RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4967
(354 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 = 110 bits (277), Expect = 8e-30
Identities = 49/129 (37%), Positives = 64/129 (49%), Gaps = 7/129 (5%)
Query: 144 VVYTDASKNDVAVSSAFCSQDTKFSSRLHPLLSIC---NAELTAILFAIHFSISAHLNNV 200
V+YTD SK + + F SR + L C +AEL AIL A+ A
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQL---ALREGR 57
Query: 201 NRAYLVICSDSLSALQTLQNIFSLNPIAGEIR-DLILTNKSKLNVRFIWVPSHVGIAGNE 259
+ I SDS +AL+ L++ S +P+ IR + + VR WVP H GI GNE
Sbjct: 58 RARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNE 117
Query: 260 EADRLAKEA 268
ADRLAKEA
Sbjct: 118 RADRLAKEA 126
>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 = 73.1 bits (180), Expect = 6e-16
Identities = 41/137 (29%), Positives = 56/137 (40%), Gaps = 19/137 (13%)
Query: 140 PDSTVVYTDAS--KNDVAVSSAFCSQDTK-FSSRLHPLLSICNAELTAILFAIHFSISAH 196
P++ VYTD S N + + + K S L P + AEL A++ A+
Sbjct: 1 PEAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPL-PGTTNQRAELLALIEALEALSGQK 59
Query: 197 LNNVNRAYLVICSDSL----SALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFIWVPSH 252
+N I +DS PI EI +L+ K V WVP H
Sbjct: 60 VN--------IYTDSQYVIGGITNGWPTKSESKPIKNEIWELLQ---KKHKVYIQWVPGH 108
Query: 253 VGIAGNEEADRLAKEAL 269
GI GNE AD+LAK+
Sbjct: 109 SGIPGNELADKLAKQGA 125
>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 = 58.0 bits (141), Expect = 2e-10
Identities = 33/109 (30%), Positives = 50/109 (45%), Gaps = 24/109 (22%)
Query: 180 AELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTL--------QNIFSLNPIAGEI 231
AEL A++ A+ I + + LVI +DS + + +N + + G+
Sbjct: 46 AELRAVIHALRL-IKEVGEGLTK--LVIATDSEYVVNGVTEWIPKWKKNGWKTS--KGKP 100
Query: 232 ---RDLIL--------TNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 269
+DLI + + V+F VP H GI GNEEADRLAK+
Sbjct: 101 VANKDLIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKGA 149
>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 = 53.3 bits (129), Expect = 7e-09
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 225 NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 269
E ++ + K K+ + F+ V +H G NE AD+LAK+AL
Sbjct: 89 KEGTKEYKEFMDKIKKKIKISFVKVKAHSGDKYNELADKLAKKAL 133
>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 = 47.7 bits (114), Expect = 5e-07
Identities = 29/98 (29%), Positives = 45/98 (45%), Gaps = 10/98 (10%)
Query: 173 PLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQN-IFSLNPIAGEI 231
P + AEL A+L A+ ++ L L+I +DS + + + +
Sbjct: 35 PAATNNEAELLALLEAL--ELALDLGLKK---LIIETDSKYVVDLINSWSKGWKKNNLLL 89
Query: 232 RDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 269
D++L +++RF VP GNE ADRLAKEA
Sbjct: 90 WDILLLLSKFIDIRFEHVPRE----GNEVADRLAKEAA 123
>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 = 47.1 bits (113), Expect = 1e-06
Identities = 14/29 (48%), Positives = 16/29 (55%)
Query: 240 SKLNVRFIWVPSHVGIAGNEEADRLAKEA 268
+K V + WV H G GNE AD LA A
Sbjct: 109 AKHQVTWHWVKGHAGHPGNERADELANAA 137
>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 = 43.0 bits (102), Expect = 3e-05
Identities = 34/147 (23%), Positives = 50/147 (34%), Gaps = 33/147 (22%)
Query: 144 VVYTDASK-NDVAVSSAFCSQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNR 202
V+TD S A + D + L S AEL A++ A+ + +N
Sbjct: 1 TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALELAKGKPVN---- 56
Query: 203 AYLVICSDSLSALQTLQNI---------FSLNPIAG--EIRDLI----LTNKSKLNVRFI 247
I +DS A L + + PIA I L V I
Sbjct: 57 ----IYTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKP----VAVI 108
Query: 248 WVPSHVG-----IAGNEEADRLAKEAL 269
+ +H G GN AD+ A++A
Sbjct: 109 HIRAHSGLPGPLALGNARADQAARQAA 135
>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 = 42.1 bits (100), Expect = 5e-05
Identities = 25/96 (26%), Positives = 39/96 (40%), Gaps = 17/96 (17%)
Query: 180 AELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF-----SLNPIAGEIRDL 234
AE A++ + ++ + L I DS + +Q + L P E R+L
Sbjct: 45 AEYEALIAGLELALELGIKK-----LEIYGDSQLVVNQIQGEYEVKNERLAPYLEEAREL 99
Query: 235 ILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALT 270
+ K V W+P N+EAD LA +AL
Sbjct: 100 L---KKFEEVEIKWIPRE----ENKEADALANQALD 128
>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 = 39.9 bits (94), Expect = 1e-04
Identities = 27/96 (28%), Positives = 40/96 (41%), Gaps = 16/96 (16%)
Query: 180 AELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNI-FSLNPIAG---EIRDLI 235
AE A+L + ++ + L++ SDS +Q +Q + + +A EIR L+
Sbjct: 5 AEAEALLEGLQLALELGIRR-----LIVESDSQLVVQQIQGEYEARSRLAALLREIRKLL 59
Query: 236 LTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS 271
S V VP N AD LAK A S
Sbjct: 60 KKFDS---VSVSHVPRE----CNRVADALAKLASAS 88
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 39.0 bits (92), Expect = 8e-04
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 243 NVRFIWVPSHVGIAGNEEADRLAKEA 268
+++ WV H G NE D LA+
Sbjct: 114 QIKWHWVKGHAGHPENERCDELARAG 139
>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 = 38.4 bits (90), Expect = 0.001
Identities = 33/126 (26%), Positives = 49/126 (38%), Gaps = 16/126 (12%)
Query: 144 VVYTDASKNDVAVSSAFCSQ--DTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVN 201
V++TDAS + A S S I EL A+L A+ A L+N
Sbjct: 1 VLFTDASLSGWG---AVLSGSWAQGLWSAEERNKHINFLELLAVLLALQ-HWGARLSN-- 54
Query: 202 RAYLVICSDSLSALQTL--QNIFSLNPIAGEIRDLIL-TNKSKLNVRFIWVPSHVGIAGN 258
R LV D+ +A+ + Q + R L+L + + +R +P N
Sbjct: 55 RKVLVRS-DNTTAVAYINRQGGTRSPELLALARQLVLWCEERNIWLRARHIPG----VLN 109
Query: 259 EEADRL 264
ADRL
Sbjct: 110 VAADRL 115
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 38.5 bits (90), Expect = 0.001
Identities = 15/37 (40%), Positives = 19/37 (51%)
Query: 232 RDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEA 268
+L K V + WV H G NE AD+LA+EA
Sbjct: 106 EELDELLKRHELVFWEWVKGHAGHPENERADQLAREA 142
>gnl|CDD|75628 PRK06548, PRK06548, ribonuclease H; Provisional.
Length = 161
Score = 32.9 bits (74), Expect = 0.11
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 233 DLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKR 290
D ++ N+ N+R WV +H G NE AD LA++A + IP P + S +
Sbjct: 107 DSLMENR---NIRMSWVNAHTGHPLNEAADSLARQAANNFSTRSAHIPGPGWTERSAK 161
>gnl|CDD|236334 PRK08719, PRK08719, ribonuclease H; Reviewed.
Length = 147
Score = 31.4 bits (71), Expect = 0.32
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 239 KSKLNVRFIWVPSHVGIAGNEEADRLAKEA 268
+++ V V +H GI GNE AD LA+ A
Sbjct: 115 RARKYVEVEKVTAHSGIEGNEAADMLAQAA 144
>gnl|CDD|180903 PRK07238, PRK07238, bifunctional RNase H/acid phosphatase;
Provisional.
Length = 372
Score = 31.9 bits (73), Expect = 0.55
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 7/47 (14%)
Query: 223 SLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 269
+ P+A + R+L V + W+P A N ADRLA EA+
Sbjct: 91 DMKPLAAQARELASQFGR---VTYTWIPR----ARNAHADRLANEAM 130
>gnl|CDD|177388 PHA02554, 13, neck protein; Provisional.
Length = 311
Score = 29.7 bits (67), Expect = 2.0
Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 10/77 (12%)
Query: 188 AIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLN-PIAGEIRDLILTNKSKL---- 242
A+ H + VN+ YL ++ Q +F L+ + ++ TN +
Sbjct: 40 ALELYGEYHYDGVNKGYLKF---KVTEEQARTGVFDLSGSNVFAVTKILRTNAGSITSMD 96
Query: 243 -NVRFIWVPSHV-GIAG 257
+ W V G+AG
Sbjct: 97 GTATYPWFTDFVLGLAG 113
>gnl|CDD|226624 COG4143, TbpA, ABC-type thiamine transport system, periplasmic
component [Coenzyme metabolism].
Length = 336
Score = 29.6 bits (67), Expect = 2.2
Identities = 19/76 (25%), Positives = 28/76 (36%), Gaps = 7/76 (9%)
Query: 76 RIRGKLLLEKYGIDHLDFLSPSPQTSAPWLIEPP--PVDYSLRKFNKDTDSKEEINISFQ 133
R R L YG+D S P W I+ P DY F D + S +
Sbjct: 95 RARETGLFAPYGVD----ASDVPV-PEGWKIDTFALPYDYGYFAFVYDKTKLKNPPKSLK 149
Query: 134 ELLQKTPDSTVVYTDA 149
+L++ ++Y D
Sbjct: 150 DLVEPEYAGKIIYQDP 165
>gnl|CDD|193535 cd05659, M18_API, M18 Peptidase Aminopeptidase I. Peptidase M18
family, Aminopeptidase I (Vacuolar aminopeptidase I;
Polypeptidase; Leucine aminopeptidase IV; LAPIV;
Aminopeptidase III; Aminopeptidase yscI; EC 3.4.11.22)
subfamily. Aminopeptidase I is widely distributed in
bacteria and eukaryotes, but only the yeast enzyme has
been characterized to date. It is a vacuolar enzyme,
synthesized as a cytosolic proform, and proteolytically
matured upon arrival in the vacuole. The
pro-aminopeptidase I (proAPI) does not enter the vacuole
via the secretory pathway. In non-starved cells, it uses
the cytoplasm to vacuole targeting (cvt) pathway and in
cells starved for nitrogen, it is targeted to the
vacuole via autophagy. Yeast aminopeptidase I is active
only in its dodecameric form with broad substrate
specificity, acting on all aminoacyl and peptidyl
derivatives that contain a free alpha-amino group; this
is in contrast to the highly selective M18 mammalian
aspartyl aminopeptidase. N-terminal leucine and most
other hydrophobic amino acid residues are the best
substrates while glycine and charged amino acid residues
in P1 position are cleaved much more slowly. This enzyme
is strongly and specifically activated by zinc (Zn2+)
and chloride (Cl-) ions.
Length = 443
Score = 29.0 bits (66), Expect = 3.9
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 80 KLLLEKYGIDHLDFLS 95
KLL EKYGI DF+S
Sbjct: 201 KLLNEKYGITEEDFIS 216
>gnl|CDD|129392 TIGR00291, RNA_SBDS, rRNA metabolism protein, SBDS family. This
protein family, possibly universal in both archaea and
eukaryotes, appears to be involved in (ribosomal) RNA
metabolism. Mutations in the human ortholog are
associated with Shwachman-Bodian-Diamond syndrome
[Protein synthesis, Other].
Length = 231
Score = 28.3 bits (63), Expect = 4.9
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 119 NKDTDSKEEINISFQELLQKTPDSTVVYTDASKNDVA 155
D +E I + F+++L V+ DASK + A
Sbjct: 26 YLAADLREGIEVDFEDVLA----IEEVFRDASKGEKA 58
>gnl|CDD|221126 pfam11518, DUF3221, Protein of unknown function (DUF3221). This
family of proteins with unknown function appears to be
restricted to Bacillus. Some members in this family of
proteins are annotated as YobA however this cannot be
confirmed. YobA is a protein with unknown function.
Length = 99
Score = 27.0 bits (60), Expect = 5.3
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 119 NKDTDSKEEINISFQELLQKTPDSTVV 145
+K ++KE N+ QEL +K P V+
Sbjct: 32 DKKFETKELQNLIEQELNEKYPSDIVL 58
>gnl|CDD|235018 PRK02256, PRK02256, putative aminopeptidase 1; Provisional.
Length = 462
Score = 28.3 bits (64), Expect = 6.3
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 80 KLLLEKYGIDHLDFLS 95
KLL EKYGI DF+S
Sbjct: 218 KLLNEKYGITEEDFVS 233
>gnl|CDD|234915 PRK01191, rpl24p, 50S ribosomal protein L24P; Validated.
Length = 120
Score = 27.2 bits (61), Expect = 7.1
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 8/37 (21%)
Query: 60 SLQQLYERKSSYEKPLRIRGKL--------LLEKYGI 88
S Q +RK+ Y PL +R KL L EKYGI
Sbjct: 5 SKQPRKQRKALYNAPLHLRQKLMSAPLSKELREKYGI 41
>gnl|CDD|218689 pfam05681, Fumerase, Fumarate hydratase (Fumerase). This family
consists of several bacterial fumarate hydratase
proteins FumA and FumB. Fumarase, or fumarate hydratase
(EC 4.2.1.2), is a component of the citric acid cycle.
In facultative anaerobes such as Escherichia coli,
fumarase also engages in the reductive pathway from
oxaloacetate to succinate during anaerobic growth. Three
fumarases, FumA, FumB, and FumC, have been reported in
E. coli. fumA and fumB genes are homologous and encode
products of identical sizes which form thermolabile
dimers of Mr 120,000. FumA and FumB are class I enzymes
and are members of the iron-dependent hydrolases, which
include aconitase and malate hydratase. The active FumA
contains a 4Fe-4S centre, and it can be inactivated upon
oxidation to give a 3Fe-4S centre.
Length = 271
Score = 27.8 bits (63), Expect = 8.6
Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 5/28 (17%)
Query: 253 VGIAGN-EEADRLAKEALT----STHPT 275
VGI G E+A LAK+AL +P
Sbjct: 181 VGIGGTSEKAALLAKKALLRPVDERNPD 208
>gnl|CDD|233475 TIGR01573, cas2, CRISPR-associated endoribonuclease Cas2. This
model describes most members of the family of Cas2, one
of the first four protein families found to mark
prokaryotic genomes that contain multiple CRISPR
elements. It is an endoribonuclease, capable of cleaving
single-stranded RNA. CRISPR is an acronym for Clustered
Regularly Interspaced Short Palindromic Repeats. The cas
genes are found near the repeats. A distinct branch of
the Cas2 family shows a very low level of sequence
identity and is modeled by TIGR01873 instead of by This
model (TIGR01573) [Mobile and extrachromosomal element
functions, Other].
Length = 95
Score = 26.5 bits (59), Expect = 8.6
Identities = 11/47 (23%), Positives = 17/47 (36%)
Query: 201 NRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFI 247
+ I + A ++ + + P G IR LT K K I
Sbjct: 35 YSVFERILEPNQLARSLIERLKRIIPDEGSIRIYPLTEKQKAKAIVI 81
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 0.134 0.395
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: 18,163,907
Number of extensions: 1743233
Number of successful extensions: 1588
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1581
Number of HSP's successfully gapped: 35
Length of query: 354
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 256
Effective length of database: 6,590,910
Effective search space: 1687272960
Effective search space used: 1687272960
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: 59 (26.4 bits)