RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6829
(369 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 = 95.8 bits (239), Expect = 4e-24
Identities = 40/133 (30%), Positives = 58/133 (43%), Gaps = 14/133 (10%)
Query: 154 WYSDFPVVDLSLYGSKTIQNTSCAVYA--GGSA-KSYILNNINSIFTAELLALVFCLDSV 210
Y+D GSK T G+ +SY L S+F AELLA++ L
Sbjct: 2 IYTD---------GSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLA 52
Query: 211 KNRPD-VNTLIVC-DSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTG 268
+ + DS +AL ++ + +S PL+ I L + G KV W P H+G
Sbjct: 53 LREGRRARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSG 112
Query: 269 ISGNEIVDRATRQ 281
I GNE DR ++
Sbjct: 113 IEGNERADRLAKE 125
>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 = 58.0 bits (141), Expect = 1e-10
Identities = 30/93 (32%), Positives = 43/93 (46%), Gaps = 11/93 (11%)
Query: 193 NSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSI----ANKNTSIPLIAHILNTW 248
+ AELLAL+ L+++ + VN I DS + I K+ S P+ I
Sbjct: 38 TTNQRAELLALIEALEALSGQK-VN--IYTDSQYVIGGITNGWPTKSESKPIKNEIWE-- 92
Query: 249 HTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQ 281
L KV W P H+GI GNE+ D+ +Q
Sbjct: 93 --LLQKKHKVYIQWVPGHSGIPGNELADKLAKQ 123
>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 = 41.6 bits (98), Expect = 9e-05
Identities = 21/92 (22%), Positives = 34/92 (36%), Gaps = 4/92 (4%)
Query: 190 NNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWH 249
+ AELLAL+ L+ + +I DS + I + + +L
Sbjct: 34 IPAATNNEAELLALLEALELALDLGLKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDIL 93
Query: 250 TLKSCGKKVAFLWCPSHTGISGNEIVDRATRQ 281
L S + F P GNE+ DR ++
Sbjct: 94 LLLSKFIDIRFEHVPR----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 = 36.5 bits (85), Expect = 0.005
Identities = 31/102 (30%), Positives = 42/102 (41%), Gaps = 22/102 (21%)
Query: 197 TAELLALVFCLDSVKNRPDVNTLIVCDS---MSALTSIA------NKNTSIPLIAH---I 244
AEL+AL+ L+ K +P VN I DS L ++ T P IA I
Sbjct: 37 RAELIALIRALELAKGKP-VN--IYTDSAYAFGILHALETIWKERGFLTGKP-IALASLI 92
Query: 245 LNTWHTLKSCGKKVAFLWCPSHTG-----ISGNEIVDRATRQ 281
L + K VA + +H+G GN D+A RQ
Sbjct: 93 LQLQKAI-QRPKPVAVIHIRAHSGLPGPLALGNARADQAARQ 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 = 33.3 bits (77), Expect = 0.076
Identities = 28/102 (27%), Positives = 38/102 (37%), Gaps = 26/102 (25%)
Query: 198 AELLALVFCLDSVKNR--PDVNTLIVCDSM--------------------SALTSIANKN 235
AEL A++ L +K +I DS S +ANK+
Sbjct: 46 AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKD 105
Query: 236 TSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDR 277
LI + L+ G +V F P H+GI GNE DR
Sbjct: 106 ----LIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADR 143
>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 = 32.1 bits (74), Expect = 0.19
Identities = 10/30 (33%), Positives = 12/30 (40%), Gaps = 1/30 (3%)
Query: 255 GKKVAFLWCPSHTGISGNEIVDR-ATRQLD 283
+V + W H G GNE D A D
Sbjct: 110 KHQVTWHWVKGHAGHPGNERADELANAAAD 139
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 31.2 bits (71), Expect = 0.40
Identities = 25/105 (23%), Positives = 37/105 (35%), Gaps = 17/105 (16%)
Query: 190 NNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDS---MSALTSIANKN------TSIPL 240
NN AEL AL+ L+++K + DS + +T K T+
Sbjct: 43 NN-----RAELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKK 97
Query: 241 IAHILNTWHTLKSCGK---KVAFLWCPSHTGISGNEIVDRATRQL 282
+ W L K V + W H G NE D+ R+
Sbjct: 98 PVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREA 142
>gnl|CDD|187701 cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI containing a
hybrid binding domain (HBD) at the N-terminus.
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 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. Some bacteria
distinguished from other bacterial RNase HI in the
presence of a hybrid binding domain (HBD) at the
N-terminus which is commonly present at the N-termini of
eukaryotic RNase HI. It has been reported that this
domain is required for dimerization and processivity of
RNase HI upon binding to RNA-DNA hybrids.
Length = 133
Score = 29.8 bits (68), Expect = 0.89
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 257 KVAFLWCPSHTGISGNEIVDR 277
K++F+ +H+G NE+ D+
Sbjct: 107 KISFVKVKAHSGDKYNELADK 127
>gnl|CDD|168661 PRK06753, PRK06753, hypothetical protein; Provisional.
Length = 373
Score = 30.0 bits (68), Expect = 2.1
Identities = 14/30 (46%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 1 MNVLKIVSN-KNYGLHRQTLLKLYQSYVSP 29
+N +K+ SN N LHRQTL+ + +SYV
Sbjct: 81 LNKVKLKSNTLNVTLHRQTLIDIIKSYVKE 110
>gnl|CDD|199847 cd03865, M14_CPE, Peptidase M14 carboxypeptidase subfamily
N/E-like; Carboxypeptidase E subgroup. Peptidase M14
Carboxypeptidase (CP) E (CPE, also known as
carboxypeptidase H, and enkephalin convertase; EC
3.4.17.10) belongs to the N/E subfamily of the M14
family of metallocarboxypeptidases (MCPs).The M14 family
are zinc-binding CPs which hydrolyze single, C-terminal
amino acids from polypeptide chains, and have a
recognition site for the free C-terminal carboxyl group,
which is a key determinant of specificity. CPE is an
important enzyme responsible for the proteolytic
processing of prohormone intermediates (such as
pro-insulin, pro-opiomelanocortin, or
pro-gonadotropin-releasing hormone) by specifically
removing C-terminal basic residues. In addition, it has
been proposed that the regulated secretory pathway (RSP)
of the nervous and endocrine systems utilizes
membrane-bound CPE as a sorting receptor. A naturally
occurring point mutation in CPE reduces the stability of
the enzyme and causes its degradation, leading to an
accumulation of numerous neuroendocrine peptides that
result in obesity and hyperglycemia. Reduced CPE enzyme
and receptor activity could underlie abnormal placental
phenotypes from the observation that CPE is
down-regulated in enlarged placentas of interspecific
hybrid (interspecies hybrid placental dysplasia, IHPD)
and cloned mice.
Length = 323
Score = 29.2 bits (65), Expect = 3.8
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 137 AVLKNTKVVPYSQGFPPWYSDFP-VVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSI 195
AV +NTK+ P ++ W D P V+ +L+G + N GSA Y ++I
Sbjct: 170 AVDENTKLAPETKAVIHWIMDIPFVLSANLHGGDLVANYPYDETRSGSAHEYSACPDDAI 229
Query: 196 FTA 198
F +
Sbjct: 230 FKS 232
>gnl|CDD|179877 PRK04778, PRK04778, septation ring formation regulator EzrA;
Provisional.
Length = 569
Score = 28.6 bits (65), Expect = 5.4
Identities = 5/15 (33%), Positives = 10/15 (66%)
Query: 306 EKWQKSWSDLTNNKL 320
E+W++ W ++ N L
Sbjct: 67 EEWRQKWDEIVTNSL 81
>gnl|CDD|219683 pfam07986, TBCC, Tubulin binding cofactor C. Members of this
family are involved in the folding pathway of tubulins
and form a beta helix structure.
Length = 119
Score = 27.2 bits (61), Expect = 5.8
Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 1/53 (1%)
Query: 313 SDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDP 365
+ + + P G + DC N V ++RI YL T S P
Sbjct: 26 DNCKDCTIILG-PVSGSVFIRDCENCTIVVACRQLRIHDCTNCDFYLHTTSRP 77
>gnl|CDD|114855 pfam06160, EzrA, Septation ring formation regulator, EzrA. During
the bacterial cell cycle, the tubulin-like cell-division
protein FtsZ polymerises into a ring structure that
establishes the location of the nascent division site.
EzrA modulates the frequency and position of FtsZ ring
formation.
Length = 559
Score = 28.7 bits (65), Expect = 6.1
Identities = 7/34 (20%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 306 EKWQKSWSDLTNNKLKCVKPTIGPWNVSDCNNRY 339
E+W++ W D+ N L ++ + + N+++
Sbjct: 63 EEWRQKWDDIVTNSLPDIEELLF--EAEELNDKF 94
>gnl|CDD|216158 pfam00860, Xan_ur_permease, Permease family. This family includes
permeases for diverse substrates such as xanthine,
uracil, and vitamin C. However many members of this
family are functionally uncharacterized and may
transport other substrates. Members of this family have
ten predicted transmembrane helices.
Length = 389
Score = 28.4 bits (64), Expect = 6.3
Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 6/79 (7%)
Query: 216 VNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVA------FLWCPSHTGI 269
V L+V D++ + S +A + T G ++ F + +
Sbjct: 20 VVPLLVGDALGLGAEDLAQLISATFLASGIGTLLQTLIFGIRLPIYLGSSFAFVTALMIA 79
Query: 270 SGNEIVDRATRQLDGAEFV 288
G A L GA V
Sbjct: 80 IGGADWGIALAGLFGAVLV 98
>gnl|CDD|184179 PRK13608, PRK13608, diacylglycerol glucosyltransferase;
Provisional.
Length = 391
Score = 28.2 bits (63), Expect = 7.2
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 8/55 (14%)
Query: 278 ATRQLDGAEFVNLSSPADLISVGKKYIHEKW-----QKSWSDLTNNKLKCVKPTI 327
AT++ +F+++ + V I K+ QK W L +N L K TI
Sbjct: 154 ATKETK-QDFIDVGIDPSTVKVTGIPIDNKFETPIDQKQW--LIDNNLDPDKQTI 205
>gnl|CDD|212098 cd10786, GH38N_AMII_like, N-terminal catalytic domain of class II
alpha-mannosidases and similar proteins; glycoside
hydrolase family 38 (GH38). Alpha-mannosidases (EC
3.2.1.24) are extensively found in eukaryotes and play
important roles in the processing of newly formed
N-glycans and in degradation of mature glycoproteins. A
deficiency of this enzyme causes the lysosomal storage
disease alpha-mannosidosis. Many bacterial and archaeal
species also possess putative alpha-mannosidases, but
their activity and specificity is largely unknown.
Based on different functional characteristics and
sequence homology, alpha-mannosidases have been
organized into two classes (class I, belonging to
glycoside hydrolase family 47, and class II, belonging
to glycoside hydrolase family 38). Members of this
family corresponds to class II alpha-mannosidases
(alphaMII), which contain intermediate Golgi
alpha-mannosidases II, acidic lysosomal
alpha-mannosidases, animal sperm and epididymal alpha
-mannosidases, neutral ER/cytosolic alpha-mannosidases,
and some putative prokaryotic alpha-mannosidases.
AlphaMII possess a-1,3, a-1,6, and a-1,2 hydrolytic
activity, and catalyzes the degradation of N-linked
oligosaccharides. The N-terminal catalytic domain of
alphaMII adopts a structure consisting of parallel
7-stranded beta/alpha barrel. Members in this family are
retaining glycosyl hydrolases of family GH38 that
employs a two-step mechanism involving the formation of
a covalent glycosyl enzyme complex. Two carboxylic acids
positioned within the active site act in concert: one as
a catalytic nucleophile and the other as a general
acid/base catalyst.
Length = 251
Score = 27.7 bits (62), Expect = 9.6
Identities = 5/25 (20%), Positives = 12/25 (48%)
Query: 328 GPWNVSDCNNRYEEVVLTRVRIGHT 352
G + + D N E ++ ++ +G
Sbjct: 81 GGYVMPDTNLPDGESLVRQILLGKR 105
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
0.319 0.135 0.413
Gapped
Lambda K H
0.267 0.0619 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,236,631
Number of extensions: 1690078
Number of successful extensions: 1230
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1228
Number of HSP's successfully gapped: 23
Length of query: 369
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 271
Effective length of database: 6,590,910
Effective search space: 1786136610
Effective search space used: 1786136610
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: 60 (27.1 bits)