQAL----------------QNVYH 456
AEL A+ + LE +K+ L + +DSK ++ + +
Sbjct: 46 AELRALIEALEALKE-----LGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVK 100
Query: 457 VSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAAR 500
L ++ ++ V + W+ H G EN+ D AR
Sbjct: 101 NKDLWEELDELLKRHE----LVFWEWVKGHAGHPENERADQLAR 140
>gnl|CDD|217143 pfam02614, UxaC, Glucuronate isomerase. This is a family of
Glucuronate isomerases also known as D-glucuronate
isomerase, uronic isomerase, uronate isomerase, or
uronic acid isomerase, EC:5.3.1.12. This enzyme
catalyzes the reactions: D-glucuronate <=>
D-fructuronate and D-galacturonate <=> D-tagaturonate.
It is not however clear where the experimental evidence
for this functional assignment came from and thus this
family has no literature reference.
Length = 469
Score = 32.2 bits (74), Expect = 0.74
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 2/32 (6%)
Query: 276 MKILSNRNWGLRRETLRRLYYSFA--LPILDY 305
MK + ++ L ET RRLY+ A LPI+DY
Sbjct: 1 MKPFLDEDFLLSNETARRLYHDHAKDLPIIDY 32
>gnl|CDD|222024 pfam13282, DUF4070, Domain of unknown function (DUF4070). This is
a bacterial domain often found at the C-terminus of
Radical_SAM methylases.
Length = 146
Score = 31.0 bits (71), Expect = 0.79
Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 9/61 (14%)
Query: 245 TRYLGLNLDSSLTWKFHIEQTKSKSLKALNVMKILSNRNW--GLRRETLRRLYYSFALPI 302
L KF Q K L+AL ++ + W G+ R+T R ++ L I
Sbjct: 58 VYRQFLEYGPPRPPKFKSPQRSWKDLRAL--LRSI----WRQGILRKT-RWQFWKLLLWI 110
Query: 303 L 303
L
Sbjct: 111 L 111
>gnl|CDD|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in
prokaryotes. Ribonuclease H (RNase H) is classified
into two evolutionarily unrelated families, type 1
(prokaryotic RNase HI, eukaryotic RNase H1 and viral
RNase H) and type 2 (prokaryotic RNase HII and HIII, and
eukaryotic RNase H2). RNase H is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. RNase H is involved in DNA
replication, repair and transcription. RNase H is widely
present in various organisms, including bacteria,
archaea and eukaryotes and most prokaryotic and
eukaryotic genomes contain multiple RNase H genes.
Despite the lack of amino acid sequence homology, Type 1
and type 2 RNase H share a main-chain fold and steric
configurations of the four acidic active-site (DEDD),
residues and have the same catalytic mechanism and
functions in cells. One of the important functions of
RNase H is to remove Okazaki fragments during DNA
replication. Prokaryotic RNase H varies greatly in
domain structures and substrate specificities.
Prokaryotes and some single-cell eukaryotes do not
require RNase H for viability.
Length = 139
Score = 30.2 bits (69), Expect = 1.2
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 477 RVSFLWIPSHLGIRENDNVDHAAR 500
+V++ W+ H G N+ D A
Sbjct: 112 QVTWHWVKGHAGHPGNERADELAN 135
>gnl|CDD|238185 cd00304, RT_like, RT_like: Reverse transcriptase (RT, RNA-dependent
DNA polymerase)_like family. An RT gene is usually
indicative of a mobile element such as a retrotransposon
or retrovirus. RTs occur in a variety of mobile
elements, including retrotransposons, retroviruses,
group II introns, bacterial msDNAs, hepadnaviruses, and
caulimoviruses. These elements can be divided into two
major groups. One group contains retroviruses and DNA
viruses whose propagation involves an RNA intermediate.
They are grouped together with transposable elements
containing long terminal repeats (LTRs). The other
group, also called poly(A)-type retrotransposons,
contain fungal mitochondrial introns and transposable
elements that lack LTRs.
Length = 98
Score = 29.6 bits (67), Expect = 1.3
Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 12/92 (13%)
Query: 183 DIRQGSSLSGDLCNIAT----SDLPQYIPTVVSHGMFVDDLAIFMRGKDMDHIEETLQNT 238
+ QGS LS L N+ + + + + + +VDDL + + + + L+
Sbjct: 11 PLPQGSPLSPALANLYMEKLEAPILKQLLDIT-LIRYVDDLVVIAKSEQQAVKKRELEEF 69
Query: 239 IQFKENTRYLGLNLDSSLTWKFHIEQTKSKSL 270
+ LGLNL T +F ++ K K L
Sbjct: 70 LAR------LGLNLSDEKT-QFTEKEKKFKFL 94
>gnl|CDD|217502 pfam03343, SART-1, SART-1 family. SART-1 is a protein involved in
cell cycle arrest and pre-mRNA splicing. It has been
shown to be a component of U4/U6 x U5 tri-snRNP complex
in human, Schizosaccharomyces pombe and Saccharomyces
cerevisiae. SART-1 is a known tumour antigen in a range
of cancers recognised by T cells.
Length = 603
Score = 29.7 bits (67), Expect = 5.3
Identities = 12/50 (24%), Positives = 18/50 (36%)
Query: 517 KIQFKKIQLGEWSKSWSDNTTTGQKLKKIKPDTRKWKSSMRWKRAEEIVI 566
KI + SD + +K KP +K K R K +E +
Sbjct: 248 KINNVSLDDDSTETPASDYYDVSEMVKFKKPKKKKKKKKKRRKDLDEDEL 297
>gnl|CDD|236005 PRK07376, PRK07376, NAD(P)H-quinone oxidoreductase subunit F;
Validated.
Length = 673
Score = 29.2 bits (66), Expect = 6.3
Identities = 20/54 (37%), Positives = 26/54 (48%), Gaps = 12/54 (22%)
Query: 322 NVVHHTGV-----RLISGAFRTSPIVSI------LAESGIPPLSNL-SKREVVH 363
VV H V RL+ G + PI +I LA SGIPP + SK E++
Sbjct: 369 EVVGHDPVLAQDMRLMGGLRKYMPITAITFLIGCLAISGIPPFAGFWSKDEILG 422
>gnl|CDD|237167 PRK12667, PRK12667, putative monovalent cation/H+ antiporter
subunit D; Reviewed.
Length = 520
Score = 28.8 bits (65), Expect = 8.3
Identities = 15/40 (37%), Positives = 18/40 (45%), Gaps = 9/40 (22%)
Query: 323 VVHHTGVRLI---SGAFRTSPIVSI------LAESGIPPL 353
+H G R I +G R PI S L+ GIPPL
Sbjct: 370 FIHAAGTRDIDELAGLGRKMPIASFAFLIGALSLVGIPPL 409
>gnl|CDD|234108 TIGR03104, trio_amidotrans, asparagine synthase family
amidotransferase. Members of this protein family are
closely related to several isoforms of asparagine
synthetase (glutamine amidotransferase) and typically
have been given this name in genome annotation to date.
Each is part of a conserved three-gene cassette sparsely
distributed across at least twenty different species
known so far, including alpha, beta, and gamma
Proteobacteria, Mycobacterium, and Prosthecochloris,
which is a member of the Chlorobi. The other two members
of the cassette are a probable protease and a member of
the GNAT family of acetyltransferases.
Length = 589
Score = 28.9 bits (65), Expect = 8.5
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 327 TGVRLISGAFRTSPIVSILAESGIPPLSNLS 357
GV L+SG +S IV +LAE+G+ L S
Sbjct: 263 VGV-LLSGGLDSSLIVGLLAEAGVDGLRTFS 292
>gnl|CDD|133345 cd04145, M_R_Ras_like, R-Ras2/TC21, M-Ras/R-Ras3. The
M-Ras/R-Ras-like subfamily contains R-Ras2/TC21,
M-Ras/R-Ras3, and related members of the Ras family.
M-Ras is expressed in lympho-hematopoetic cells. It
interacts with some of the known Ras effectors, but
appears to also have its own effectors. Expression of
mutated M-Ras leads to transformation of several types
of cell lines, including hematopoietic cells, mammary
epithelial cells, and fibroblasts. Overexpression of
M-Ras is observed in carcinomas from breast, uterus,
thyroid, stomach, colon, kidney, lung, and rectum. In
addition, expression of a constitutively active M-Ras
mutant in murine bone marrow induces a malignant mast
cell leukemia that is distinct from the monocytic
leukemia induced by H-Ras. TC21, along with H-Ras, has
been shown to regulate the branching morphogenesis of
ureteric bud cell branching in mice. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 28.1 bits (63), Expect = 9.2
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 38 HDRKITKDEIYNIKRQLPRPYIICSDMNAHN 68
H R+++++E + RQL PYI S + N
Sbjct: 121 HQRQVSREEGQELARQLKIPYIETSAKDRVN 151
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 0.135 0.407
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,619,110
Number of extensions: 2757166
Number of successful extensions: 2175
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2163
Number of HSP's successfully gapped: 33
Length of query: 570
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 468
Effective length of database: 6,413,494
Effective search space: 3001515192
Effective search space used: 3001515192
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 (27.5 bits)