RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14885
(483 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-29
Identities = 35/124 (28%), Positives = 63/124 (50%), Gaps = 6/124 (4%)
Query: 222 VVF-DLSKRNSNTGFAFII---NNENFQYRLPHEASIFTAEAIAIFYCIKKISDMK--IK 275
V++ D SK TG F I + Y+L S+F AE +AI ++ +
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60
Query: 276 KAIIFSDNKSVLNGIDNIQQRNNIIQLIKQEYYFASTNGSQISFMWIPSHSNIALNDKAD 335
K IFSD+++ L + + + + ++ I++ + +G ++ W+P HS I N++AD
Sbjct: 61 KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERAD 120
Query: 336 QLAK 339
+LAK
Sbjct: 121 RLAK 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 = 67.7 bits (166), Expect = 1e-13
Identities = 28/114 (24%), Positives = 52/114 (45%), Gaps = 5/114 (4%)
Query: 227 SKRNSNTGFAFIINNE-NFQYRLPHEASIFTAEAIAIFYCIKKISDMKIKKAIIFSDNKS 285
+ G ++ + LP + AE +A+ ++ +S +K I++D++
Sbjct: 13 NGNPGPGGAGYVTDGGKQRSKPLPG-TTNQRAELLALIEALEALSG---QKVNIYTDSQY 68
Query: 286 VLNGIDNIQQRNNIIQLIKQEYYFASTNGSQISFMWIPSHSNIALNDKADQLAK 339
V+ GI N + + IK E + ++ W+P HS I N+ AD+LAK
Sbjct: 69 VIGGITNGWPTKSESKPIKNEIWELLQKKHKVYIQWVPGHSGIPGNELADKLAK 122
>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 = 65.8 bits (161), Expect = 3e-13
Identities = 24/118 (20%), Positives = 48/118 (40%), Gaps = 9/118 (7%)
Query: 230 NSNTGFAFIINNENFQYRL-----PHEASIFTAEAIAIFYCIKKISDMKIKKAIIFSDNK 284
G ++ + + A+ AE +A+ ++ D+ +KK II +D+K
Sbjct: 10 PGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLKKLIIETDSK 69
Query: 285 SVLNGIDNIQQRNNIIQLIKQEYYFASTNGSQISFMWIPSHSNIALNDKADQLAKNSI 342
V++ I++ + L+ + + I F +P N AD+LAK +
Sbjct: 70 YVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPREGNEV----ADRLAKEAA 123
>gnl|CDD|214480 smart00034, CLECT, C-type lectin (CTL) or
carbohydrate-recognition domain (CRD). Many of these
domains function as calcium-dependent carbohydrate
binding modules.
Length = 124
Score = 57.2 bits (138), Expect = 3e-10
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 1/63 (1%)
Query: 29 CPQHWVQYRDSCYRFVKSPLKTRNDAKLNCKSLDSDLANVNDADEHGFIMYQLFWQDPQR 88
CP W+ Y CY+F KT DA+ C+SL LA+++ E+ F+ L
Sbjct: 1 CPSGWISYGGKCYKFSTEK-KTWEDAQAFCQSLGGHLASIHSEAENDFVASLLKNSGSSD 59
Query: 89 RKW 91
W
Sbjct: 60 YYW 62
>gnl|CDD|153063 cd03593, CLECT_NK_receptors_like, C-type lectin-like domain
(CTLD) of the type found in natural killer cell
receptors (NKRs). CLECT_NK_receptors_like: C-type
lectin-like domain (CTLD) of the type found in natural
killer cell receptors (NKRs), including proteins
similar to oxidized low density lipoprotein (OxLDL)
receptor (LOX-1), CD94, CD69, NKG2-A and -D, osteoclast
inhibitory lectin (OCIL), dendritic cell-associated
C-type lectin-1 (dectin-1), human myeloid inhibitory
C-type lectin-like receptor (MICL), mast
cell-associated functional antigen (MAFA), killer cell
lectin-like receptors: subfamily F, member 1 (KLRF1)
and subfamily B, member 1 (KLRB1), and lys49 receptors.
CTLD refers to a domain homologous to the
carbohydrate-recognition domains (CRDs) of the C-type
lectins. NKRs are variously associated with activation
or inhibition of natural killer (NK) cells. Activating
NKRs stimulate cytolysis by NK cells of virally
infected or transformed cells; inhibitory NKRs block
cytolysis upon recognition of markers of healthy self
cells. Most Lys49 receptors are inhibitory; some are
stimulatory. OCIL inhibits NK cell function via
binding to the receptor NKRP1D. Murine OCIL in
addition to inhibiting NK cell function inhibits
osteoclast differentiation. MAFA clusters with the type
I Fc epsilon receptor (FcepsilonRI) and inhibits the
mast cells secretory response to FcepsilonRI stimulus.
CD72 is a negative regulator of B cell receptor
signaling. NKG2D is an activating receptor for
stress-induced antigens; human NKG2D ligands include
the stress induced MHC-I homologs, MICA, MICB, and ULBP
family of glycoproteins Several NKRs have a
carbohydrate-binding capacity which is not mediated
through calcium ions (e.g. OCIL binds a range of high
molecular weight sulfated glycosaminoglycans including
dextran sulfate, fucoidan, and gamma-carrageenan
sugars). Dectin-1 binds fungal beta-glucans and in
involved in the innate immune responses to fungal
pathogens. MAFA binds saccharides having terminal
alpha-D mannose residues in a calcium-dependent manner.
LOX-1 is the major receptor for OxLDL in endothelial
cells and thought to play a role in the pathology of
atherosclerosis. Some NKRs exist as homodimers
(e.g.Lys49, NKG2D, CD69, LOX-1) and some as
heterodimers (e.g. CD94/NKG2A). Dectin-1 can function
as a monomer in vitro.
Length = 116
Score = 53.1 bits (128), Expect = 9e-09
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 5/59 (8%)
Query: 29 CPQHWVQYRDSCYRFVKSPLKTRNDAKLNCKSLDSDLANVNDADEHGFIMYQL----FW 83
CP+ W+ Y + CY F KT N++K C S +S L ++D +E F+ Q+ +W
Sbjct: 1 CPKDWICYGNKCYYFSMEK-KTWNESKEACSSKNSSLLKIDDEEELEFLQSQIGSSSYW 58
>gnl|CDD|153060 cd03590, CLECT_DC-SIGN_like, C-type lectin-like domain (CTLD) of
the type found in human dendritic cell (DC)-specific
intercellular adhesion molecule 3-grabbing non-integrin
(DC-SIGN) and the related receptor, DC-SIGN receptor
(DC-SIGNR). CLECT_DC-SIGN_like: C-type lectin-like
domain (CTLD) of the type found in human dendritic cell
(DC)-specific intercellular adhesion molecule 3-grabbing
non-integrin (DC-SIGN) and the related receptor, DC-SIGN
receptor (DC-SIGNR). This group also contains proteins
similar to hepatic asialoglycoprotein receptor (ASGP-R)
and langerin in human. These proteins are type II
membrane proteins with a CTLD ectodomain. CTLD refers
to a domain homologous to the carbohydrate-recognition
domains (CRDs) of the C-type lectins. DC-SIGN is
thought to mediate the initial contact between dendritic
cells and resting T cells, and may also mediate the
rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind
to oligosaccharides present on human tissues, as well
as, on pathogens including parasites, bacteria, and
viruses. DC-SIGN and DC-SIGNR bind to HIV enhancing
viral infection of T cells. DC-SIGN and DC-SIGNR are
homotetrameric, and contain four CTLDs stabilized by a
coiled coil of alpha helices. The hepatic ASGP-R is an
endocytic recycling receptor which binds and
internalizes desialylated glycoproteins having a
terminal galactose or N-acetylgalactosamine residues on
their N-linked carbohydrate chains, via the
clathrin-coated pit mediated endocytic pathway, and
delivers them to lysosomes for degradation. It has been
proposed that glycoproteins bearing terminal Sia (sialic
acid) alpha2, 6GalNAc and Sia alpha2, 6Gal are
endogenous ligands for ASGP-R and that ASGP-R
participates in regulating the relative concentration of
serum glycoproteins bearing alpha 2,6-linked Sia. The
human ASGP-R is a hetero-oligomer composed of two
subunits, both of which are found within this group.
Langerin is expressed in a subset of dendritic
leukocytes, the Langerhans cells (LC). Langerin induces
the formation of Birbeck Granules (BGs) and associates
with these BGs following internalization. Langerin
binds, in a calcium-dependent manner, to
glyco-conjugates containing mannose and related sugars
mediating their uptake and degradation. Langerin
molecules oligomerize as trimers with three CTLDs held
together by a coiled-coil of alpha helices.
Length = 126
Score = 50.4 bits (121), Expect = 1e-07
Identities = 26/113 (23%), Positives = 46/113 (40%), Gaps = 24/113 (21%)
Query: 29 CPQHWVQYRDSCYRFVKSPLKTRNDAKLNCKSLDSDLANVNDADEHGFIMYQL-----FW 83
CP +W ++ SCY F + K+ +++ C+ + + L +N +E FI L +W
Sbjct: 1 CPTNWKSFQSSCY-FFSTEKKSWEESRQFCEDMGAHLVIINSQEEQEFISKILSGNRSYW 59
Query: 84 ---QDPQR-RKWYFGGTQQSPNLWVNEDDPQRRKWYFGGTQQSPNLW--VNED 130
D + +W WV+ K ++ + PN W ED
Sbjct: 60 IGLSDEETEGEW----------KWVDGTPLNSSKTFWHPGE--PNNWGGGGED 100
>gnl|CDD|153057 cd00037, CLECT, C-type lectin (CTL)/C-type lectin-like (CTLD)
domain. CLECT: C-type lectin (CTL)/C-type lectin-like
(CTLD) domain; protein domains homologous to the
carbohydrate-recognition domains (CRDs) of the C-type
lectins. This group is chiefly comprised of eukaryotic
CTLDs, but contains some, as yet functionally
uncharacterized, bacterial CTLDs. Many CTLDs are
calcium-dependent carbohydrate binding modules; other
CTLDs bind protein ligands, lipids, and inorganic
surfaces, including CaCO3 and ice. Animal C-type
lectins are involved in such functions as extracellular
matrix organization, endocytosis, complement activation,
pathogen recognition, and cell-cell interactions. For
example: mannose-binding lectin and lung surfactant
proteins A and D bind carbohydrates on surfaces (e.g.
pathogens, allergens, necrotic, and apoptotic cells) and
mediate functions associated with killing and
phagocytosis; P (platlet)-, E (endothelial)-, and L
(leukocyte)- selectins (sels) mediate the initial
attachment, tethering, and rolling of lymphocytes on
inflamed vascular walls enabling subsequent lymphocyte
adhesion and transmigration. CTLDs may bind a variety
of carbohydrate ligands including mannose,
N-acetylglucosamine, galactose, N-acetylgalactosamine,
and fucose. Several CTLDs bind to protein ligands, and
only some of these binding interactions are
Ca2+-dependent; including the CTLDs of Coagulation
Factors IX/X (IX/X) and Von Willebrand Factor (VWF)
binding proteins, and natural killer cell receptors.
C-type lectins, such as lithostathine, and some type II
antifreeze glycoproteins function in a Ca2+-independent
manner to bind inorganic surfaces. Many proteins in
this group contain a single CTLD; these CTLDs associate
with each other through several different surfaces to
form dimers, trimers, or tetramers, from which
ligand-binding sites project in different orientations.
Various vertebrate type 1 transmembrane proteins
including macrophage mannose receptor, endo180,
phospholipase A2 receptor, and dendritic and epithelial
cell receptor (DEC205) have extracellular domains
containing 8 or more CTLDs; these CTLDs remain in the
parent model. In some members (IX/X and VWF binding
proteins), a loop extends to the adjoining domain to
form a loop-swapped dimer. A similar conformation is
seen in the macrophage mannose receptor CRD4's putative
non-sugar bound form of the domain in the acid
environment of the endosome. Lineage specific
expansions of CTLDs have occurred in several animal
lineages including Drosophila melanogaster and
Caenorhabditis elegans; these CTLDs also remain in the
parent model.
Length = 116
Score = 46.5 bits (110), Expect = 2e-06
Identities = 31/143 (21%), Positives = 48/143 (33%), Gaps = 28/143 (19%)
Query: 39 SCYRFVKSPLKTRNDAKLNCKSLDSDLANVNDADEHGFIMYQLFWQDPQRRKWYFGGTQQ 98
SCY+F T +A+ C+SL LA+++ +E+ F+ L + + G
Sbjct: 1 SCYKFSTEK-LTWEEAQEYCRSLGGHLASIHSEEENDFLASLL--KKSSSSDVWIGLNDL 57
Query: 99 SPNLWVNEDDPQRRKWYFGGTQQSPNLWVNEDGTNLNELDAAFLPEPADNVQRDYLAYSF 158
S W DG+ L + EP D + S
Sbjct: 58 SSE----------------------GTWKWSDGSPLVDYTNWAPGEPNPGGSEDCVVLSS 95
Query: 159 SQSLKRWGFERVTGMEPLLFICE 181
S + V+ L FICE
Sbjct: 96 SSD---GKWNDVSCSSKLPFICE 115
>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 = 46.3 bits (111), Expect = 2e-06
Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 12/86 (13%)
Query: 261 AIFYCIKKISDMKIKKAIIFSDNKSVLNGIDN----IQQRNNIIQLIKQEYYFASTNGSQ 316
A+ Y ++ IKK I+ D GI+ + N +E+ +
Sbjct: 56 AMEYAVEN----GIKKITIYYD----YEGIEKWATGEWKANKEGTKEYKEFMDKIKKKIK 107
Query: 317 ISFMWIPSHSNIALNDKADQLAKNSI 342
ISF+ + +HS N+ AD+LAK ++
Sbjct: 108 ISFVKVKAHSGDKYNELADKLAKKAL 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 = 46.8 bits (112), Expect = 3e-06
Identities = 25/101 (24%), Positives = 51/101 (50%), Gaps = 18/101 (17%)
Query: 257 AEAIAIFYCIKKISDMK--IKKAIIFSDNKSVLNGI-DNIQQ--RNN------------- 298
AE A+ + ++ I ++ + K +I +D++ V+NG+ + I + +N
Sbjct: 46 AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKD 105
Query: 299 IIQLIKQEYYFASTNGSQISFMWIPSHSNIALNDKADQLAK 339
+I+ + + G ++ F +P HS I N++AD+LAK
Sbjct: 106 LIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146
>gnl|CDD|218599 pfam05473, Herpes_UL45, UL45 protein. This family consists several
UL45 proteins. The herpes simplex virus UL45 gene
encodes an 18 kDa virion envelope protein whose function
remains unknown. It has been suggested that the 18 kDa
UL45 gene product is required for efficient growth in
the central nervous system at low doses and may play an
important role under the conditions of a naturally
acquired infection. This family also contains several
Varicellovirus UL45 or gene 15 proteins. The Equine
herpesvirus 1 UL45 protein represents a type II membrane
glycoprotein which has found to be non-essential for
EHV-1 growth in vitro but deletion reduces the viruses'
replication efficiency.
Length = 191
Score = 43.3 bits (102), Expect = 7e-05
Identities = 21/66 (31%), Positives = 28/66 (42%), Gaps = 2/66 (3%)
Query: 8 LFIFV-SFHSVFSQTIDELEL-RCPQHWVQYRDSCYRFVKSPLKTRNDAKLNCKSLDSDL 65
L +FV VF+ LE CP W+ DSC R +P T +A C + S L
Sbjct: 53 LTMFVIVATFVFTVPRMALESGPCPAEWIGLGDSCIRPDGTPADTYEEAVATCAAYPSKL 112
Query: 66 ANVNDA 71
+ A
Sbjct: 113 IPRSTA 118
>gnl|CDD|153059 cd03589, CLECT_CEL-1_like, C-type lectin-like domain (CTLD) of
the type found in CEL-1 from Cucumaria echinata and
Echinoidin from Anthocidaris crassispina.
CLECT_CEL-1_like: C-type lectin-like domain (CTLD) of
the type found in CEL-1 from Cucumaria echinata and
Echinoidin from Anthocidaris crassispina. CTLD refers
to a domain homologous to the carbohydrate-recognition
domains (CRDs) of the C-type lectins. The CEL-1 CTLD
binds three calcium ions and has a high specificity for
N-acteylgalactosamine (GalNAc). CEL-1 exhibits strong
cytotoxicity which is inhibited by GalNAc. This
protein may play a role as a toxin defending against
predation. Echinoidin is found in the coelomic fluid
of the sea urchin and is specific for GalBeta1-3GalNAc.
Echinoidin has a cell adhesive activity towards human
cancer cells which is not mediated through the CTLD.
Both CEL-1 and Echinoidin are multimeric proteins
comprised of multiple dimers linked by disulfide bonds.
Length = 137
Score = 40.8 bits (96), Expect = 2e-04
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 29 CPQHWVQYRDSCYRFVKSPLKTRNDAKLNCKSLDS-----DLANVNDADEHGFIMYQLF 82
CP W + CYRF T +A+L C+S L +++ +E+ F+ Y LF
Sbjct: 1 CPTFWTAFGGYCYRFF-GDRLTWEEAELRCRSFSIPGLIAHLVSIHSQEENDFV-YDLF 57
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 40.8 bits (96), Expect = 3e-04
Identities = 18/95 (18%), Positives = 41/95 (43%), Gaps = 12/95 (12%)
Query: 257 AEAIAIFYCIKKISDMKIKKAIIFSDNKSVLNGID-------NIQQRNNIIQLIK----- 304
AE A+ ++ + ++ + +++D+K V+ GI + + +K
Sbjct: 46 AELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLW 105
Query: 305 QEYYFASTNGSQISFMWIPSHSNIALNDKADQLAK 339
+E + + W+ H+ N++ADQLA+
Sbjct: 106 EELDELLKRHELVFWEWVKGHAGHPENERADQLAR 140
>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 = 39.1 bits (92), Expect = 4e-04
Identities = 22/99 (22%), Positives = 41/99 (41%), Gaps = 18/99 (18%)
Query: 253 SIFTAEAIAIFYCIKKISDMKIKKAIIFSDNKSVLNGIDNIQQRN-------NIIQLIKQ 305
S AEA A+ ++ ++ I++ I+ SD++ V + IQ +++ I++
Sbjct: 1 SPLEAEAEALLEGLQLALELGIRRLIVESDSQLV---VQQIQGEYEARSRLAALLREIRK 57
Query: 306 EYYFASTNGSQISFMWIPSHSNIALNDKADQLAKNSINS 344
+S +P N AD LAK + S
Sbjct: 58 ---LLKKF-DSVSVSHVPRECNRV----ADALAKLASAS 88
>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 = 0.001
Identities = 25/117 (21%), Positives = 44/117 (37%), Gaps = 25/117 (21%)
Query: 236 AFIINNENFQYR----LPHEASIFTAEAIAIFYCIKKISDMKIKKAIIFSDNKSVLNGID 291
I + + L A+ AE A+ ++ ++ IKK I+ D++ V+N I
Sbjct: 20 IVIKSPDGEVLEQSIPLGFPATNNEAEYEALIAGLELALELGIKKLEIYGDSQLVVNQIQ 79
Query: 292 NIQQRNN---------IIQLIKQEYYFASTNGSQISFMWIPSHSNIALNDKADQLAK 339
+ N +L+K+ ++ WIP N +AD LA
Sbjct: 80 GEYEVKNERLAPYLEEARELLKK--------FEEVEIKWIPREENK----EADALAN 124
>gnl|CDD|153064 cd03594, CLECT_REG-1_like, C-type lectin-like domain (CTLD) of the
type found in Human REG-1 (lithostathine), REG-4, and
avian eggshell-specific proteins: ansocalcin,
structhiocalcin-1(SCA-1), and -2(SCA-2).
CLECT_REG-1_like: C-type lectin-like domain (CTLD) of
the type found in Human REG-1 (lithostathine), REG-4,
and avian eggshell-specific proteins: ansocalcin,
structhiocalcin-1(SCA-1), and -2(SCA-2). CTLD refers to
a domain homologous to the carbohydrate-recognition
domains (CRDs) of the C-type lectins. REG-1 is a
proliferating factor which participates in various kinds
of tissue regeneration including pancreatic beta-cell
regeneration, regeneration of intestinal mucosa,
regeneration of motor neurons, and perhaps in tissue
regeneration of damaged heart. REG-1 may play a role on
the pathophysiology of Alzheimer's disease and in the
development of gastric cancers. Its expression is
correlated with reduced survival from early-stage
colorectal cancer. REG-1 also binds and aggregates
several bacterial strains from the intestinal flora and
it has been suggested that it is involved in the control
of the intestinal bacterial ecosystem. Rat
lithostathine has calcium carbonate crystal inhibitor
activity in vitro. REG-IV is unregulated in pancreatic,
gastric, hepatocellular, and prostrate adenocarcinomas.
REG-IV activates the EGF receptor/Akt/AP-1 signaling
pathway in colorectal carcinoma. Ansocalcin, SCA-1 and
-2 are found at high concentration in the calcified egg
shell layer of goose and ostrich, respectively and tend
to form aggregates. Ansocalcin nucleates calcite
crystal aggregates in vitro.
Length = 129
Score = 38.9 bits (91), Expect = 0.001
Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 15/89 (16%)
Query: 29 CPQHWVQYRDSCYRFVKSPLKTRNDAKLNCKSL--DSDLANVNDADEHGFIMYQLFWQDP 86
CP+ W+ Y+ +CY + + P + +DA+L C+ + LA+++ E I +
Sbjct: 1 CPKGWLPYKGNCYGYFRQP-LSWSDAELFCQKYGPGAHLASIHSPAEAAAIASLI----- 54
Query: 87 QRRKWYFGGTQQSPNLWVNEDDP-QRRKW 114
Y Q +W+ DP Q R W
Sbjct: 55 ---SSYQKAYQ---PVWIGLHDPQQSRGW 77
>gnl|CDD|222982 PHA03097, PHA03097, C-type lectin-like protein; Provisional.
Length = 157
Score = 38.3 bits (89), Expect = 0.002
Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 1/70 (1%)
Query: 8 LFIFVSFHSVFSQTIDELELRCPQHWVQYRDSCYRFVKSPLKTRNDAKLNCKSLDSDLAN 67
L V S D L C WV Y + CY F ++ + ++ A C +D L
Sbjct: 25 LIALVIILSCKLSPGDRSGLNCRSGWVGYNNKCYTFSEN-ITNKHLAIERCADMDGILTL 83
Query: 68 VNDADEHGFI 77
++D E F+
Sbjct: 84 IDDQKEVLFV 93
>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 = 37.5 bits (88), Expect = 0.004
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 13/59 (22%)
Query: 281 SDNKSVLNGIDNIQQRNNIIQLIKQEYYFASTNGSQISFMWIPSHSNIALNDKADQLAK 339
+D K V N +D Q+ + L+ + Q+++ W+ H+ N++AD+LA
Sbjct: 90 ADGKPVKN-VDLWQE---LDALLAKH---------QVTWHWVKGHAGHPGNERADELAN 135
>gnl|CDD|165201 PHA02867, PHA02867, C-type lectin protein; Provisional.
Length = 167
Score = 35.8 bits (82), Expect = 0.019
Identities = 18/75 (24%), Positives = 28/75 (37%), Gaps = 12/75 (16%)
Query: 3 LISSCLFIFVSFHSVFSQTIDELELRCPQHWVQYRDSCYRFVKSPLKTRNDAKLNCKSLD 62
+ + F F V CP W+ Y CY F + ND+K C +D
Sbjct: 34 VTCKWYYAFPYFSKV-----------CPDEWIGYNSKCYYFTINE-TNWNDSKKLCDVMD 81
Query: 63 SDLANVNDADEHGFI 77
S L ++ + F+
Sbjct: 82 SSLIRFDNIETLNFV 96
>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 = 33.4 bits (77), Expect = 0.082
Identities = 28/143 (19%), Positives = 49/143 (34%), Gaps = 36/143 (25%)
Query: 222 VVF-DLSKRNSNTGFA-FIINNENFQYRLPHEASIFTAEAIAIFYCIKKISDMKIKKAII 279
VF D S G+A + LP+ S AE IA+ ++ + I
Sbjct: 1 TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALELAKGKPVN---I 57
Query: 280 FSDNKSV----------------LNGIDNIQQR--NNIIQLIKQEYYFASTNGSQISFMW 321
++D+ L G + + I++ ++ +
Sbjct: 58 YTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPK--------PVAVIH 109
Query: 322 IPSHSN----IAL-NDKADQLAK 339
I +HS +AL N +ADQ A+
Sbjct: 110 IRAHSGLPGPLALGNARADQAAR 132
>gnl|CDD|200477 cd11338, AmyAc_CMD, Alpha amylase catalytic domain found in
cyclomaltodextrinases and related proteins.
Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase
(NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC
3.2.1.133) catalyze the hydrolysis of alpha-(1,4)
glycosidic linkages on a number of substrates including
cyclomaltodextrins (CDs), pullulan, and starch. These
enzymes hydrolyze CDs and starch to maltose and pullulan
to panose by cleavage of alpha-1,4 glycosidic bonds
whereas alpha-amylases essentially lack activity on CDs
and pullulan. They also catalyze transglycosylation of
oligosaccharides to the C3-, C4- or C6-hydroxyl groups
of various acceptor sugar molecules. Since these
proteins are nearly indistinguishable from each other,
they are referred to as cyclomaltodextrinases (CMDs).
The Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 389
Score = 32.8 bits (76), Expect = 0.33
Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 9/52 (17%)
Query: 77 IMYQLF---------WQDPQRRKWYFGGTQQSPNLWVNEDDPQRRKWYFGGT 119
+ YQ+F DP+ ++ + G P+ R+ ++GG
Sbjct: 3 VFYQIFPDRFANGDPSNDPKGGEYNYFGWPDLPDYPPPWGGEPTRRDFYGGD 54
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 30.6 bits (70), Expect = 0.88
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 316 QISFMWIPSHSNIALNDKADQLAKNSINSKLL 347
QI + W+ H+ N++ D+LA+ L
Sbjct: 114 QIKWHWVKGHAGHPENERCDELARAGAEEATL 145
>gnl|CDD|132709 TIGR03670, rpoB_arch, DNA-directed RNA polymerase subunit B. This
model represents the archaeal version of DNA-directed
RNA polymerase subunit B (rpoB) and is observed in all
archaeal genomes.
Length = 599
Score = 31.9 bits (73), Expect = 0.94
Identities = 27/99 (27%), Positives = 43/99 (43%), Gaps = 28/99 (28%)
Query: 130 DGTNLNELDAAFLPEPADNVQRDYLAYSFSQSLKRWGFERVTG--MEPLLFICEASIQKL 187
DGT F EP + ++++ L F K ++ +TG +E +FI QKL
Sbjct: 421 DGT-------PFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKL 473
Query: 188 HYLLNDDRTYQYGMDIENPDKI---PRGPYFI--KQPTD 221
H+++ DKI RGP + +QPT+
Sbjct: 474 HHMV--------------ADKIHARSRGPVQVLTRQPTE 498
>gnl|CDD|152929 pfam12495, Vip3A_N, Vegetative insecticide protein 3A N terminal.
This family of proteins is found in bacteria. Proteins
in this family are typically between 170 and 789 amino
acids in length. The family is found in association with
pfam02018. Vip3A represents a novel class of proteins
insecticidal to lepidopteran insect larvae.
Length = 177
Score = 30.8 bits (69), Expect = 1.1
Identities = 30/90 (33%), Positives = 44/90 (48%), Gaps = 8/90 (8%)
Query: 309 FASTNGSQISFMWIPSHSNIALNDKADQLAKNSINSKLLDFYIQDDLKNHLRKNIVKLYN 368
F + G ++ I + + LND + +L + +N L D Q +L L K I+K+ N
Sbjct: 27 FKTDTGGNLTLDEILKNQQL-LNDISGKL--DGVNGSLNDLIAQGNLNTELSKEILKIAN 83
Query: 369 DQ--WTNIQNNKLRTIKDNTTLWKTSLRKI 396
+Q N NNKL I NT L + L KI
Sbjct: 84 EQNQVLNDVNNKLDAI--NTML-RVYLPKI 110
>gnl|CDD|153067 cd03597, CLECT_attractin_like, C-type lectin-like domain (CTLD) of
the type found in human and mouse attractin (AtrN) and
attractin-like protein (ALP). CLECT_attractin_like:
C-type lectin-like domain (CTLD) of the type found in
human and mouse attractin (AtrN) and attractin-like
protein (ALP). CTLD refers to a domain homologous to
the carbohydrate-recognition domains (CRDs) of the
C-type lectins. Mouse AtrN (the product of the mahogany
gene) has been shown to bind Agouti protein and to
function in agouti-induced pigmentation and obesity.
Mutations in AtrN have also been shown to cause
spongiform encephalopathy and hypomyelination in rats
and hamsters. The cytoplasmic region of mouse ALP has
been shown to binds to melanocortin receptor (MCR4).
Signaling through MCR4 plays a role in appetite
suppression. Attractin may have therapeutic potential
in the treatment of obesity. Human attractin (hAtrN)
has been shown to be expressed on activated T cells and
released extracellularly. The circulating serum
attractin induces the spreading of monocytes that become
the focus of the clustering of non-proliferating T
cells.
Length = 129
Score = 29.5 bits (66), Expect = 2.0
Identities = 30/136 (22%), Positives = 57/136 (41%), Gaps = 23/136 (16%)
Query: 29 CPQHWVQYRDSCYRFVKSPLKTRNDAKLNCKSLDSDLANVNDADEHGFIMYQLFWQDPQR 88
C + W +SC + + ++ ++AKL C++L++ LA++ + F++ +L
Sbjct: 1 CGEGWHLVGNSCLKINTAR-ESYDNAKLYCRNLNAVLASLTTQKKVEFVLKEL------- 52
Query: 89 RKWYFGGTQQSPNLWVNEDDPQRRKWYFGGTQQSPNLWVNEDGTNLNELDAAFLP-EPAD 147
+K + +P WV G + + + W ED + +LP EP+D
Sbjct: 53 QKHQMTKQKLTP--WV------------GLRKINVSYWCWEDMSPFTNTTLQWLPGEPSD 98
Query: 148 NVQRDYLAYSFSQSLK 163
YL LK
Sbjct: 99 AGFCGYLEEPAVSGLK 114
>gnl|CDD|237997 cd00032, CASc, Caspase, interleukin-1 beta converting enzyme (ICE)
homologues; Cysteine-dependent aspartate-directed
proteases that mediate programmed cell death
(apoptosis). Caspases are synthesized as inactive
zymogens and activated by proteolysis of the peptide
backbone adjacent to an aspartate. The resulting two
subunits associate to form an (alpha)2(beta)2-tetramer
which is the active enzyme. Activation of caspases can
be mediated by other caspase homologs.
Length = 243
Score = 30.3 bits (69), Expect = 2.1
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 229 RNSNTGFAFIINNENFQYRLP 249
+ G A IINNENF L
Sbjct: 5 NSKRRGLALIINNENFDKGLK 25
>gnl|CDD|222979 PHA03093, PHA03093, EEV glycoprotein; Provisional.
Length = 185
Score = 29.7 bits (67), Expect = 2.3
Identities = 16/34 (47%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 36 YRDSCYRFVKSPLKTRNDAKLNCKSLDSDLANVN 69
Y SCY F P KT +DAK +C S L N N
Sbjct: 106 YDGSCYIFHSEP-KTFSDAKADCAKKSSTLPNSN 138
>gnl|CDD|215684 pfam00059, Lectin_C, Lectin C-type domain. This family includes
both long and short form C-type.
Length = 108
Score = 28.5 bits (64), Expect = 3.0
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 48 LKTRNDAKLNCKSLDSDLANVNDADEHGFIMY 79
KT +A+ C+ L L ++ A+E F+
Sbjct: 2 SKTWAEAEAACQKLGGHLVSIQSAEEQDFLTS 33
>gnl|CDD|185407 PTZ00035, PTZ00035, Rad51 protein; Provisional.
Length = 337
Score = 29.6 bits (67), Expect = 3.4
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 251 EASIFTAEAIAI-----FYCIKKISDMK---IKKAIIFSDNKSVLNGIDNIQQRNNIIQL 302
EA I T E++A IK IS+ K IK+A ++ + ++ R NII++
Sbjct: 41 EAGICTVESVAYATKKDLCNIKGISEAKVEKIKEAASKLVPMGFISATEYLEARKNIIRI 100
>gnl|CDD|153073 cd03603, CLECT_VCBS, A bacterial subgroup of the C-type lectin-like
(CTLD) domain; a subgroup of bacterial protein domains
homologous to the carbohydrate-recognition domains
(CRDs) of the C-type lectins. CLECT_VCBS: A bacterial
subgroup of the C-type lectin-like (CTLD) domain; a
subgroup of bacterial protein domains homologous to the
carbohydrate-recognition domains (CRDs) of the C-type
lectins. Many CTLDs are calcium-dependent carbohydrate
binding modules; other CTLDs bind protein ligands,
lipids, and inorganic surfaces including CaCO3 and ice.
Bacterial CTLDs within this group are functionally
uncharacterized. Animal C-type lectins are involved in
such functions as extracellular matrix organization,
endocytosis, complement activation, pathogen
recognition, and cell-cell interactions. CTLDs may bind
a variety of carbohydrate ligands including mannose,
N-acetylglucosamine, galactose, N-acetylgalactosamine,
and fucose. CTLDs associate with each other through
several different surfaces to form dimers, trimers, or
tetramers from which ligand-binding sites project in
different orientations. In some CTLDs a loop extends to
the adjoining domain to form a loop-swapped dimer.
Length = 118
Score = 28.5 bits (64), Expect = 3.5
Identities = 21/93 (22%), Positives = 34/93 (36%), Gaps = 10/93 (10%)
Query: 41 YRFVKSPLKTRNDAKLNCKSLDSDLANVNDADEHGFIMYQLFWQDPQRRKWYFGGTQ-QS 99
Y+FV T A+ +SL L +N A+E+ ++ F + G + +
Sbjct: 3 YKFVDGG-MTWEAAQTLAESLGGHLVTINSAEENDWL-LSNF---GGYGASWIGASDAAT 57
Query: 100 PNLWVNEDDPQRRKWY--FGGTQQSPNLWVNED 130
W D Y +G + N NED
Sbjct: 58 EGTWKWSDGE--ESTYTNWGSGEPHNNGGGNED 88
>gnl|CDD|216687 pfam01763, Herpes_UL6, Herpesvirus UL6 like. This family consists
of various proteins from the herpesviridae that are
similar to herpes simplex virus type I UL6 virion
protein. UL6 is essential for cleavage and packaging of
the viral genome.
Length = 556
Score = 29.5 bits (67), Expect = 4.4
Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 4/66 (6%)
Query: 351 IQDDLKNHLRKNIVKLYNDQWTNIQNNKLRTIKDNTTLWKTSLRKIRNEEILLTRLRIGH 410
+ + + ++ K Q I N + TI+D + L+K+R E L+RLR
Sbjct: 351 TRQAFRKSVSNSVNKCLEGQ---I-NEQFDTIEDLKEENEDLLKKLRELESELSRLREEA 406
Query: 411 TRITHS 416
S
Sbjct: 407 RASRGS 412
>gnl|CDD|165262 PHA02953, PHA02953, IEV and EEV membrane glycoprotein;
Provisional.
Length = 170
Score = 27.8 bits (62), Expect = 8.4
Identities = 11/41 (26%), Positives = 15/41 (36%), Gaps = 1/41 (2%)
Query: 29 CPQHWVQYRDSCYRFVKSPLKTRNDAKLNCKSLDSDLANVN 69
C + W+ Y + CY L T L C + L N
Sbjct: 47 CAKGWIPYDNYCYLDTNIQLSTYGAVYL-CNKYRARLPKPN 86
>gnl|CDD|185494 PTZ00168, PTZ00168, mitochondrial carrier protein; Provisional.
Length = 259
Score = 28.4 bits (63), Expect = 8.8
Identities = 19/69 (27%), Positives = 29/69 (42%), Gaps = 3/69 (4%)
Query: 240 NNENFQYRLPHEASIFTAEAIAIFYCIKKISDMKIKKAIIFSDNKSVLNGIDNIQQRNNI 299
EN + S AE A CI ++ +K+ + S N SVL I I QR +
Sbjct: 77 YRENISKTNLYLISTSIAEITA---CIVRLPFEIVKQNMQVSGNISVLKTIYEITQREGL 133
Query: 300 IQLIKQEYY 308
+ + Y+
Sbjct: 134 PSFLGKSYF 142
>gnl|CDD|227036 COG4692, COG4692, Predicted neuraminidase (sialidase) [Carbohydrate
transport and metabolism].
Length = 381
Score = 28.3 bits (63), Expect = 9.1
Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 9/52 (17%)
Query: 92 YFGGTQQSPN---LWVNEDD------PQRRKWYFGGTQQSPNLWVNEDGTNL 134
+FGGT + + L V PQR F ++Q+P L+ D L
Sbjct: 50 WFGGTLEGKSDIFLSVLASSLNSWGEPQRLSADFSHSEQNPVLFKASDNLWL 101
>gnl|CDD|233891 TIGR02487, NrdD, anaerobic ribonucleoside-triphosphate reductase.
This model represents the oxygen-sensitive (anaerobic,
class III) ribonucleotide reductase. The mechanism of
the enzyme involves a glycine-centered radical , a
C-terminal zinc binding site , and a set of conserved
active site cysteines and asparagines. This enzyme
requires an activating component, NrdG, a radical-SAM
domain containing enzyme (TIGR02491). Together the two
form an alpha-2/beta-2 heterodimer [Purines,
pyrimidines, nucleosides, and nucleotides,
2'-Deoxyribonucleotide metabolism].
Length = 579
Score = 28.5 bits (64), Expect = 9.4
Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 298 NIIQLIK-QEYYFASTNGSQISFMWIPS--HSNIALNDKADQLAKNSIN 343
N+ + I + + TNG I+++ + AL D + KN I
Sbjct: 468 NLGEKIDIEAPFHPLTNGGHITYIELDEAIPDPEALKDITKKAMKNGIG 516
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
0.321 0.136 0.417
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,657,987
Number of extensions: 2391038
Number of successful extensions: 1977
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1963
Number of HSP's successfully gapped: 60
Length of query: 483
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 382
Effective length of database: 6,457,848
Effective search space: 2466897936
Effective search space used: 2466897936
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 (21.9 bits)
S2: 61 (27.3 bits)