RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5610
(237 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 = 90.4 bits (225), Expect = 4e-23
Identities = 37/89 (41%), Positives = 47/89 (52%), Gaps = 4/89 (4%)
Query: 7 ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLNPIAGEIR-DLILTNK 65
EL AIL A+ A + I SDS +AL+ L++ S +P+ IR +
Sbjct: 41 ELLAILEALQL---ALREGRRARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELAN 97
Query: 66 SKLNVRFIWVPSHVGIAGNEEADRLAKEA 94
+ VR WVP H GI GNE ADRLAKEA
Sbjct: 98 HGVKVRLHWVPGHSGIEGNERADRLAKEA 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 = 63.4 bits (155), Expect = 6e-13
Identities = 29/95 (30%), Positives = 38/95 (40%), Gaps = 15/95 (15%)
Query: 5 VLELTAILFAIHFSISAHLNNVNRAYLVICSDSL----SALQTLQNIFSLNPIAGEIRDL 60
EL A++ A+ +N I +DS PI EI +L
Sbjct: 42 RAELLALIEALEALSGQKVN--------IYTDSQYVIGGITNGWPTKSESKPIKNEIWEL 93
Query: 61 ILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
+ K V WVP H GI GNE AD+LAK+
Sbjct: 94 LQ---KKHKVYIQWVPGHSGIPGNELADKLAKQGA 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 = 53.7 bits (130), Expect = 2e-09
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 51 NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
E ++ + K K+ + 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 = 53.0 bits (128), Expect = 6e-09
Identities = 32/108 (29%), Positives = 49/108 (45%), Gaps = 24/108 (22%)
Query: 7 ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTL--------QNIFSLNPIAGEI- 57
EL A++ A+ I + + LVI +DS + + +N + + G+
Sbjct: 47 ELRAVIHALRL-IKEVGEGLTK--LVIATDSEYVVNGVTEWIPKWKKNGWKTS--KGKPV 101
Query: 58 --RDLIL--------TNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
+DLI + + V+F VP H GI GNEEADRLAK+
Sbjct: 102 ANKDLIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKGA 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 = 45.6 bits (109), Expect = 2e-06
Identities = 14/29 (48%), Positives = 16/29 (55%)
Query: 66 SKLNVRFIWVPSHVGIAGNEEADRLAKEA 94
+K V + 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 = 43.1 bits (102), Expect = 1e-05
Identities = 27/90 (30%), Positives = 42/90 (46%), Gaps = 10/90 (11%)
Query: 7 ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQN-IFSLNPIAGEIRDLILTNK 65
EL A+L A+ ++ L L+I +DS + + + + D++L
Sbjct: 43 ELLALLEAL--ELALDLGLKK---LIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLS 97
Query: 66 SKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
+++RF VP GNE ADRLAKEA
Sbjct: 98 KFIDIRFEHVPRE----GNEVADRLAKEAA 123
>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 = 39.0 bits (92), Expect = 3e-04
Identities = 24/95 (25%), Positives = 38/95 (40%), Gaps = 17/95 (17%)
Query: 7 ELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIF-----SLNPIAGEIRDLI 61
E A++ + ++ + L I DS + +Q + L P E R+L+
Sbjct: 46 EYEALIAGLELALELGIKK-----LEIYGDSQLVVNQIQGEYEVKNERLAPYLEEARELL 100
Query: 62 LTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALT 96
K V W+P N+EAD LA +AL
Sbjct: 101 ---KKFEEVEIKWIPRE----ENKEADALANQALD 128
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 38.3 bits (90), Expect = 0.001
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 69 NVRFIWVPSHVGIAGNEEADRLAKEA 94
+++ WV H G NE D LA+
Sbjct: 114 QIKWHWVKGHAGHPENERCDELARAG 139
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 37.7 bits (88), Expect = 0.001
Identities = 15/37 (40%), Positives = 19/37 (51%)
Query: 58 RDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEA 94
+L K V + WV H G NE AD+LA+EA
Sbjct: 106 EELDELLKRHELVFWEWVKGHAGHPENERADQLAREA 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 = 35.6 bits (83), Expect = 0.003
Identities = 26/97 (26%), Positives = 39/97 (40%), Gaps = 16/97 (16%)
Query: 5 VLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNI-FSLNPIAG---EIRDL 60
E A+L + ++ + L++ SDS +Q +Q + + +A EIR L
Sbjct: 4 EAEAEALLEGLQLALELGIRR-----LIVESDSQLVVQQIQGEYEARSRLAALLREIRKL 58
Query: 61 ILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS 97
+ S V VP N AD LAK A S
Sbjct: 59 LKKFDS---VSVSHVPRE----CNRVADALAKLASAS 88
>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 = 33.4 bits (77), Expect = 0.029
Identities = 25/88 (28%), Positives = 38/88 (43%), Gaps = 11/88 (12%)
Query: 6 LELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTL--QNIFSLNPIAGEIRDLIL- 62
LEL A+L A+ A L+ NR LV D+ +A+ + Q + R L+L
Sbjct: 36 LELLAVLLALQ-HWGARLS--NRKVLVRS-DNTTAVAYINRQGGTRSPELLALARQLVLW 91
Query: 63 TNKSKLNVRFIWVPSHVGIAGNEEADRL 90
+ + +R +P N ADRL
Sbjct: 92 CEERNIWLRARHIPG----VLNVAADRL 115
>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 = 32.6 bits (75), Expect = 0.070
Identities = 25/111 (22%), Positives = 38/111 (34%), Gaps = 32/111 (28%)
Query: 5 VLELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNI---------FSLNPIAG 55
EL A++ A+ + +N I +DS A L + + PIA
Sbjct: 37 RAELIALIRALELAKGKPVN--------IYTDSAYAFGILHALETIWKERGFLTGKPIAL 88
Query: 56 --EIRDLI----LTNKSKLNVRFIWVPSHVG-----IAGNEEADRLAKEAL 95
I L V I + +H G GN AD+ A++A
Sbjct: 89 ASLILQLQKAIQRPKP----VAVIHIRAHSGLPGPLALGNARADQAARQAA 135
>gnl|CDD|75628 PRK06548, PRK06548, ribonuclease H; Provisional.
Length = 161
Score = 32.5 bits (73), Expect = 0.093
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 59 DLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTSTHPTINKIPIPDYKAYSKR 116
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 = 0.17
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 65 KSKLNVRFIWVPSHVGIAGNEEADRLAKEA 94
+++ 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 = 32.3 bits (74), Expect = 0.22
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 7/47 (14%)
Query: 49 SLNPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 95
+ 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 = 30.9 bits (70), Expect = 0.52
Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 10/77 (12%)
Query: 14 AIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSLN-PIAGEIRDLILTNKSKL---- 68
A+ H + VN+ YL ++ Q +F L+ + ++ TN +
Sbjct: 40 ALELYGEYHYDGVNKGYLKF---KVTEEQARTGVFDLSGSNVFAVTKILRTNAGSITSMD 96
Query: 69 -NVRFIWVPSHV-GIAG 83
+ W V G+AG
Sbjct: 97 GTATYPWFTDFVLGLAG 113
>gnl|CDD|215451 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 29.0 bits (65), Expect = 2.1
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 218 LKDNDISPILEFLRRTQIK 236
+ D S +LE++RRTQ K
Sbjct: 398 VSREDCSHVLEWIRRTQCK 416
>gnl|CDD|222135 pfam13445, zf-RING_LisH, RING-type zinc-finger, LisH dimerisation
motif. This zinc-finger is the dimerisation motif for
LisH proteins, and is also a typical RING-type of plant
ubiquitin ligases.
Length = 55
Score = 26.1 bits (58), Expect = 2.9
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 176 KENPPICVPCGCVISVKHILTDCQTHSNIRAP 207
+ENPP+ +PCG V S K + + + P
Sbjct: 23 EENPPVMLPCGHVYSRKALEKLAKNGGKFKCP 54
>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 = 26.9 bits (60), Expect = 4.1
Identities = 11/47 (23%), Positives = 17/47 (36%)
Query: 27 NRAYLVICSDSLSALQTLQNIFSLNPIAGEIRDLILTNKSKLNVRFI 73
+ I + A ++ + + P G IR LT K K I
Sbjct: 35 YSVFERILEPNQLARSLIERLKRIIPDEGSIRIYPLTEKQKAKAIVI 81
>gnl|CDD|193541 cd05665, M20_Acy1_IAAspH_bact, M20 Peptidases Aminoacyclase-1
indole-3-acetic-L-aspartic acid hydrolase from bacteria
and archaea. Peptidase M20 family, Bacterial and
archaeal Aminoacyclase-1 indole-3-acetic-L-aspartic acid
hydrolase (IAA-Asp hydrolase; IAAspH; IAAH; IAA
amidohydrolase; EC 3.5.1.-) subfamily. IAAspH hydrolyzes
indole-3-acetyl-N-aspartic acid (IAA or auxin) to
indole-3-acetic acid. Genes encoding IAA-amidohydrolases
were first cloned from Arabidopsis; ILR1, IAR3, ILL1 and
ILL2 encode active IAA- amino acid hydrolases, and three
additional amidohydrolase-like genes (ILL3, ILL5, ILL6)
have been isolated. In higher plants, the growth
regulator indole-3-acetic acid (IAA or auxin) is found
both free and conjugated via amide bonding to a variety
of amino acids and peptides, and via an ester linkage to
carbohydrates. IAA-Asp conjugates are involved in
homeostatic control, protection, storing and subsequent
use of free IAA. IAA-Asp is also found in some plants as
a unique intermediate for entering into IAA
non-decarboxylative oxidative pathway. IAA
amidohydrolase cleaves the amide bond between the auxin
and the conjugated amino acid. Enterobacter agglomerans
IAAspH has very strong enzyme activity and substrate
specificity towards IAA-Asp, although its substrate
affinity is weaker compared to Arabidopsis enzymes of
the ILR1 gene family. Enhanced IAA-hydrolase activity
has been observed during clubroot disease in Chinese
cabbage.
Length = 415
Score = 27.5 bits (62), Expect = 7.2
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 66 SKLNVRFIWVPSHVGIAGNE 85
+KL+V F V +H G A E
Sbjct: 217 TKLDVTFTGVSAHAGGAPEE 236
>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 = 27.3 bits (61), Expect = 7.6
Identities = 12/58 (20%), Positives = 23/58 (39%), Gaps = 13/58 (22%)
Query: 123 NSEWHNLQNNKLHQIKLENKPWNP-------PYLINRKEQVSLTRLRIGHTNTTHIHL 173
SEW +NNK +N+ PY + E+ + + +++ T H+
Sbjct: 286 ESEWQRFKNNK------KNEALLDRIIKVKVPYCLRVSEEAQIYEKLLRNSDLTEAHI 337
>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 = 27.0 bits (61), Expect = 8.7
Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 5/28 (17%)
Query: 79 VGIAGN-EEADRLAKEALT----STHPT 101
VGI G E+A LAK+AL +P
Sbjct: 181 VGIGGTSEKAALLAKKALLRPVDERNPD 208
>gnl|CDD|213227 cd03260, ABC_PstB_phosphate_transporter, ATP-binding cassette
domain of the phosphate transport system. Phosphate
uptake is of fundamental importance in the cell
physiology of bacteria because phosphate is required as
a nutrient. The Pst system of E. coli comprises four
distinct subunits encoded by the pstS, pstA, pstB, and
pstC genes. The PstS protein is a phosphate-binding
protein located in the periplasmic space. PstA and PstC
are hydrophobic and they form the transmembrane portion
of the Pst system. PstB is the catalytic subunit, which
couples the energy of ATP hydrolysis to the import of
phosphate across cellular membranes through the Pst
system, often referred as ABC-protein. PstB belongs to
one of the largest superfamilies of proteins
characterized by a highly conserved adenosine
triphosphate (ATP) binding cassette (ABC), which is also
a nucleotide binding domain (NBD).
Length = 227
Score = 26.8 bits (60), Expect = 8.8
Identities = 15/46 (32%), Positives = 17/46 (36%), Gaps = 11/46 (23%)
Query: 51 NPIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALT 96
NP G I D NV + GI EE D +EAL
Sbjct: 91 NPFPGSIYD---------NVAY--GLRLHGIKLKEELDERVEEALR 125
>gnl|CDD|241493 cd13339, PH-GRAM_MTMR13, Myotubularian (MTM) related 13 protein
Pleckstrin Homology-Glucosyltransferases, Rab-like
GTPase activators and Myotubularins (PH-GRAM) domain.
MTMR13 (also called SBF2/SET binding factor 2) is a
catalytically inactive phosphatase that plays a role as
an adapter for the phosphatase myotubularin to regulate
myotubularintracellular location. It contains a Leu
residue instead of a conserved Cys residue in the
dsPTPase catalytic loop which renders it catalytically
inactive as a phosphatase. MTMR13 has high sequence
similarity to MTMR5 and has recently been shown to be a
second gene mutated in type 4B Charcot-Marie-Tooth
syndrome. Both MTMR5 and MTMR13 contain an N-terminal
DENN domain, a PH-GRAM domain, an inactive PTP domain, a
SET interaction domain, a coiled-coil domain, and a
C-terminal PH domain. Myotubularin-related proteins are
a subfamily of protein tyrosine phosphatases (PTPs) that
dephosphorylate D3-phosphorylated inositol lipids.
Mutations in this family cause the human neuromuscular
disorders myotubular myopathy and type 4B
Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs
5, 9-13) contain naturally occurring substitutions of
residues required for catalysis by PTP family enzymes.
Although these proteins are predicted to be
enzymatically inactive, they are thought to function as
antagonists of endogenous phosphatase activity or
interaction modules. Most MTMRs contain a N-terminal
PH-GRAM domain, a Rac-induced recruitment domain (RID)
domain, a PTP domain (which may be active or inactive),
a SET-interaction domain, and a C-terminal coiled-coil
region. In addition some members contain DENN domain
N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH
domains C-terminal to the coiled-coil region. The GRAM
domain, found in myotubularins, glucosyltransferases,
and other putative membrane-associated proteins, is part
of a larger motif with a pleckstrin homology (PH) domain
fold. The PH domain family possesses multiple functions
including the ability to bind phosphoinositides via its
beta1/beta2, beta3/beta4, and beta6/beta7 connecting
loops and to other proteins. However, no
phosphoinositide binding sites have been found for the
MTMRs to date.
Length = 184
Score = 26.5 bits (58), Expect = 9.8
Identities = 21/95 (22%), Positives = 42/95 (44%), Gaps = 4/95 (4%)
Query: 147 PYLINRKEQVSLTRLRIGHTNTTHIHLMKKENPPICVPCGCVISVKHILTDCQTHSNIRA 206
P+++ + + LT RI T H L+ ++ P + K I Q N++
Sbjct: 60 PHILPAEGALFLTTYRIIFKGTPHDQLVGEQTVIRSFPIASITKEKKITIQNQLQQNMQE 119
Query: 207 PLNLSSTLLSCLK---DNDISP-ILEFLRRTQIKI 237
L ++S +K D ++SP ++E ++ +K
Sbjct: 120 GLQITSASFQLIKVAFDEEVSPEVVEIFKKQLMKF 154
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 0.134 0.403
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: 11,600,088
Number of extensions: 1046920
Number of successful extensions: 916
Number of sequences better than 10.0: 1
Number of HSP's gapped: 913
Number of HSP's successfully gapped: 31
Length of query: 237
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 143
Effective length of database: 6,768,326
Effective search space: 967870618
Effective search space used: 967870618
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: 57 (25.7 bits)