RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7728
(65 letters)
>gnl|CDD|143238 cd05761, Ig2_Necl-1-4_like, Second immunoglobulin (Ig)-like
domain of the nectin-like molecules Necl-1 - Necl-4
(also known as cell adhesion molecules CADM3, CADM1,
CADM2, and CADM4, respectively). Ig2_Necl-1-4_like:
domain similar to the second immunoglobulin (Ig)-like
domain of the nectin-like molecules Necl-1 (also known
as cell adhesion molecule 3 (CADM3)), Necl-2 (CADM1),
Necl-3 (CADM2) and Necl-4 (CADM4). These nectin-like
molecules have similar domain structures to those of
nectins. At least five nectin-like molecules have been
identified (Necl-1 - Necl-5). These have an
extracellular region containing three Ig-like domains,
one transmembrane region, and one cytoplasmic region.
The N-terminal Ig-like domain of the extracellular
region belongs to the V-type subfamily of Ig domains,
is essential to cell-cell adhesion, and plays a part in
the interaction with the envelope glycoprotein D of
various viruses. Necl-1 and Necl-2 have
Ca(2+)-independent homophilic and heterophilic
cell-cell adhesion activity. Necl-1 is specifically
expressed in neural tissue and is important to the
formation of synapses, axon bundles, and myelinated
axons. Necl-2 is expressed in a wide variety of
tissues, and is a putative tumour suppressor gene,
which is downregulated in aggressive neuroblastoma.
Necl-3 has been shown to accumulate in tissues of the
central and peripheral nervous system, where it is
expressed in ependymal cells and myelinated axons. It
is observed at the interface between the axon shaft and
the myelin sheath. Necl-4 is expressed on Schwann
cells, and plays a key part in initiating peripheral
nervous system (PNS) myelination. Necl-4 participates
in cell-cell adhesion and is proposed to play a role in
tumor suppression.
Length = 82
Score = 43.5 bits (103), Expect = 1e-07
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 38 EITLECLVKNAKPAAKIVWYRGNTELK 64
E+ L C +KPAA I W++G+ ELK
Sbjct: 1 EVELTCTSSGSKPAATIRWFKGDKELK 27
>gnl|CDD|143329 cd07705, Ig2_Necl-1, Second immunoglobulin (Ig)-like domain of
nectin-like molcule-1 (Necl-1, also known as cell
adhesion molecule3 (CADM3)). Ig2_Necl-1: second
immunoglobulin (Ig)-like domain of nectin-like
molcule-1 (Necl-1, also known as cell adhesion
molecule3 (CADM3)). These nectin-like molecules have
similar domain structures to those of nectins. At least
five nectin-like molecules have been identified (Necl-1
- Necl-5). These have an extracellular region
containing three Ig-like domains, one transmembrane
region, and one cytoplasmic region. The N-terminal
Ig-like domain of the extracellular region belongs to
the V-type subfamily of Ig domains, is essential to
cell-cell adhesion, and plays a part in the interaction
with the envelope glycoprotein D of various viruses.
Necl-1 and Necl-2 have Ca(2+)-independent homophilic
and heterophilic cell-cell adhesion activity. Necl-1 is
specifically expressed in neural tissue and is
important to the formation of synapses, axon bundles,
and myelinated axons. Necl-2 is expressed in a wide
variety of tissues, and is a putative tumour suppressor
gene, which is downregulated in aggressive
neuroblastoma. Ig domains are likely to participate in
ligand binding and recognition.
Length = 83
Score = 37.3 bits (86), Expect = 3e-05
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 40 TLECLVKNAKPAAKIVWYRGNTELK 64
L C +KPAA I W +G+ EL+
Sbjct: 3 KLRCTSSGSKPAANIKWRKGDQELE 27
>gnl|CDD|219745 pfam08205, C2-set_2, CD80-like C2-set immunoglobulin domain.
These domains belong to the immunoglobulin superfamily.
Length = 89
Score = 35.5 bits (82), Expect = 2e-04
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 35 ENQEITLECLVKNAKPAAKIVWYRGNTEL 63
EN E+ C KPA +I WY EL
Sbjct: 13 ENLEVVATCSSAGGKPAPRITWYLDGREL 41
>gnl|CDD|143291 cd05883, Ig2_Necl-2, Second immunoglobulin (Ig)-like domain of
nectin-like molecule 2 (also known as cell adhesion
molecule 1 (CADM1)). Ig2_Necl-2: second immunoglobulin
(Ig)-like domain of nectin-like molecule 2 (also known
as cell adhesion molecule 1 (CADM1)). Nectin-like
molecules (Necls) have similar domain structures to
those of nectins. At least five nectin-like molecules
have been identified (Necl-1 - Necl-5). These have an
extracellular region containing three Ig-like domains,
one transmembrane region, and one cytoplasmic region.
Necl-2 has Ca(2+)-independent homophilic and
heterophilic cell-cell adhesion activity. Necl-1 is
expressed in a wide variety of tissues, and is a
putative tumour suppressor gene, which is downregulated
in aggressive neuroblastoma. Ig domains are likely to
participate in ligand binding and recognition.
Length = 82
Score = 35.3 bits (81), Expect = 2e-04
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 38 EITLECLVKNAKPAAKIVWYRGNTELK 64
EI L C +KPAA I W++GN EL
Sbjct: 1 EIELNCTAMASKPAATIRWFKGNKELT 27
>gnl|CDD|143232 cd05755, Ig2_ICAM-1_like, Second immunoglobulin (Ig)-like domain
of intercellular cell adhesion molecule-1 (ICAM-1,
CD54) and similar proteins. Ig2_ ICAM-1_like: domain
similar to the second immunoglobulin (Ig)-like domain
of intercellular cell adhesion molecule-1 (ICAM-1,
CD54). During the inflammation process, these molecules
recruit leukocytes onto the vascular endothelium before
extravasation to the injured tissues. ICAM-1 may be
involved in organ targeted tumor metastasis. The
interaction of ICAM-1 with leukocyte
function-associated antigen-1 (LFA-1) plays a part in
leukocyte-endothelial cell recognition. This group also
contains ICAM-2, which also interacts with LFA-1.
Transmigration of immature dendritic cells across
resting endothelium is dependent on the interaction of
ICAM-2 with, yet unidentified, ligand(s) on the
dendritic cells. ICAM-1 has five Ig-like domains and
ICAM-2 has two. ICAM-1 may also act as host receptor
for viruses and parasites.
Length = 100
Score = 35.2 bits (81), Expect = 4e-04
Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 6/50 (12%)
Query: 17 PSSIEIVGHPSNSKIEIRENQEITLECLVKNAKPAAK--IVWYRGNTELK 64
P S+E+ PS + TL+C V P +V RGN L
Sbjct: 1 PDSVELSPLPSWQP----VGKNYTLQCDVPGVAPRQNLTVVLLRGNETLS 46
>gnl|CDD|143293 cd05885, Ig2_Necl-4, Second immunoglobulin (Ig)-like domain of
nectin-like molecule-4 (Necl-4, also known as cell
adhesion molecule 4 (CADM4)). Ig2_Necl-4: second
immunoglobulin (Ig)-like domain of nectin-like
molecule-4 (Necl-4, also known as cell adhesion
molecule 4 (CADM4)). Nectin-like molecules have similar
domain structures to those of nectins. At least five
nectin-like molecules have been identified
(Necl-1-Necl-5). These have an extracellular region
containing three Ig-like domains, one transmembrane
region, and one cytoplasmic region. Ig domains are
likely to participate in ligand binding and
recognition. Necl-4 is expressed on Schwann cells, and
plays a key part in initiating peripheral nervous
system (PNS) myelination. In injured peripheral nerve
cells, the mRNA signal for both Necl-4 and Necl-5 was
observed to be elevated. Necl-4 participates in
cell-cell adhesion and is proposed to play a role in
tumor suppression.
Length = 80
Score = 32.6 bits (74), Expect = 0.002
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 38 EITLECLVKNAKPAAKIVWYRGNTELK 64
E+ L CL +KPAA + WYR ELK
Sbjct: 1 EVELTCLSPRSKPAATLRWYRDRKELK 27
>gnl|CDD|191810 pfam07679, I-set, Immunoglobulin I-set domain.
Length = 90
Score = 33.0 bits (76), Expect = 0.002
Identities = 8/44 (18%), Positives = 18/44 (40%), Gaps = 3/44 (6%)
Query: 21 EIVGHPSNSKIEIRENQEITLECLVKNAKPAAKIVWYRGNTELK 64
+ P + +E++E + C V P + W++ L+
Sbjct: 2 KFTQKPKD--VEVQEGESARFTCTVT-GDPDPTVSWFKDGQPLR 42
>gnl|CDD|206066 pfam13895, Ig_2, Immunoglobulin domain. This domain contains
immunoglobulin-like domains.
Length = 80
Score = 32.8 bits (75), Expect = 0.002
Identities = 9/36 (25%), Positives = 14/36 (38%), Gaps = 1/36 (2%)
Query: 29 SKIEIRENQEITLECLVKNAKPAAKIVWYRGNTELK 64
S + E +++TL C P WY+ L
Sbjct: 7 SPTVVFEGEDVTLTCSA-PGNPPPNYTWYKDGVPLS 41
>gnl|CDD|143236 cd05759, Ig2_KIRREL3-like, Second immunoglobulin (Ig)-like domain
of Kirrel (kin of irregular chiasm-like) 3 (also known
as Neph2). Ig2_KIRREL3-like: domain similar to the
second immunoglobulin (Ig)-like domain of Kirrel (kin
of irregular chiasm-like) 3 (also known as Neph2). This
protein has five Ig-like domains, one transmembrane
domain, and a cytoplasmic tail. Included in this group
is mammalian Kirrel (Neph1), Kirrel2 (Neph3), and
Drosophila RST (irregular chiasm C-roughest) protein.
These proteins contain multiple Ig domains, have
properties of cell adhesion molecules, and are
important in organ development.
Length = 82
Score = 31.6 bits (72), Expect = 0.005
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 41 LECLVKNAKPAAKIVWYR 58
L C + AKPAA+I+W+R
Sbjct: 4 LTCRARGAKPAAEIIWFR 21
>gnl|CDD|143292 cd05884, Ig2_Necl-3, Second immunoglobulin (Ig)-like domain of
nectin-like molecule-3 (Necl-3, also known as cell
adhesion molecule 2 (CADM2)). Ig2_Necl-3: second
immunoglobulin (Ig)-like domain of nectin-like
molecule-3 (Necl-3, also known as cell adhesion
molecule 2 (CADM2)). Nectin-like molecules have similar
domain structures to those of nectins. At least five
nectin-like molecules have been identified (Necl-1 -
Necl-5). These have an extracellular region containing
three Ig-like domains, one transmembrane region, and
one cytoplasmic region. Necl-3 has been shown to
accumulate in tissues of the central and peripheral
nervous system, where it is expressed in ependymal
cells and myelinated axons. It is observed at the
interface between the axon shaft and the myelin sheath.
Ig domains are likely to participate in ligand binding
and recognition.
Length = 83
Score = 31.5 bits (71), Expect = 0.007
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 39 ITLECLVKNAKPAAKIVWYRGNTELK 64
+ L C +KPAA I W++ + E+K
Sbjct: 2 MQLTCKTSGSKPAADIRWFKNDKEIK 27
>gnl|CDD|197706 smart00408, IGc2, Immunoglobulin C-2 Type.
Length = 63
Score = 30.1 bits (68), Expect = 0.015
Identities = 9/30 (30%), Positives = 11/30 (36%), Gaps = 1/30 (3%)
Query: 35 ENQEITLECLVKNAKPAAKIVWYRGNTELK 64
E Q +TL C P I W + L
Sbjct: 1 EGQSVTLTCPA-EGNPVPNITWLKDGKPLP 29
>gnl|CDD|143231 cd05754, Ig3_Perlecan_like, Third immunoglobulin (Ig)-like domain
found in Perlecan and similar proteins.
Ig3_Perlecan_like: domain similar to the third
immunoglobulin (Ig)-like domain found in Perlecan.
Perlecan is a large multi-domain heparin sulfate
proteoglycan, important in tissue development and
organogenesis. Perlecan can be represented as 5 major
portions; its fourth major portion (domain IV) is a
tandem repeat of immunoglobulin-like domains
(Ig2-Ig15), which can vary in size due to alternative
splicing. Perlecan binds many cellular and
extracellular ligands. Its domain IV region has many
binding sites. Some of these have been mapped at the
level of individual Ig-like domains, including a site
restricted to the Ig5 domain for heparin/sulfatide, a
site restricted to the Ig3 domain for nidogen-1 and
nidogen-2, a site restricted to Ig4-5 for fibronectin,
and sites restricted to Ig2 and to Ig13-15 for
fibulin-2.
Length = 85
Score = 30.2 bits (68), Expect = 0.022
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 20 IEIVGHPSNSKIEIRENQEITLECLVKNAKPAAKIVWYRGNTEL 63
I++ S+ E+R +++ C K+ PA +VW R L
Sbjct: 1 IQVTVEEPRSQ-EVRPGADVSFICRAKSKSPAYTLVWTRVGGGL 43
>gnl|CDD|222457 pfam13927, Ig_3, Immunoglobulin domain. This family contains
immunoglobulin-like domains.
Length = 74
Score = 27.7 bits (61), Expect = 0.16
Identities = 8/27 (29%), Positives = 11/27 (40%)
Query: 38 EITLECLVKNAKPAAKIVWYRGNTELK 64
+TL C + P I WYR +
Sbjct: 17 GVTLTCSAEGGPPPPTISWYRNGSISG 43
>gnl|CDD|143165 cd00096, Ig, Immunoglobulin domain. Ig: immunoglobulin (Ig)
domain found in the Ig superfamily. The Ig superfamily
is a heterogenous group of proteins, built on a common
fold comprised of a sandwich of two beta sheets.
Members of this group are components of immunoglobulin,
neuroglia, cell surface glycoproteins, such as, T-cell
receptors, CD2, CD4, CD8, and membrane glycoproteins,
such as, butyrophilin and chondroitin sulfate
proteoglycan core protein. A predominant feature of
most Ig domains is a disulfide bridge connecting the
two beta-sheets with a tryptophan residue packed
against the disulfide bond.
Length = 74
Score = 27.8 bits (61), Expect = 0.17
Identities = 8/25 (32%), Positives = 10/25 (40%), Gaps = 1/25 (4%)
Query: 39 ITLECLVKNAKPAAKIVWYRGNTEL 63
+TL CL P I W + L
Sbjct: 1 VTLTCLASG-PPPPTITWLKNGKPL 24
>gnl|CDD|143180 cd04979, Ig_Semaphorin_C, Immunoglobulin (Ig)-like domain of
semaphorin. Ig_Semaphorin_C; Immunoglobulin (Ig)-like
domain in semaphorins. Semaphorins are transmembrane
protein that have important roles in a variety of
tissues. Functionally, semaphorins were initially
characterized for their importance in the development
of the nervous system and in axonal guidance. Later
they have been found to be important for the formation
and functioning of the cardiovascular, endocrine,
gastrointestinal, hepatic, immune, musculoskeletal,
renal, reproductive, and respiratory systems.
Semaphorins function through binding to their receptors
and transmembrane semaphorins also serves as receptors
themselves. Although molecular mechanism of semaphorins
is poorly understood, the Ig-like domains may involve
in ligand binding or dimerization.
Length = 89
Score = 27.7 bits (62), Expect = 0.21
Identities = 9/34 (26%), Positives = 14/34 (41%), Gaps = 2/34 (5%)
Query: 30 KIEIRENQEITLECLVKNAKPAAKIVWYRGNTEL 63
+ + E + LEC K+ A +VW L
Sbjct: 5 VVTVVEGNSVFLECSPKS--NLASVVWLFQGGPL 36
>gnl|CDD|179654 PRK03818, PRK03818, putative transporter; Validated.
Length = 552
Score = 27.9 bits (63), Expect = 0.27
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 2 LSRYGPRTRLYQFAPPS 18
L R G +LY F PPS
Sbjct: 413 LGRIGSIGKLYWFMPPS 429
>gnl|CDD|219514 pfam07686, V-set, Immunoglobulin V-set domain. This domain is
found in antibodies as well as neural protein P0 and
CTL4 amongst others.
Length = 114
Score = 26.8 bits (59), Expect = 0.54
Identities = 6/27 (22%), Positives = 12/27 (44%)
Query: 35 ENQEITLECLVKNAKPAAKIVWYRGNT 61
E +TL C ++ + + WY+
Sbjct: 15 EGGSVTLPCSFSSSSGSTSVYWYKQPL 41
>gnl|CDD|184794 PRK14697, PRK14697, bifunctional
5'-methylthioadenosine/S-adenosylhomocysteine
nucleosidase/phosphatase; Provisional.
Length = 233
Score = 26.5 bits (58), Expect = 0.98
Identities = 11/29 (37%), Positives = 20/29 (68%)
Query: 27 SNSKIEIRENQEITLECLVKNAKPAAKIV 55
S+ IEI E + ++ EC V+++K AK++
Sbjct: 133 SSLHIEIHEGRIVSGECFVEDSKLKAKLI 161
>gnl|CDD|129467 TIGR00370, TIGR00370, sensor histidine kinase inhibitor, KipI
family. [Hypothetical proteins, Conserved].
Length = 202
Score = 25.6 bits (56), Expect = 1.7
Identities = 8/37 (21%), Positives = 17/37 (45%)
Query: 6 GPRTRLYQFAPPSSIEIVGHPSNSKIEIRENQEITLE 42
G +T +Y + P +++G + + +EN L
Sbjct: 158 GLQTGVYPISTPGGWQLIGKTPLALFDPQENPPTLLR 194
>gnl|CDD|182799 PRK10874, PRK10874, cysteine sulfinate desulfinase; Provisional.
Length = 401
Score = 25.8 bits (57), Expect = 1.7
Identities = 10/16 (62%), Positives = 10/16 (62%)
Query: 47 NAKPAAKIVWYRGNTE 62
NA A IVW RG TE
Sbjct: 77 NAPDAKNIVWTRGTTE 92
>gnl|CDD|236179 PRK08188, PRK08188, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 714
Score = 25.4 bits (56), Expect = 2.1
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 15/47 (31%)
Query: 4 RYGPRTRLYQFAPP-----------SSIEIVGHPSNSKIEIRENQEI 39
R+G + Q PP SSI HP SKIEIR+ +I
Sbjct: 575 RHGIYNQNLQAVPPTGSISYINHSTSSI----HPIVSKIEIRKEGKI 617
>gnl|CDD|143166 cd00098, IgC, Immunoglobulin Constant domain. IgC:
Immunoglobulin constant domain (IgC). Members of the
IgC family are components of immunoglobulin, T-cell
receptors, CD1 cell surface glycoproteins, secretory
glycoproteins A/C, and Major Histocompatibility Complex
(MHC) class I/II molecules. In immunoglobulins, each
chain is composed of one variable domain (IgV) and one
or more IgC domains. These names reflect the fact that
the variability in sequences is higher in the variable
domain than in the constant domain. The IgV domain is
responsible for antigen binding, and the IgC domain is
involved in oligomerization and molecular interactions.
Length = 95
Score = 24.7 bits (54), Expect = 2.7
Identities = 9/40 (22%), Positives = 12/40 (30%), Gaps = 1/40 (2%)
Query: 25 HPSNSKIEIRENQEITLECLVKNAKPA-AKIVWYRGNTEL 63
E +TL CL P + W + EL
Sbjct: 2 FLLPPSPEELLGGSVTLTCLATGFYPPDITVTWLKNGKEL 41
>gnl|CDD|110031 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA insert domain.
Members of this family include: alpha subunit from
eubacteria alpha subunits from chloroplasts Rpb3
subunits from eukaryotes RpoD subunits from archaeal.
Length = 117
Score = 24.5 bits (54), Expect = 3.3
Identities = 9/36 (25%), Positives = 13/36 (36%), Gaps = 5/36 (13%)
Query: 13 QFAPPSSIEIV--GHPSNSKIEIRENQEITLECLVK 46
+EIV +R+ QE+ LE K
Sbjct: 58 DLESDPDVEIVNPDILI---ATLRKGQELELEAYAK 90
>gnl|CDD|143246 cd05769, IgC_TCR_beta, T cell receptor (TCR) beta chain constant
immunoglobulin domain. IgC_TCR_beta: Constant domain
of the beta chain of alpha/beta T-cell antigen
receptors (TCRs). TCRs mediate antigen recognition by T
lymphocytes, and are composed of alpha and beta, or
gamma and delta, polypeptide chains with variable (V)
and constant (C) regions. This group includes the
variable domain of the beta chain. Alpha/beta TCRs
recognize antigen as peptide fragments presented by
major histocompatibility complex (MHC) molecules. The
antigen binding site is formed by the variable domains
of the alpha and beta chains, located at the N-terminus
of each chain. Alpha/beta TCRs recognize antigens
differently from gamma/delta TCRs.
Length = 115
Score = 24.6 bits (54), Expect = 3.5
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 29 SKIEIRENQEITLECLVKNAKP 50
S+ EIR ++ TL CL P
Sbjct: 11 SEAEIRNKRKATLVCLATGFYP 32
>gnl|CDD|153378 cd07366, 3MGA_Dioxygenase, Subunit B of the Class III Extradiol
ring-cleavage dioxygenase, 3-O-Methylgallate
Dioxygenase, which catalyzes the oxidization and
subsequent ring-opening of 3-O-Methylgallate.
3-O-Methylgallate Dioxygenase catalyzes the oxidization
and subsequent ring-opening of 3-O-Methylgallate (3MGA)
between carbons 2 and 3. 3-O-Methylgallate Dioxygenase
is a key enzyme in the syringate degradation pathway, in
which the syringate is first converted to
3-O-Methylgallate by O-demethylase. This enzyme is a
member of the class III extradiol dioxygenase family, a
group of enzymes which uses a non-heme Fe(II) to cleave
aromatic rings between a hydroxylated carbon and an
adjacent non-hydroxylated carbon. LigAB-like enzymes are
usually composed of two subunits, designated A and B,
which form a tetramer composed of two copies of each
subunit. This model represents the catalytic subunit, B.
Length = 328
Score = 24.7 bits (54), Expect = 3.5
Identities = 8/37 (21%), Positives = 13/37 (35%)
Query: 2 LSRYGPRTRLYQFAPPSSIEIVGHPSNSKIEIRENQE 38
L R P +AP + HP ++ I+
Sbjct: 127 LDRMPPHEAAAGYAPDEARTYPCHPELARHLIKHTVA 163
>gnl|CDD|220554 pfam10076, DUF2313, Uncharacterized protein conserved in bacteria
(DUF2313). Members of this family of proteins comprise
various hypothetical and putative bacteriophage tail
proteins.
Length = 161
Score = 24.6 bits (54), Expect = 4.4
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 33 IRENQEITLECLVKNAKPAAKIVWY 57
+R + LECL++ KPA IV +
Sbjct: 134 LRSWGDAALECLLERIKPAHTIVIF 158
>gnl|CDD|133006 cd02513, CMP-NeuAc_Synthase, CMP-NeuAc_Synthase activates
N-acetylneuraminic acid by adding CMP moiety.
CMP-N-acetylneuraminic acid synthetase (CMP-NeuAc
synthetase) or acylneuraminate cytidylyltransferase
catalyzes the transfer the CMP moiety of CTP to the
anomeric hydroxyl group of NeuAc in the presence of
Mg++. It is the second to last step in the sialylation
of the oligosaccharide component of glycoconjugates by
providing the activated sugar-nucleotide cytidine
5'-monophosphate N-acetylneuraminic acid (CMP-Neu5Ac),
the substrate for sialyltransferases. Eukaryotic
CMP-NeuAc synthetases are predominantly located in the
nucleus. The activated CMP-Neu5Ac diffuses from the
nucleus into the cytoplasm.
Length = 223
Score = 23.7 bits (52), Expect = 7.7
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 3 SRYGPRTRLYQFAPPSSIEI 22
S +G +T Y+ SI+I
Sbjct: 191 SFFGGKTGPYEMPRERSIDI 210
>gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA
polymerase III (RNAP III), C-terminal domain.
Eukaryotic RNA polymerase III (RNAP III) is a large
multi-subunit complex responsible for the synthesis of
tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is
also known as C160 in yeast. Structure studies suggest
that different RNA polymerase complexes share a similar
crab-claw-shape structure. The C-terminal domain of
Rpb1, the largest subunit of RNAP II, makes up part of
the foot and jaw structures of RNAP II. The similarity
between this domain and the C-terminal domain of Rpb1,
its counterpart in RNAP II, suggests a similar
functional and structural role.
Length = 300
Score = 23.7 bits (52), Expect = 7.8
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 8 RTRLYQFAPPSSIEIVGHPSNSKIEIRENQEI 39
+T L + A S IE V P + I I+ +++I
Sbjct: 87 KTYLGEVA--SYIEEVYSPDDCYILIKLDKKI 116
>gnl|CDD|165528 PHA03270, PHA03270, envelope glycoprotein C; Provisional.
Length = 466
Score = 23.7 bits (51), Expect = 8.6
Identities = 18/63 (28%), Positives = 25/63 (39%), Gaps = 9/63 (14%)
Query: 3 SRYGPRTRLYQFAPPSSIEIVGHPSNSKIEIRENQEITLECLVKNAKPA--AKIVWYRGN 60
RYG TR+ F P S+ I H + E + C+ N P A W+ G
Sbjct: 208 HRYGTWTRVRMFRRP-SLSIRPH------AVLEGEPFGATCVAANYYPGDRAAFRWFEGG 260
Query: 61 TEL 63
E+
Sbjct: 261 DEV 263
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
0.316 0.133 0.394
Gapped
Lambda K H
0.267 0.0682 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,173,028
Number of extensions: 215772
Number of successful extensions: 221
Number of sequences better than 10.0: 1
Number of HSP's gapped: 219
Number of HSP's successfully gapped: 31
Length of query: 65
Length of database: 10,937,602
Length adjustment: 36
Effective length of query: 29
Effective length of database: 9,340,858
Effective search space: 270884882
Effective search space used: 270884882
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.3 bits)