RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3199
(1144 letters)
>gnl|CDD|187699 cd09275, RNase_HI_RT_DIRS1, DIRS1 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 eukaryotes. 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. The structural features of DIRS1-group
elements are different from typical LTR elements. RNase
H inhibitors have been explored as an anti-HIV drug
target because RNase H inactivation inhibits reverse
transcription.
Length = 120
Score = 117 bits (295), Expect = 8e-31
Identities = 49/118 (41%), Positives = 72/118 (61%)
Query: 871 VTSDASDSGWGARVDNRMIKGSWTECQKKWHINVKELFAVQMSLEKNLAYVQNKVVLIQS 930
+ +DAS SGWGA + +G W+ ++ HIN EL AV ++L+ A + N+ VL++S
Sbjct: 2 LFTDASLSGWGAVLSGSWAQGLWSAEERNKHINFLELLAVLLALQHWGARLSNRKVLVRS 61
Query: 931 DNLTVVCYIQKQGGTKSINLLRGVEEIFRIATVHNITVQAQYIPGMYNNIADSLSRSQ 988
DN T V YI +QGGT+S LL ++ NI ++A++IPG+ N AD LSR Q
Sbjct: 62 DNTTAVAYINRQGGTRSPELLALARQLVLWCEERNIWLRARHIPGVLNVAADRLSRLQ 119
>gnl|CDD|187698 cd09274, RNase_HI_RT_Ty3, Ty3/Gypsy 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 eukaryotes. 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. Ty3/Gypsy family widely distributed among
the genomes of plants, fungi and animals. RNase H
inhibitors have been explored as an anti-HIV drug target
because RNase H inactivation inhibits reverse
transcription.
Length = 121
Score = 53.6 bits (130), Expect = 2e-08
Identities = 35/135 (25%), Positives = 59/135 (43%), Gaps = 35/135 (25%)
Query: 870 FVTSDASDSGWGARVDNRMIKGSW----------TECQKKWHINVKELFAVQMSLEKNLA 919
+ +DASD G GA V +++ G T ++ + KEL A+ +L+K
Sbjct: 1 VLETDASDFGIGA-VLSQLDDGKERPIAFASRKLTPAERNYSTYEKELLAIVFALKKFRH 59
Query: 920 YVQNKVVLIQSD--NLTVVCYIQKQGGTKSIN--LLRGVEEI----FRIATVHNITVQAQ 971
Y+ + + +D +L Y+ + K +N L R + + F I +
Sbjct: 60 YLLGRKFTVYTDHKSLK---YLLTK---KDLNPRLARWLLLLQEFDFEI----------E 103
Query: 972 YIPGMYNNIADSLSR 986
Y PG N +AD+LSR
Sbjct: 104 YRPGKENVVADALSR 118
>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 = 38.9 bits (91), Expect = 0.002
Identities = 25/127 (19%), Positives = 44/127 (34%), Gaps = 21/127 (16%)
Query: 873 SDASDS------GWGA-----RVDNRMIKGSWTECQKKWHINVKELFAVQMSLEKNLAYV 921
+D S G G N EL A+ +LE +
Sbjct: 2 TDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAA---TNNEAELLALLEALEL-ALDL 57
Query: 922 QNKVVLIQSDNLTVVCYIQKQGGTKSINLLRGVEEIFRI--ATVHNITVQAQYIPGMYNN 979
K ++I++D+ VV I N L ++ I I ++ +++P N
Sbjct: 58 GLKKLIIETDSKYVVDLINSWSKGWKKNNL----LLWDILLLLSKFIDIRFEHVPREGNE 113
Query: 980 IADSLSR 986
+AD L++
Sbjct: 114 VADRLAK 120
>gnl|CDD|187703 cd09279, RNase_HI_archaeal_like, RNAse HI family that includes
Archaeal RNase HI. 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. Most archaeal genomes contain
only type 2 RNase H (RNase HII); however, a few contain
RNase HI as well. Although archaeal RNase HI sequences
conserve the DEDD active-site motif, they lack other
common features important for catalytic function, such
as the basic protrusion region. Archaeal RNase HI
homologs are more closely related to retroviral RNase HI
than bacterial and eukaryotic type I RNase H in
enzymatic properties.
Length = 128
Score = 33.3 bits (77), Expect = 0.19
Identities = 24/84 (28%), Positives = 36/84 (42%), Gaps = 2/84 (2%)
Query: 903 NVKELFAVQMSLEKNLAYVQNKVVLIQSDNLTVVCYIQKQGGTKSINLLRGVEEIFRIAT 962
N E A+ LE L K + I D+ VV IQ + K+ L +EE +
Sbjct: 43 NEAEYEALIAGLELALEL-GIKKLEIYGDSQLVVNQIQGEYEVKNERLAPYLEEARELLK 101
Query: 963 VHNITVQAQYIPGMYNNIADSLSR 986
V+ ++IP N AD+L+
Sbjct: 102 -KFEEVEIKWIPREENKEADALAN 124
>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 = 29.8 bits (68), Expect = 1.8
Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 926 VLIQSDNLTVVCYIQKQGGTKSI--NLLRGVEEIFRIATVHNITVQAQYIPGMYNNIADS 983
++++SD+ VV IQ + +S LLR + ++ + +V ++P N +AD+
Sbjct: 25 LIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLK----KFDSVSVSHVPRECNRVADA 80
Query: 984 LSR 986
L++
Sbjct: 81 LAK 83
>gnl|CDD|203567 pfam07017, PagP, Antimicrobial peptide resistance and lipid A
acylation protein PagP. This family consists of several
bacterial antimicrobial peptide resistance and lipid A
acylation (PagP) proteins. The bacterial outer membrane
enzyme PagP transfers a palmitate chain from a
phospholipid to lipid A. In a number of pathogenic
Gram-negative bacteria, PagP confers resistance to
certain cationic antimicrobial peptides produced during
the host innate immune response.
Length = 147
Score = 30.8 bits (70), Expect = 2.0
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 965 NITVQAQYIPGMYNN 979
+T QA YIPG YNN
Sbjct: 124 QLTFQATYIPGTYNN 138
>gnl|CDD|178695 PLN03150, PLN03150, hypothetical protein; Provisional.
Length = 623
Score = 31.7 bits (72), Expect = 2.5
Identities = 29/93 (31%), Positives = 41/93 (44%), Gaps = 14/93 (15%)
Query: 870 FVTSDASDSGWGARVDNRMIKGSWTECQKKWHINVKELFAVQMSLEKNLAYVQNKVVLIQ 929
F D S + G RV + +I G K++ V+MS E+ A V NK V +
Sbjct: 286 FAEIDNSITAEGKRVFDVLING---------DTAFKDVDIVKMSGERYTALVLNKTVAVS 336
Query: 930 SDNLTVVCYIQKQGGTKSINLLRGVEEIFRIAT 962
LT+V K+G IN + E+F I T
Sbjct: 337 GRTLTIV-LQPKKGTHAIINAI----EVFEIIT 364
>gnl|CDD|185536 PTZ00275, PTZ00275, biotin-acetyl-CoA-carboxylase ligase;
Provisional.
Length = 285
Score = 31.3 bits (71), Expect = 2.6
Identities = 16/43 (37%), Positives = 24/43 (55%)
Query: 922 QNKVVLIQSDNLTVVCYIQKQGGTKSINLLRGVEEIFRIATVH 964
++K VLI DN +V Y+Q S+ LLR ++ R+ T H
Sbjct: 236 KDKKVLIDQDNELIVGYLQGLLHDGSLLLLREKNKLVRVNTGH 278
>gnl|CDD|235718 PRK06154, PRK06154, hypothetical protein; Provisional.
Length = 565
Score = 31.3 bits (71), Expect = 3.0
Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 19/76 (25%)
Query: 402 PAIRVP---PRILKDIPP-------------SEEYLFDPKSLAEAMRAQSSSGKNGKQRI 445
P + +P PR D+ P E + P + E MR + +NG+
Sbjct: 109 PVLFLPTGYPRGSTDVAPNFESLRNYRHITKWCEQVTLPDEVPELMRRAFTRLRNGRPG- 167
Query: 446 PSIPSVNINVDMMSEP 461
P + + + VD+++E
Sbjct: 168 PVV--LELPVDVLAEE 181
>gnl|CDD|176513 cd08571, GDPD_SHV3_plant, Glycerophosphodiester phosphodiesterase
domain of glycerophosphodiester phosphodiesterase-like
protein SHV3 and SHV3-like proteins. This subfamily
corresponds to the glycerophosphodiester
phosphodiesterase (GDPD) domain present in
glycerophosphodiester phosphodiesterase (GP-GDE)-like
protein SHV3 and SHV3-like proteins (SVLs), which may
play an important role in cell wall organization. The
prototype of this family is a
glycosylphosphatidylinositol (GPI) anchored protein SHV3
encoded by shaven3 (shv3) gene from Arabidopsis
thaliana. Members in this family show sequence homology
to bacterial GP-GDEs (EC 3.1.4.46) that catalyze the
hydrolysis of various glycerophosphodiesters, and
produce sn-glycerol-3-phosphate (G3P) and the
corresponding alcohols. Both, SHV3 and SVLs, have two
tandemly repeated GDPD domains whose biochemical
functions remain unclear. The residues essential for
interactions with the substrates and calcium ions in
bacterial GP-GDEs are not conserved in SHV3 and SVLs,
which suggests that the function of GDPD domains in
these proteins might be distinct from those in typical
bacterial GP-GDEs. In addition, the two tandem repeats
show low sequence similarity to each other, suggesting
they have different biochemical function. Most members
of this family are Arabidopsis-specific gene products.
To date, SHV3 orthologues are only found in
Physcomitrella patens.
Length = 302
Score = 31.1 bits (71), Expect = 3.3
Identities = 17/59 (28%), Positives = 28/59 (47%)
Query: 909 AVQMSLEKNLAYVQNKVVLIQSDNLTVVCYIQKQGGTKSINLLRGVEEIFRIATVHNIT 967
AV SL K K V I S + +V+ +K+ GTK + + V++ + N+T
Sbjct: 154 AVLTSLSKAGYDQTAKKVYISSPDSSVLKSFKKRVGTKLVFRVLDVDDTEPDTLLSNLT 212
>gnl|CDD|182241 PRK10100, PRK10100, DNA-binding transcriptional regulator CsgD;
Provisional.
Length = 216
Score = 30.6 bits (69), Expect = 3.5
Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 7/47 (14%)
Query: 58 LNKLRFALPTLEIVRAFDPSANCLKEYPYRDMKK-------KMLSWA 97
LNKLR EI R+ S N +K + Y KK + +SWA
Sbjct: 164 LNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWA 210
>gnl|CDD|143635 cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain.
Diguanylate-cyclase (DGC) or GGDEF domain: Originally
named after a conserved residue pattern, and initially
described as a domain of unknown function 1 (DUF1). This
domain is widely present in bacteria, linked to a wide
range of non-homologous domains in a variety of cell
signaling proteins. The domain shows homology to the
adenylyl cyclase catalytic domain. This correlates with
the functional information available on two
GGDEF-containing proteins, namely diguanylate cyclase
and phosphodiesterase A of Acetobacter xylinum, both of
which regulate the turnover of cyclic diguanosine
monophosphate. Together with the EAL domain, GGDEF might
be involved in regulating cell surface adhesion in
bacteria.
Length = 158
Score = 29.8 bits (68), Expect = 4.1
Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 7/50 (14%)
Query: 108 AFSKQIRGSSHSHDIVAR-------AVAPLKSEFVSRETADRILSNIEKP 150
++++R S D+VAR + P + A+R+ IE+P
Sbjct: 60 EVAERLRSSLRESDLVARLGGDEFAILLPGTDLEEAEALAERLREAIEEP 109
>gnl|CDD|236829 PRK11045, pagP, phospholipid:lipid A palmitoyltransferase;
Provisional.
Length = 184
Score = 30.0 bits (68), Expect = 4.9
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 966 ITVQAQYIPGMYNN 979
+T Q YIPG YNN
Sbjct: 159 LTFQMTYIPGTYNN 172
>gnl|CDD|240415 PTZ00429, PTZ00429, beta-adaptin; Provisional.
Length = 746
Score = 30.3 bits (68), Expect = 6.8
Identities = 19/96 (19%), Positives = 39/96 (40%), Gaps = 16/96 (16%)
Query: 183 MGRINETINS---LFSR-LQSELP--AFNREESSHSETEESEFPERDVSPPPDSWEAPP- 235
M + +++N+ +F+R QS LP E +TE+ + E +P + + P
Sbjct: 576 MADLKKSLNTAAIVFARPYQSFLPPYGLADVELDEEDTEDDDAVELPSTPSMGTQDGSPA 635
Query: 236 ---------LFDSPEEITVSPDLPFSFAPCVKEREP 262
+F+ + T +P S + + +P
Sbjct: 636 PSAAPAGYDIFEFAGDGTGAPHPVASGSNGAQHADP 671
Score = 30.3 bits (68), Expect = 6.8
Identities = 19/96 (19%), Positives = 39/96 (40%), Gaps = 16/96 (16%)
Query: 541 MGRINETINS---LFSR-LQSELP--AFNREESSHSETEESEFPERDVSPPPDSWEAPP- 593
M + +++N+ +F+R QS LP E +TE+ + E +P + + P
Sbjct: 576 MADLKKSLNTAAIVFARPYQSFLPPYGLADVELDEEDTEDDDAVELPSTPSMGTQDGSPA 635
Query: 594 ---------LFDSPEEITVSPDLPFSFAPCVKEREP 620
+F+ + T +P S + + +P
Sbjct: 636 PSAAPAGYDIFEFAGDGTGAPHPVASGSNGAQHADP 671
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
0.317 0.132 0.392
Gapped
Lambda K H
0.267 0.0779 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 59,422,088
Number of extensions: 5959468
Number of successful extensions: 5269
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5260
Number of HSP's successfully gapped: 38
Length of query: 1144
Length of database: 10,937,602
Length adjustment: 107
Effective length of query: 1037
Effective length of database: 6,191,724
Effective search space: 6420817788
Effective search space used: 6420817788
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: 64 (28.3 bits)