RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15899
(104 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 = 81.9 bits (203), Expect = 1e-21
Identities = 35/92 (38%), Positives = 49/92 (53%), Gaps = 3/92 (3%)
Query: 3 HCSNGIAELIAILLCLRSIKN--HPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWC 60
+CS AEL+AIL L+ A + + SDS +L A+ +P S P++ +I A
Sbjct: 34 YCSVFDAELLAILEALQLALREGRRARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIR 93
Query: 61 DLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAK 92
+L G V+L W P H GI GNE D+ AK
Sbjct: 94 ELANHGVK-VRLHWVPGHSGIEGNERADRLAK 124
>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 = 54.6 bits (132), Expect = 5e-11
Identities = 27/95 (28%), Positives = 43/95 (45%), Gaps = 12/95 (12%)
Query: 3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPY----LSCPIISQIYSA 58
+N AEL+A++ L ++ + +DS + I N + S PI ++I+
Sbjct: 37 GTTNQRAELLALIEALEALSGQK---VNIYTDSQYVIGGITNGWPTKSESKPIKNEIW-- 91
Query: 59 WCDLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAKD 93
+L V + W P H GI GNE D+ AK
Sbjct: 92 --ELLQKKHK-VYIQWVPGHSGIPGNELADKLAKQ 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 = 43.1 bits (102), Expect = 1e-06
Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 5/93 (5%)
Query: 3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDL 62
+N AEL+A+L L + + ++ +DS + I + + + L
Sbjct: 36 AATNNEAELLALLEALELALDLGLKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLL 95
Query: 63 KTVGQYYVKLMWCPSHCGIRGNEAVDQAAKDPL 95
+ ++ P GNE D+ AK+
Sbjct: 96 LS-KFIDIRFEHVPRE----GNEVADRLAKEAA 123
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 35.4 bits (82), Expect = 0.001
Identities = 23/101 (22%), Positives = 36/101 (35%), Gaps = 11/101 (10%)
Query: 3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIA---------NPYLSCPIIS 53
+N AEL A++ L ++K A L +DS + I +
Sbjct: 40 RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPV 99
Query: 54 QIYSAWCDLKTVGQ--YYVKLMWCPSHCGIRGNEAVDQAAK 92
+ W +L + + V W H G NE DQ A+
Sbjct: 100 KNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAR 140
>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 = 0.007
Identities = 27/109 (24%), Positives = 40/109 (36%), Gaps = 27/109 (24%)
Query: 6 NGIAELIAILLCLRSIKNH--PAMRFLLVSDSMGSLSAI--------------------A 43
N AEL A++ LR IK + ++ +DS ++ + A
Sbjct: 43 NQRAELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVA 102
Query: 44 NPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAK 92
N L I ++ + VK P H GI GNE D+ AK
Sbjct: 103 NKDL----IKEL-DKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146
>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 = 0.013
Identities = 23/100 (23%), Positives = 33/100 (33%), Gaps = 21/100 (21%)
Query: 9 AELIAILLCLRSIKNHPAMRFLLVSDS---MGSLSAIA----NPYLSCPIISQIYSAWCD 61
AELIA++ L K + +DS G L A+ + S
Sbjct: 38 AELIALIRALELAKG---KPVNIYTDSAYAFGILHALETIWKERGFLTGKPIALASLILQ 94
Query: 62 LKTV----GQYYVKLMWCPSHCG-----IRGNEAVDQAAK 92
L+ V + +H G GN DQAA+
Sbjct: 95 LQKAIQRPKPVAV--IHIRAHSGLPGPLALGNARADQAAR 132
>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 = 29.8 bits (68), Expect = 0.15
Identities = 9/23 (39%), Positives = 10/23 (43%)
Query: 70 VKLMWCPSHCGIRGNEAVDQAAK 92
V W H G GNE D+ A
Sbjct: 113 VTWHWVKGHAGHPGNERADELAN 135
>gnl|CDD|152066 pfam11630, DUF3254, Protein of unknown function (DUF3254). This
family of proteins is most likely a family of
anti-lipopolysaccharide factor proteins however this
cannot be confirmed.
Length = 97
Score = 28.5 bits (64), Expect = 0.25
Identities = 11/33 (33%), Positives = 13/33 (39%), Gaps = 7/33 (21%)
Query: 68 YYVKLMWCPSHCGIRGN-------EAVDQAAKD 93
YY MWCP I G V+ A +D
Sbjct: 44 YYKGKMWCPGWTPITGESRTRSRSGVVEHAVRD 76
>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 = 28.2 bits (64), Expect = 0.46
Identities = 9/29 (31%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 69 YVKLMWC--PSHCGIRGNEAVDQAAKDPL 95
+K+ + +H G + NE D+ AK L
Sbjct: 105 KIKISFVKVKAHSGDKYNELADKLAKKAL 133
>gnl|CDD|238006 cd00047, PTPc, Protein tyrosine phosphatases (PTP) catalyze the
dephosphorylation of phosphotyrosine peptides; they
regulate phosphotyrosine levels in signal transduction
pathways. The depth of the active site cleft renders the
enzyme specific for phosphorylated Tyr (pTyr) residues,
instead of pSer or pThr. This family has a distinctive
active site signature motif, HCSAGxGRxG. Characterized
as either transmembrane, receptor-like or
non-transmembrane (soluble) PTPs. Receptor-like PTP
domains tend to occur in two copies in the cytoplasmic
region of the transmembrane proteins, only one copy may
be active.
Length = 231
Score = 28.3 bits (64), Expect = 0.63
Identities = 8/28 (28%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 3 HCSNGIAE---LIAILLCLRSIKNHPAM 27
HCS G+ IAI + L+ ++ +
Sbjct: 172 HCSAGVGRTGTFIAIDILLQRLEAEGVV 199
>gnl|CDD|215717 pfam00102, Y_phosphatase, Protein-tyrosine phosphatase.
Length = 233
Score = 28.0 bits (63), Expect = 0.70
Identities = 8/28 (28%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 3 HCSNGI---AELIAILLCLRSIKNHPAM 27
HCS G+ IAI + L+ ++ +
Sbjct: 174 HCSAGVGRTGTFIAIDILLQQLEAEGEV 201
>gnl|CDD|214550 smart00194, PTPc, Protein tyrosine phosphatase, catalytic domain.
Length = 259
Score = 27.6 bits (62), Expect = 0.97
Identities = 8/25 (32%), Positives = 13/25 (52%), Gaps = 3/25 (12%)
Query: 3 HCSNGI---AELIAILLCLRSIKNH 24
HCS G+ IAI + L+ ++
Sbjct: 200 HCSAGVGRTGTFIAIDILLQQLEAG 224
>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 = 27.5 bits (62), Expect = 0.99
Identities = 8/35 (22%), Positives = 13/35 (37%)
Query: 2 FHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSM 36
F +N AE A++ L + + DS
Sbjct: 38 FPATNNEAEYEALIAGLELALELGIKKLEIYGDSQ 72
>gnl|CDD|217764 pfam03856, SUN, Beta-glucosidase (SUN family). Members of this
family include Nca3, Sun4 and Sim1. This is a family of
yeast proteins, involved in a diverse set of functions
(DNA replication, aging, mitochondrial biogenesis and
cell septation). BGLA from Candida wickerhamii has been
characterized as a Beta-glucosidase EC:3.2.1.21.
Length = 248
Score = 27.2 bits (61), Expect = 1.4
Identities = 10/25 (40%), Positives = 11/25 (44%), Gaps = 1/25 (4%)
Query: 46 YLSCPIISQIYSAWCDLKTVGQYYV 70
L+ P Y W KT QYYV
Sbjct: 135 PLAVPDGDTYYY-WQGKKTSAQYYV 158
>gnl|CDD|75628 PRK06548, PRK06548, ribonuclease H; Provisional.
Length = 161
Score = 26.3 bits (57), Expect = 2.7
Identities = 29/104 (27%), Positives = 45/104 (43%), Gaps = 23/104 (22%)
Query: 5 SNGIAELIAILLCLRSIKNHPAMRFLLVSDS---MGSLS-------------AIANPYLS 48
+N IAEL A+ L + + H L++SDS + SL+ A P L+
Sbjct: 41 TNNIAELTAVRELLIATR-HTDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLN 99
Query: 49 CPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAK 92
II +I S + +++ W +H G NEA D A+
Sbjct: 100 QEIIQEIDS------LMENRNIRMSWVNAHTGHPLNEAADSLAR 137
>gnl|CDD|185387 PRK15490, PRK15490, Vi polysaccharide biosynthesis protein TviE;
Provisional.
Length = 578
Score = 26.2 bits (57), Expect = 3.6
Identities = 13/25 (52%), Positives = 17/25 (68%), Gaps = 2/25 (8%)
Query: 19 RSIKNHPAMRFLLVSDSMGSLSAIA 43
R +++HPA RF+LV D G L A A
Sbjct: 422 RYLQHHPATRFVLVGD--GDLRAEA 444
>gnl|CDD|212121 cd10810, GH38N_AMII_LAM_like, N-terminal catalytic domain of
lysosomal alpha-mannosidase and similar proteins;
glycoside hydrolase family 38 (GH38). The subfamily is
represented by lysosomal alpha-mannosidase (LAM,
Man2B1, EC 3.2.1.114), which is a broad specificity
exoglycosidase hydrolyzing all known alpha 1,2-, alpha
1,3-, and alpha 1,6-mannosidic linkages from numerous
high mannose type oligosaccharides. LAM is expressed in
all tissues and in many species. In mammals, the
absence of LAM can cause the autosomal recessive
disease alpha-mannosidosis. LAM has an acidic pH
optimum at 4.0-4.5. It is stimulated by zinc ion and is
inhibited by cobalt ion and plant alkaloids, such as
swainsonine (SW). LAM catalyzes hydrolysis by a double
displacement mechanism in which a glycosyl-enzyme
intermediate is formed and hydrolyzed via oxacarbenium
ion-like transition states. A carboxylic acid in the
active site acts as the catalytic nucleophile in the
formation of the covalent intermediate while a second
carboxylic acid acts as a general acid catalyst. The
same residue is thought to assist in the hydrolysis
(deglycosylation) step, this time acting as a general
base.
Length = 278
Score = 26.0 bits (58), Expect = 4.1
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 4/38 (10%)
Query: 59 WCDLKTVGQYYVKLMWCPSHCGIRG--NEAVDQAAKDP 94
W LKTV QYY H G++ + +++ K+P
Sbjct: 15 W--LKTVDQYYYGSNNSIQHAGVQYILDSVIEELLKNP 50
>gnl|CDD|178801 PRK00024, PRK00024, hypothetical protein; Reviewed.
Length = 224
Score = 25.8 bits (58), Expect = 4.7
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 8/40 (20%)
Query: 9 AELIAILLCLRS-IKNHPAM---RFLLVSDSMGSLSAIAN 44
AEL+AIL LR+ K + R LL GSL + +
Sbjct: 27 AELLAIL--LRTGTKGKSVLDLARELL--QRFGSLRGLLD 62
>gnl|CDD|223700 COG0627, COG0627, Predicted esterase [General function prediction
only].
Length = 316
Score = 25.9 bits (57), Expect = 5.0
Identities = 12/63 (19%), Positives = 15/63 (23%), Gaps = 13/63 (20%)
Query: 34 DSMGSLSAIANPYLSCPIISQIYSAWCDLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAKD 93
S S S I +P + W G M P + D
Sbjct: 178 KSASSFSGILSPSSPWGPTLAMGDPW------GGKAFNAMLGP-------DSDPAWQEND 224
Query: 94 PLL 96
PL
Sbjct: 225 PLS 227
>gnl|CDD|236334 PRK08719, PRK08719, ribonuclease H; Reviewed.
Length = 147
Score = 25.6 bits (56), Expect = 5.2
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 69 YVKLMWCPSHCGIRGNEAVDQAA 91
YV++ +H GI GNEA D A
Sbjct: 119 YVEVEKVTAHSGIEGNEAADMLA 141
>gnl|CDD|181869 PRK09453, PRK09453, phosphodiesterase; Provisional.
Length = 182
Score = 25.2 bits (56), Expect = 6.1
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 27 MRFLLVSDSMGSLSA 41
M+ + SD+ GSL A
Sbjct: 1 MKLMFASDTHGSLPA 15
>gnl|CDD|214649 smart00404, PTPc_motif, Protein tyrosine phosphatase, catalytic
domain motif.
Length = 105
Score = 25.0 bits (55), Expect = 6.7
Identities = 7/26 (26%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 1 MFHCSNGI---AELIAILLCLRSIKN 23
+ HCS G+ +AI + L+ ++
Sbjct: 43 VVHCSAGVGRTGTFVAIDILLQQLEA 68
>gnl|CDD|214469 smart00012, PTPc_DSPc, Protein tyrosine phosphatase, catalytic
domain, undefined specificity. Protein tyrosine
phosphatases. Homologues detected by this profile and
not by those of "PTPc" or "DSPc" are predicted to be
protein phosphatases with a similar fold to DSPs and
PTPs, yet with unpredicted specificities.
Length = 105
Score = 25.0 bits (55), Expect = 6.7
Identities = 7/26 (26%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 1 MFHCSNGI---AELIAILLCLRSIKN 23
+ HCS G+ +AI + L+ ++
Sbjct: 43 VVHCSAGVGRTGTFVAIDILLQQLEA 68
>gnl|CDD|180839 PRK07103, PRK07103, polyketide beta-ketoacyl:acyl carrier protein
synthase; Validated.
Length = 410
Score = 25.4 bits (56), Expect = 7.3
Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 3 HC--SNGIAELIAILLCLRSIKNHP 25
H + GI ELIA LL +R+ HP
Sbjct: 341 HGLSAAGIVELIATLLQMRAGFLHP 365
>gnl|CDD|234752 PRK00413, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 638
Score = 25.0 bits (56), Expect = 8.4
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 67 QYYVKLMWCPSHCGI 81
+Y +K M CP H I
Sbjct: 326 EYALKPMNCPGHVQI 340
>gnl|CDD|176208 cd08246, crotonyl_coA_red, crotonyl-CoA reductase. Crotonyl-CoA
reductase, a member of the medium chain
dehydrogenase/reductase family, catalyzes the
NADPH-dependent conversion of crotonyl-CoA to
butyryl-CoA, a step in (2S)-methylmalonyl-CoA
production for straight-chain fatty acid biosynthesis.
Like enoyl reductase, another enzyme in fatty acid
synthesis, crotonyl-CoA reductase is a member of the
zinc-dependent alcohol dehydrogenase-like medium chain
dehydrogenase/reductase family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 393
Score = 25.1 bits (55), Expect = 8.5
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 78 HCGIRGNEAVDQAAKDPLLSP 98
HC + ++A DP+ P
Sbjct: 112 HCSVWDGNDPERAGGDPMFDP 132
>gnl|CDD|236567 PRK09559, PRK09559, putative global regulator; Reviewed.
Length = 327
Score = 25.0 bits (55), Expect = 8.9
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 24 HPAMRFLLVSD 34
HPA RFLLV+D
Sbjct: 156 HPAERFLLVTD 166
>gnl|CDD|203321 pfam05733, Tenui_N, Tenuivirus/Phlebovirus nucleocapsid protein.
This family consists of several Tenuivirus and
Phlebovirus nucleocapsid proteins. These are ssRNA
viruses.
Length = 224
Score = 25.0 bits (55), Expect = 9.4
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 6/46 (13%)
Query: 41 AIANPYLSCPIISQIYSAW-----CDLKTVGQYYVKLMWCPSHCGI 81
A A +C + + SA D+ T G Y + M P G+
Sbjct: 109 AAAFAGWTCQALKVV-SAKLAVTGSDMDTSGPDYPRWMMHPQFAGL 153
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
0.325 0.137 0.441
Gapped
Lambda K H
0.267 0.0705 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,081,084
Number of extensions: 401486
Number of successful extensions: 421
Number of sequences better than 10.0: 1
Number of HSP's gapped: 418
Number of HSP's successfully gapped: 35
Length of query: 104
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 35
Effective length of database: 7,877,176
Effective search space: 275701160
Effective search space used: 275701160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.2 bits)