RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5302
(333 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 = 111 bits (280), Expect = 2e-30
Identities = 49/129 (37%), Positives = 65/129 (50%), Gaps = 7/129 (5%)
Query: 100 VIYTDASKTDVAVSSAFCSQDIKFSTRLHSLLSIC---NAELTSILFAIHFLLSSCLNEH 156
VIYTD SK + + F +R + L C +AEL +IL A+ L
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60
Query: 157 TQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILENKSK-LSIRFIWVPSHVGIAGNE 215
I SDS +AL+ L++ S +P+ IR I E + + +R WVP H GI GNE
Sbjct: 61 K---ITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNE 117
Query: 216 EADRLAKEA 224
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 = 71.1 bits (175), Expect = 2e-15
Identities = 29/91 (31%), Positives = 44/91 (48%), Gaps = 9/91 (9%)
Query: 136 AELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILE-N 194
AEL +++ A+ L +N I +DS + + N + + I+N I E
Sbjct: 43 AELLALIEALEALSGQKVN--------IYTDSQYVIGGITNGWPTKSESKPIKNEIWELL 94
Query: 195 KSKLSIRFIWVPSHVGIAGNEEADRLAKEAL 225
+ K + WVP H GI GNE AD+LAK+
Sbjct: 95 QKKHKVYIQWVPGHSGIPGNELADKLAKQGA 125
>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 = 55.6 bits (135), Expect = 1e-09
Identities = 17/45 (37%), Positives = 25/45 (55%)
Query: 181 NPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEAL 225
E + + + K K+ I F+ V +H G NE AD+LAK+AL
Sbjct: 89 KEGTKEYKEFMDKIKKKIKISFVKVKAHSGDKYNELADKLAKKAL 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 = 52.6 bits (127), Expect = 2e-08
Identities = 30/107 (28%), Positives = 48/107 (44%), Gaps = 20/107 (18%)
Query: 136 AELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTL--------QNVFSL---NPIA 184
AEL +++ A+ + VI +DS + + +N + P+A
Sbjct: 46 AELRAVIHALRLIKEVGEGLTK---LVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVA 102
Query: 185 -----SEIRNLILE-NKSKLSIRFIWVPSHVGIAGNEEADRLAKEAL 225
E+ L+ E + + ++F VP H GI GNEEADRLAK+
Sbjct: 103 NKDLIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKGA 149
>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 = 44.8 bits (107), Expect = 6e-06
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 196 SKLSIRFIWVPSHVGIAGNEEADRLAKEA 224
+K + + WV H G GNE AD LA A
Sbjct: 109 AKHQVTWHWVKGHAGHPGNERADELANAA 137
>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 = 43.5 bits (103), Expect = 1e-05
Identities = 28/91 (30%), Positives = 40/91 (43%), Gaps = 10/91 (10%)
Query: 136 AELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVFSLNPIASEIRNLILE-N 194
AEL ++L A+ L+ L +I +DS + + + + + IL
Sbjct: 42 AELLALLEAL--ELALDLGLKK---LIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLL 96
Query: 195 KSKLSIRFIWVPSHVGIAGNEEADRLAKEAL 225
+ IRF VP GNE ADRLAKEA
Sbjct: 97 SKFIDIRFEHVPRE----GNEVADRLAKEAA 123
>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 = 42.3 bits (100), Expect = 4e-05
Identities = 27/126 (21%), Positives = 48/126 (38%), Gaps = 16/126 (12%)
Query: 100 VIYTDASKTDVAVSSAFCSQ--DIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHT 157
V++TDAS + A S + I EL ++L A+ + N
Sbjct: 1 VLFTDASLSGWG---AVLSGSWAQGLWSAEERNKHINFLELLAVLLALQHWGARLSNRKV 57
Query: 158 QACFVICSDSLSALQTL--QNVFSLNPIASEIRNLILE-NKSKLSIRFIWVPSHVGIAGN 214
++ SD+ +A+ + Q + + R L+L + + +R +P N
Sbjct: 58 ----LVRSDNTTAVAYINRQGGTRSPELLALARQLVLWCEERNIWLRARHIPG----VLN 109
Query: 215 EEADRL 220
ADRL
Sbjct: 110 VAADRL 115
>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 = 39.8 bits (94), Expect = 3e-04
Identities = 27/113 (23%), Positives = 42/113 (37%), Gaps = 21/113 (18%)
Query: 121 IKFSTRLHSLLSICN--AELTSILFAIHFLLSSCLNEHTQACFVICSDSLSALQTLQNVF 178
++ S L + N AE +++ + L E I DS + +Q +
Sbjct: 30 LEQSIPLGFPAT--NNEAEYEALIAGLELAL-----ELGIKKLEIYGDSQLVVNQIQGEY 82
Query: 179 -----SLNPIASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALT 226
L P E R L+ K + W+P N+EAD LA +AL
Sbjct: 83 EVKNERLAPYLEEARELL---KKFEEVEIKWIPRE----ENKEADALANQALD 128
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 38.7 bits (91), Expect = 0.001
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 199 SIRFIWVPSHVGIAGNEEADRLAKEA 224
I++ WV H G NE D LA+
Sbjct: 114 QIKWHWVKGHAGHPENERCDELARAG 139
>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 = 38.0 bits (89), Expect = 0.001
Identities = 29/146 (19%), Positives = 51/146 (34%), Gaps = 31/146 (21%)
Query: 100 VIYTDASKTDVAVSSAFCS-QDIKFSTRLHSLLSICNAELTSILFAIHFLLSSCLNEHTQ 158
++TD S A + D+ L S AEL +++ A+ +N
Sbjct: 1 TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALELAKGKPVN---- 56
Query: 159 ACFVICSDSLSALQTLQNV--------------FSLNPIASEIRNLILENKSKLSIRFIW 204
I +DS A L + +L + +++ I K + I
Sbjct: 57 ----IYTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKP---VAVIH 109
Query: 205 VPSHVG-----IAGNEEADRLAKEAL 225
+ +H G GN AD+ A++A
Sbjct: 110 IRAHSGLPGPLALGNARADQAARQAA 135
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 37.7 bits (88), Expect = 0.003
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 204 WVPSHVGIAGNEEADRLAKEA 224
WV H G NE AD+LA+EA
Sbjct: 122 WVKGHAGHPENERADQLAREA 142
>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 = 34.1 bits (79), Expect = 0.012
Identities = 22/67 (32%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 162 VICSDSLSALQTLQNVFSLNPIASEIRNLILENKSKLSIRFI-WVPSHVGIAGNEEADRL 220
++ SDS +Q +Q S + L+ E + KL +F SHV N AD L
Sbjct: 26 IVESDSQLVVQQIQG---EYEARSRLAALLREIR-KLLKKFDSVSVSHVPRECNRVADAL 81
Query: 221 AKEALTS 227
AK A S
Sbjct: 82 AKLASAS 88
>gnl|CDD|75628 PRK06548, PRK06548, ribonuclease H; Provisional.
Length = 161
Score = 33.2 bits (75), Expect = 0.084
Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 183 IASEIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKA 242
I EI +L +EN++ IR WV +H G NE AD LA++A + IP P +
Sbjct: 102 IIQEIDSL-MENRN---IRMSWVNAHTGHPLNEAADSLARQAANNFSTRSAHIPGPGWTE 157
Query: 243 YSKR 246
S +
Sbjct: 158 RSAK 161
>gnl|CDD|236334 PRK08719, PRK08719, ribonuclease H; Reviewed.
Length = 147
Score = 31.8 bits (72), Expect = 0.25
Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 182 PIAS-EIRNLILENKSKLSIRFIWVPSHVGIAGNEEADRLAKEA 224
P+A+ ++ + E +++ + V +H GI GNE AD LA+ A
Sbjct: 101 PVANRDLWQQVDELRARKYVEVEKVTAHSGIEGNEAADMLAQAA 144
>gnl|CDD|180903 PRK07238, PRK07238, bifunctional RNase H/acid phosphatase;
Provisional.
Length = 372
Score = 31.5 bits (72), Expect = 0.52
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 4/27 (14%)
Query: 199 SIRFIWVPSHVGIAGNEEADRLAKEAL 225
+ + W+P A N ADRLA EA+
Sbjct: 108 RVTYTWIPR----ARNAHADRLANEAM 130
>gnl|CDD|226637 COG4167, SapF, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 267
Score = 30.2 bits (68), Expect = 1.3
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 185 SEIRNLILENKSKLSIRFIWVPSHVGI 211
S++ NL+LE + K I +I+V H+G+
Sbjct: 186 SQLINLMLELQEKQGISYIYVTQHIGM 212
>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 = 29.7 bits (68), Expect = 2.0
Identities = 20/68 (29%), Positives = 26/68 (38%), Gaps = 29/68 (42%)
Query: 193 ENKSKLS-----------IRFI--WVPSH-----------VGIAGN-EEADRLAKEALT- 226
ENKSKL+ +F+ V VGI G E+A LAK+AL
Sbjct: 141 ENKSKLAMLNPSDGIEGIKKFVLETVKEAGPNACPPGVVGVGIGGTSEKAALLAKKALLR 200
Query: 227 ---STHPT 231
+P
Sbjct: 201 PVDERNPD 208
>gnl|CDD|214810 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 361
Score = 29.2 bits (66), Expect = 3.0
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 11/62 (17%)
Query: 248 ILTSWNSEWHNLQNNKLHE------IKVENKPWNPPYLINRKEQVSLTRLRIGHTNTTHI 301
I S SEW +NNK +E IKV+ PY + E+ + + +++ T
Sbjct: 281 IAHSNESEWQRFKNNKKNEALLDRIIKVK-----VPYCLRVSEEAQIYEKLLRNSDLTEA 335
Query: 302 HL 303
H+
Sbjct: 336 HI 337
>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 = 3.3
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 35 KLLLEKYGIEYLDFLS 50
KLL EKYGI DF+S
Sbjct: 201 KLLNEKYGITEEDFIS 216
>gnl|CDD|193521 cd05643, M28_like_7, M28 Zn-Peptidases. Peptidase family M28 (also
called aminopeptidase Y family), uncharacterized
subfamily. The M28 family contains aminopeptidases as
well as carboxypeptidases. They typically have
co-catalytic zinc ions; each zinc ion is tetrahedrally
co-ordinated, with three amino acid ligands plus
activated water; one aspartate residue binds both metal
ions. This protein subfamily conserves some of the
metal-coordinating residues of the typically
co-catalytic M28 family which might suggest binding of a
single metal ion.
Length = 288
Score = 28.5 bits (64), Expect = 4.6
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 192 LENKSKLSIRFIWVPSHVGIAG--NEEADRLAK 222
L N+ K I F+WVP + G + DRL K
Sbjct: 117 LLNRPKRGICFLWVPEYTGTVAYFAKHPDRLKK 149
>gnl|CDD|185067 PRK15112, PRK15112, antimicrobial peptide ABC system ATP-binding
protein SapF; Provisional.
Length = 267
Score = 28.6 bits (64), Expect = 4.9
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 185 SEIRNLILENKSKLSIRFIWVPSHVGI 211
S++ NL+LE + K I +I+V H+G+
Sbjct: 186 SQLINLMLELQEKQGISYIYVTQHLGM 212
>gnl|CDD|235018 PRK02256, PRK02256, putative aminopeptidase 1; Provisional.
Length = 462
Score = 28.6 bits (65), Expect = 5.1
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 35 KLLLEKYGIEYLDFLS 50
KLL EKYGI DF+S
Sbjct: 218 KLLNEKYGITEEDFVS 233
>gnl|CDD|215922 pfam00443, UCH, Ubiquitin carboxyl-terminal hydrolase.
Length = 313
Score = 27.8 bits (62), Expect = 9.0
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 297 NTTHIHLMKKENPPICVPCGC-VMSVKHIHINRLPNLL 333
N + ++KE C CG ++K + I+RLP +L
Sbjct: 173 NFLKLEELEKEEKYYCPKCGGKQNAIKKLDISRLPPVL 210
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 0.133 0.400
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,520,724
Number of extensions: 1546182
Number of successful extensions: 1466
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1461
Number of HSP's successfully gapped: 32
Length of query: 333
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 236
Effective length of database: 6,635,264
Effective search space: 1565922304
Effective search space used: 1565922304
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: 59 (26.5 bits)