RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14103
(78 letters)
>gnl|CDD|143170 cd04969, Ig5_Contactin_like, Fifth Ig domain of contactin.
Ig5_Contactin_like: Fifth Ig domain of contactins.
Contactins are neural cell adhesion molecules and are
comprised of six Ig domains followed by four
fibronectin type III(FnIII) domains anchored to the
membrane by glycosylphosphatidylinositol. The first
four Ig domains form the intermolecular binding
fragment, which arranges as a compact U-shaped module
via contacts between Ig domains 1 and 4, and between Ig
domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play
a part in the neuronal processes of neurite outgrowth,
axon guidance and fasciculation, and neuronal
migration. This group also includes contactin-1 and
contactin-5. The different contactins show different
expression patterns in the central nervous system.
During development and in adulthood, contactin-2 is
transiently expressed in subsets of central and
peripheral neurons. Contactin-5 is expressed
specifically in the rat postnatal nervous system,
peaking at about 3 weeks postnatal, and a lack of
contactin-5 (NB-2) results in an impairment of neuronal
act ivity in the rat auditory system. Contactin-5 is
highly expressed in the adult human brain in the
occipital lobe and in the amygdala. Contactin-1 is
differentially expressed in tumor tissues and may,
through a RhoA mechanism, facilitate invasion and
metastasis of human lung adenocarcinoma.
Length = 73
Score = 34.3 bits (79), Expect = 6e-04
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 16 WKRGIAILTAGSTKVTPDKRIQLVDGYNLQITDLQTTDAGSYQCQ 60
W +G +LT S RI + +L+I ++ +D G Y C
Sbjct: 20 WSKGTELLTNSS-------RICIWPDGSLEILNVTKSDEGKYTCF 57
>gnl|CDD|143201 cd05724, Ig2_Robo, Second immunoglobulin (Ig)-like domain in Robo
(roundabout) receptors. Ig2_Robo: domain similar to
the second immunoglobulin (Ig)-like domain in Robo
(roundabout) receptors. Robo receptors play a role in
the development of the central nervous system (CNS),
and are receptors of Slit protein. Slit is a repellant
secreted by the neural cells in the midline. Slit acts
through Robo to prevent most neurons from crossing the
midline from either side. Three mammalian Robo homologs
(robo1, -2, and -3), and three mammalian Slit homologs
(Slit-1,-2, -3), have been identified. Commissural
axons, which cross the midline, express low levels of
Robo; longitudinal axons, which avoid the midline,
express high levels of Robo. robo1, -2, and -3 are
expressed by commissural neurons in the vertebrate
spinal cord and Slits 1, -2, -3 are expressed at the
ventral midline. Robo-3 is a divergent member of the
Robo family which instead of being a positive regulator
of slit responsiveness, antagonizes slit responsiveness
in precrossing axons. The Slit-Robo interaction is
mediated by the second leucine-rich repeat (LRR) domain
of Slit and the two N-terminal Ig domains of Robo, Ig1
and Ig2. The primary Robo binding site for Slit2 has
been shown by surface plasmon resonance experiments and
mutational analysis to be is the Ig1 domain, while the
Ig2 domain has been proposed to harbor a weak secondary
binding site.
Length = 86
Score = 34.7 bits (80), Expect = 6e-04
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 26 GSTKVTPDKRIQLVDGYNLQITDLQTTDAGSYQC 59
G ++R+++VD NL I + + +D G+Y+C
Sbjct: 35 GQPLNLDNERVRIVDDGNLLIAEARKSDEGTYKC 68
>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 = 34.0 bits (77), Expect = 0.001
Identities = 9/46 (19%), Positives = 16/46 (34%)
Query: 16 WKRGIAILTAGSTKVTPDKRIQLVDGYNLQITDLQTTDAGSYQCQI 61
W + L + R L I+++ D+G+Y C
Sbjct: 17 WLKNGKPLPSSVLTRVRSSRGTSSGSSTLTISNVTLEDSGTYTCVA 62
>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 = 34.1 bits (78), Expect = 0.002
Identities = 7/24 (29%), Positives = 17/24 (70%)
Query: 40 DGYNLQITDLQTTDAGSYQCQIGT 63
+ ++L I++L+ +D+G+Y C +
Sbjct: 77 NDFSLTISNLRLSDSGTYTCAVSN 100
>gnl|CDD|214653 smart00410, IG_like, Immunoglobulin like. IG domains that cannot
be classified into one of IGv1, IGc1, IGc2, IG.
Length = 85
Score = 32.9 bits (75), Expect = 0.003
Identities = 9/55 (16%), Positives = 19/55 (34%), Gaps = 9/55 (16%)
Query: 9 DKNYVLAWKRGIAILTAGSTKVTPDKRIQLVDGYN---LQITDLQTTDAGSYQCQ 60
+ W + G + R + + L I+++ D+G+Y C
Sbjct: 21 SPPPEVTWYKQ------GGKLLAESGRFSVSRSGSTSTLTISNVTPEDSGTYTCA 69
>gnl|CDD|214652 smart00409, IG, Immunoglobulin.
Length = 85
Score = 32.9 bits (75), Expect = 0.003
Identities = 9/55 (16%), Positives = 19/55 (34%), Gaps = 9/55 (16%)
Query: 9 DKNYVLAWKRGIAILTAGSTKVTPDKRIQLVDGYN---LQITDLQTTDAGSYQCQ 60
+ W + G + R + + L I+++ D+G+Y C
Sbjct: 21 SPPPEVTWYKQ------GGKLLAESGRFSVSRSGSTSTLTISNVTPEDSGTYTCA 69
>gnl|CDD|143202 cd05725, Ig3_Robo, Third immunoglobulin (Ig)-like domain in Robo
(roundabout) receptors. Ig3_Robo: domain similar to
the third immunoglobulin (Ig)-like domain in Robo
(roundabout) receptors. Robo receptors play a role in
the development of the central nervous system (CNS),
and are receptors of Slit protein. Slit is a repellant
secreted by the neural cells in the midline. Slit acts
through Robo to prevent most neurons from crossing the
midline from either side. Three mammalian Robo homologs
(robo1, -2, and -3), and three mammalian Slit homologs
(Slit-1,-2, -3), have been identified. Commissural
axons, which cross the midline, express low levels of
Robo; longitudinal axons, which avoid the midline,
express high levels of Robo. robo1, -2, and -3 are
expressed by commissural neurons in the vertebrate
spinal cord and Slits 1, -2, -3 are expressed at the
ventral midline. Robo-3 is a divergent member of the
Robo family which instead of being a positive regulator
of slit responsiveness, antagonizes slit responsiveness
in precrossing axons. The Slit-Robo interaction is
mediated by the second leucine-rich repeat (LRR) domain
of Slit and the two N-terminal Ig domains of Robo, Ig1
and Ig2. The primary Robo binding site for Slit2 has
been shown by surface plasmon resonance experiments and
mutational analysis to be is the Ig1 domain, while the
Ig2 domain has been proposed to harbor a weak secondary
binding site.
Length = 69
Score = 32.4 bits (74), Expect = 0.003
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 32 PDKRIQLVDGYNLQITDLQTTDAGSYQCQ 60
P R +++D +L+I ++ D GSY C+
Sbjct: 25 PKGRAEILDDKSLKIRNVTAGDEGSYTCE 53
>gnl|CDD|143252 cd05775, Ig_SLAM-CD84_like_N, N-terminal immunoglobulin (Ig)-like
domain of the signaling lymphocyte activation molecule
(SLAM) family, CD84_like. Ig_SLAM-CD84_like_N: The
N-terminal immunoglobulin (Ig)-like domain of the
signaling lymphocyte activation molecule (SLAM) family,
CD84_like. The SLAM family is a group of immune-cell
specific receptors that can regulate both adaptive and
innate immune responses. Members of this group include
proteins such as CD84, SLAM (CD150), Ly-9 (CD229),
NTB-A (ly-108, SLAM6), 19A (CRACC), and SLAMF9. The
genes coding for the SLAM family are nested on
chromosome 1, in humans at 1q23, and in mice at 1H2.
The SLAM family is a subset of the CD2 family, which
also includes CD2 and CD58 located on chromosome 1 at
1p13 in humans. In mice, CD2 is located on chromosome
3, and there is no CD58 homolog. The SLAM family
proteins are organized as an extracellular domain with
either two or four Ig-like domains, a single
transmembrane segment, and a cytoplasmic region having
Tyr-based motifs. The extracellular domain is organized
as a membrane-distal Ig variable (IgV) domain that is
responsible for ligand recognition and a
membrane-proximal truncated Ig constant-2 (IgC2)
domain.
Length = 97
Score = 32.7 bits (75), Expect = 0.004
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 9/63 (14%)
Query: 17 KRGIAILTAGSTK----VTPDKRIQ-----LVDGYNLQITDLQTTDAGSYQCQIGTLEPK 67
+AI+T G + D + + Y+LQI++L+ DAGSY+ +I T
Sbjct: 27 NTSLAIITPGEETAPEIIVTDPSYKERVNFSQNDYSLQISNLKMEDAGSYRAEINTKNGV 86
Query: 68 EIT 70
IT
Sbjct: 87 TIT 89
>gnl|CDD|143218 cd05741, Ig_CEACAM_D1_like, First immunoglobulin (Ig)-like domain
of carcinoembryonic antigen (CEA) related cell adhesion
molecule (CEACAM) and similar proteins.
Ig_CEACAM_D1_like : immunoglobulin (IG)-like domain 1
in carcinoembryonic antigen (CEA) related cell adhesion
molecule (CEACAM) protein subfamily-like. The CEA
family is a group of anchored or secreted
glycoproteins, expressed by epithelial cells,
leukocytes, endothelial cells and placenta. The CEA
family is divided into the CEACAM and
pregnancy-specific glycoprotein (PSG) subfamilies. This
group represents the CEACAM subfamily. CEACAM1 has many
important cellular functions, it is a cell adhesion
molecule, and a signaling molecule that regulates the
growth of tumor cells, it is an angiogenic factor, and
is a receptor for bacterial and viral pathogens,
including mouse hepatitis virus (MHV). In mice, four
isoforms of CEACAM1 generated by alternative splicing
have either two [D1, D4] or four [D1-D4] Ig-like
domains on the cell surface. This family corresponds to
the D1 Ig-like domain. Also belonging to this group is
the N-terminal immunoglobulin (Ig)-like domain of the
signaling lymphocyte activation molecule (SLAM) family,
CD84-like family. The SLAM family is a group of
immune-cell specific receptors that can regulate both
adaptive and innate immune responses. SLAM family
proteins are organized as an extracellular domain with
having two or four Ig-like domains, a single
transmembrane segment, and a cytoplasmic region having
tyr-based motifs. The extracellular domain is organized
as a membrane-distal Ig variable (IgV) domain that is
responsible for ligand recognition and a
membrane-proximal truncated Ig constant-2 (IgC2)
domain.
Length = 92
Score = 31.9 bits (73), Expect = 0.006
Identities = 17/80 (21%), Positives = 29/80 (36%), Gaps = 11/80 (13%)
Query: 4 LSGLPDKNYVLAWKRG------IAILTAGSTKVTP-----DKRIQLVDGYNLQITDLQTT 52
+S LP+ + W +G I + +T T R + +L I +L
Sbjct: 8 VSNLPENLQEITWYKGKDKSVEAEIASYIATNSTVFGPAYSGRETIYPNGSLLIQNLTKE 67
Query: 53 DAGSYQCQIGTLEPKEITHT 72
D+G+Y QI +
Sbjct: 68 DSGTYTLQIISTNGVTENAK 87
>gnl|CDD|143258 cd05850, Ig1_Contactin-2, First Ig domain of contactin-2.
Ig1_Contactin-2: First Ig domain of the neural cell
adhesion molecule contactin-2-like. Contactins are
comprised of six Ig domains followed by four
fibronectin type III (FnIII) domains anchored to the
membrane by glycosylphosphatidylinositol. Contactin-2
(TAG-1, axonin-1) facilitates cell adhesion by
homophilic binding between molecules in apposed
membranes. It may play a part in the neuronal processes
of neurite outgrowth, axon guidance and fasciculation,
and neuronal migration. The first four Ig domains form
the intermolecular binding fragment, which arranges as
a compact U-shaped module by contacts between IG
domains 1 and 4, and domains 2 and 3. The different
contactins show different expression patterns in the
central nervous system. During development and in
adulthood, contactin-2 is transiently expressed in
subsets of central and peripheral neurons. Contactin-2
is also expressed in retinal amacrine cells in the
developing chick retina, corresponding to the period of
formation and maturation of AC processes.
Length = 94
Score = 31.1 bits (70), Expect = 0.016
Identities = 17/32 (53%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 29 KVTPDKRIQLVDGYNLQITDLQTT-DAGSYQC 59
K P+ R LV G NL I + Q DAGSYQC
Sbjct: 46 KFAPESRYTLVAG-NLVINNPQKARDAGSYQC 76
>gnl|CDD|143285 cd05877, Ig_LP_like, Immunoglobulin (Ig)-like domain of human
cartilage link protein (LP). Ig_LP_like: immunoglobulin
(Ig)-like domain similar to that that found in human
cartilage link protein (LP). In cartilage,
chondroitin-keratan sulfate proteoglycan (CSPG),
aggrecan, forms cartilage link protein stabilized
aggregates with hyaluronan (HA). These aggregates
contribute to the tissue's load bearing properties.
Aggregates having other CSPGs substituting for aggrecan
may contribute to the structural integrity of many
different tissues. Members of the vertebrate HPLN
(hyaluronan/HA and proteoglycan binding link) protein
family are physically linked adjacent to CSPG genes.
Length = 106
Score = 31.1 bits (71), Expect = 0.020
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 44 LQITDLQTTDAGSYQCQ-IGTLEPKEITHTLEILG 77
L ITDL+ D G Y+C+ I LE + + L + G
Sbjct: 70 LVITDLRLEDYGRYRCEVIDGLEDESVVVALRLRG 104
>gnl|CDD|143222 cd05745, Ig3_Peroxidasin, Third immunoglobulin (Ig)-like domain
of peroxidasin. Ig3_Peroxidasin: the third
immunoglobulin (Ig)-like domain in peroxidasin.
Peroxidasin has a peroxidase domain and interacting
extracellular motifs containing four Ig-like domains.
It has been suggested that peroxidasin is secreted and
has functions related to the stabilization of the
extracellular matrix. It may play a part in various
other important processes such as removal and
destruction of cells which have undergone programmed
cell death, and protection of the organism against
non-self.
Length = 74
Score = 30.3 bits (68), Expect = 0.025
Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 7/48 (14%)
Query: 13 VLAWKRGIAILTAGSTKVTPDKRIQLVDGYNLQITDLQTTDAGSYQCQ 60
V+AW T G ++++ D+R ++ L+I+ + D G Y+CQ
Sbjct: 18 VIAW-------TKGGSQLSVDRRHLVLSSGTLRISRVALHDQGQYECQ 58
>gnl|CDD|143209 cd05732, Ig5_NCAM-1_like, Fifth immunoglobulin (Ig)-like domain
of Neural Cell Adhesion Molecule NCAM-1 (NCAM) and
similar proteins. Ig5_NCAM-1 like: domain similar to
the fifth immunoglobulin (Ig)-like domain of Neural
Cell Adhesion Molecule NCAM-1 (NCAM). NCAM plays
important roles in the development and regeneration of
the central nervous system, in synaptogenesis and
neural migration. NCAM mediates cell-cell and
cell-substratum recognition and adhesion via homophilic
(NCAM-NCAM), and heterophilic (NCAM-non-NCAM),
interactions. NCAM is expressed as three major isoforms
having different intracellular extensions. The
extracellular portion of NCAM has five N-terminal
Ig-like domains and two fibronectin type III domains.
The double zipper adhesion complex model for NCAM
homophilic binding involves Ig1, Ig2, and Ig3. By this
model, Ig1 and Ig2 mediate dimerization of NCAM
molecules situated on the same cell surface (cis
interactions), and Ig3 domains mediate interactions
between NCAM molecules expressed on the surface of
opposing cells (trans interactions), through binding to
the Ig1 and Ig2 domains. The adhesive ability of NCAM
is modulated by the addition of polysialic acid chains
to the fifth Ig-like domain. Also included in this
group is NCAM-2 (also known as OCAM/mamFas II and
RNCAM) NCAM-2 is differentially expressed in the
developing and mature olfactory epithelium (OE).
Length = 96
Score = 30.6 bits (69), Expect = 0.026
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 14 LAWKRGIAILTAGSTKVTPDKRIQLVDGY---NLQITDLQTTDAGSYQC 59
+ W+R + G + D RI + +L + D+Q TDAG Y C
Sbjct: 33 ITWRRATRNFSEGDK--SLDGRIVVRGHARVSSLTLKDVQLTDAGRYDC 79
>gnl|CDD|143194 cd05717, Ig1_Necl-1-3_like, First (N-terminal) immunoglobulin
(Ig)-like domain of the nectin-like molecules Necl-1 -
Necl-3 (also known as cell adhesion molecules CADM3,
CADM1, and CADM2 respectively). Ig1_Necl-1-3_like:
N-terminal immunoglobulin (Ig)-like domain of the
nectin-like molecules Necl-1 (also known as cell
adhesion molecule 3 (CADM3)), Necl-2 (CADM1), and
Necl-3 (CADM2). At least five nectin-like molecules
have been identified (Necl-1 - Necl-5). They all have
an extracellular region containing three Ig-like
domains, a transmembrane region, and a 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, Necl-2, and
Necl-3 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 accumulates in central and
peripheral nervous system tissue, and has been shown to
selectively interact with oligodendrocytes. This group
also contains Class-I MHC-restricted T-cell-associated
molecule (CRTAM), whose expression pattern is
consistent with its expression in Class-I
MHC-restricted T-cells.
Length = 95
Score = 30.5 bits (69), Expect = 0.030
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 4/45 (8%)
Query: 33 DKRIQLVDGYNLQ----ITDLQTTDAGSYQCQIGTLEPKEITHTL 73
D RIQLV+ + I+++ +D G Y C + T+ + T+
Sbjct: 49 DNRIQLVNFSANELSISISNVSLSDEGRYTCSLYTMPVQTAKATV 93
>gnl|CDD|143168 cd04967, Ig1_Contactin, First Ig domain of contactin.
Ig1_Contactin: First Ig domain of contactins.
Contactins are neural cell adhesion molecules and are
comprised of six Ig domains followed by four
fibronectin type III(FnIII) domains anchored to the
membrane by glycosylphosphatidylinositol. The first
four Ig domains form the intermolecular binding
fragment, which arranges as a compact U-shaped module
via contacts between Ig domains 1 and 4, and between Ig
domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play
a part in the neuronal processes of neurite outgrowth,
axon guidance and fasciculation, and neuronal
migration. This group also includes contactin-1 and
contactin-5. The different contactins show different
expression patterns in the central nervous system.
During development and in adulthood, contactin-2 is
transiently expressed in subsets of central and
peripheral neurons. Contactin-5 is expressed
specifically in the rat postnatal nervous system,
peaking at about 3 weeks postnatal, and a lack of
contactin-5 (NB-2) results in an impairment of neuronal
activity in the rat auditory system. Contactin-5 is
highly expressed in the adult human brain in the
occipital lobe and in the amygdala. Contactin-1 is
differentially expressed in tumor tissues and may,
through a RhoA mechanism, facilitate invasion and
metastasis of human lung adenocarcinoma.
Length = 91
Score = 29.7 bits (67), Expect = 0.047
Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 29 KVTPDKRIQLVDGYNLQITDLQTT-DAGSYQC----QIGTLEPKEIT 70
PD R LV G NL I++ DAG YQC +GT+ +E T
Sbjct: 46 DDEPDSRYSLVGG-NLVISNPSKAKDAGRYQCLASNIVGTVLSREAT 91
>gnl|CDD|143191 cd05714, Ig_CSPGs_LP, Immunoglobulin (Ig)-like domain of
chondroitin sulfate proteoglycans (CSPGs), human
cartilage link protein (LP) and similar proteins.
Ig_CSPGs_LP: immunoglobulin (Ig)-like domain similar to
that found in chondroitin sulfate proteoglycans (CSPGs)
and human cartilage link protein (LP). Included in this
group are the CSPGs aggrecan, versican, and neurocan. In
CSPGs this Ig-like domain is followed by hyaluronan
(HA)-binding tandem repeats, and a C-terminal region
with epidermal growth factor-like, lectin-like, and
complement regulatory protein-like domains. Separating
these N- and C-terminal regions is a nonhomologous
glycosaminoglycan attachment region. In cartilage,
aggrecan forms cartilage link protein stabilized
aggregates with hyaluronan (HA). These aggregates
contribute to the tissue's load bearing properties.
Aggrecan and versican have a wide distribution in
connective tissue and extracellular matrices. Neurocan
is localized almost exclusively in nervous tissue.
Aggregates having other CSPGs substituting for aggrecan
may contribute to the structural integrity of many
different tissues. There is considerable evidence that
HA-binding CSPGs are involved in developmental processes
in the central nervous system. Members of the vertebrate
HPLN (hyaluronan/HA and proteoglycan binding link)
protein family are physically linked adjacent to CSPG
genes.
Length = 106
Score = 29.9 bits (68), Expect = 0.049
Identities = 15/35 (42%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 44 LQITDLQTTDAGSYQCQ-IGTLEPKEITHTLEILG 77
L ITDL+ D+G Y+C+ I +E ++ T LE+ G
Sbjct: 70 LVITDLRLEDSGRYRCEVIDGIEDEQDTVELEVRG 104
>gnl|CDD|191810 pfam07679, I-set, Immunoglobulin I-set domain.
Length = 90
Score = 29.5 bits (67), Expect = 0.055
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 29 KVTPDKRIQLV---DGYNLQITDLQTTDAGSYQCQ 60
+ R ++ Y L I+++Q D G Y C
Sbjct: 40 PLRSSDRFKVTYEGGTYTLTISNVQPDDEGKYTCV 74
>gnl|CDD|143278 cd05870, Ig5_NCAM-2, Fifth immunoglobulin (Ig)-like domain of
Neural Cell Adhesion Molecule NCAM-2 (also known as
OCAM/mamFas II and RNCAM). Ig5_NCAM-2: the fifth
immunoglobulin (Ig)-like domain of Neural Cell Adhesion
Molecule NCAM-2 (also known as OCAM/mamFas II and
RNCAM). NCAM-2 is organized similarly to NCAM ,
including five N-terminal Ig-like domains and two
fibronectin type III domains. NCAM-2 is differentially
expressed in the developing and mature olfactory
epithelium (OE), and may function like NCAM, as an
adhesion molecule.
Length = 98
Score = 29.6 bits (66), Expect = 0.057
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 14 LAWKRGIAILTAGSTKVTPDKRIQLVDGY---NLQITDLQTTDAGSYQCQ 60
+ WKR T +PD RI++ + +L I D++ +D+G Y C+
Sbjct: 33 ITWKRASDGHTFSEGDKSPDGRIEVKGQHGESSLHIKDVKLSDSGRYDCE 82
>gnl|CDD|143289 cd05881, Ig1_Necl-2, First (N-terminal) immunoglobulin (Ig)-like
domain of nectin-like molecule 2 (also known as cell
adhesion molecule 1 (CADM1)). Ig1_Necl-2: domain
similar to the N-terminal immunoglobulin (Ig)-like
domain of nectin-like molecule-2, Necl-2 (also known as
cell adhesion molecule 1 (CADM1), SynCAM1, IGSF4A,
Tslc1, sgIGSF, and RA175). Nectin-like molecules have
similar domain structures to those of nectins. At least
five nectin-like molecules have been identified (Necl-1
- Necl-5). They all have an extracellular region
containing three Ig-like domains, a transmembrane
region, and a 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-2 has Ca(2+)-independent homophilic and
heterophilic cell-cell adhesion activity. Necl-2 is
expressed in a wide variety of tissues, and is a
putative tumour suppressor gene, which is downregulated
in aggressive neuroblastoma.
Length = 95
Score = 29.2 bits (65), Expect = 0.075
Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 4/47 (8%)
Query: 33 DKRIQLVDGYN----LQITDLQTTDAGSYQCQIGTLEPKEITHTLEI 75
D R QLV+ + + ++++ +D G Y CQ+ T P+E T+ +
Sbjct: 49 DSRFQLVNFSSNELRVSLSNVSLSDEGRYFCQLYTDPPQEAYTTITV 95
>gnl|CDD|212460 cd05723, Ig4_Neogenin, Fourth immunoglobulin (Ig)-like domain in
neogenin and similar proteins. Ig4_Neogenin: fourth
immunoglobulin (Ig)-like domain in neogenin and related
proteins. Neogenin is a cell surface protein which is
expressed in the developing nervous system of
vertebrate embryos in the growing nerve cells. It is
also expressed in other embryonic tissues, and may play
a general role in developmental processes such as cell
migration, cell-cell recognition, and tissue growth
regulation. Included in this group is the tumor
suppressor protein DCC, which is deleted in colorectal
carcinoma . DCC and neogenin each have four Ig-like
domains followed by six fibronectin type III domains, a
transmembrane domain, and an intracellular domain.
Length = 71
Score = 28.4 bits (63), Expect = 0.11
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 30 VTPDKRIQLVDGYNLQITDLQTTDAGSYQC 59
V P ++V +NLQ+ L +D G YQC
Sbjct: 25 VIPSDYFKIVKEHNLQVLGLVKSDEGFYQC 54
>gnl|CDD|197706 smart00408, IGc2, Immunoglobulin C-2 Type.
Length = 63
Score = 27.8 bits (62), Expect = 0.16
Identities = 11/56 (19%), Positives = 15/56 (26%), Gaps = 10/56 (17%)
Query: 5 SGLPDKNYVLAWKRGIAILTAGSTKVTPDKRIQLVDGYNLQITDLQTTDAGSYQCQ 60
G P N W + + R L I + D+G Y C
Sbjct: 12 EGNPVPNIT--WLKD-------GKPLPESNRFVASGST-LTIKSVSLEDSGLYTCV 57
>gnl|CDD|143290 cd05882, Ig1_Necl-1, First (N-terminal) immunoglobulin (Ig)-like
domain of nectin-like molcule-1 (Necl-1, also known as
cell adhesion molecule3 (CADM3)). Ig1_Necl-1: domain
similar to the N-terminal immunoglobulin (Ig)-like
domain of nectin-like molecule-1, Necl-1 (also known as
celll adhesion molecule 3 (CADM3), SynCAM2, IGSF4).
Nectin-like molecules have similar domain structures to
those of nectins. At least five nectin-like molecules
have been identified (Necl-1 - Necl-5). They all have
an extracellular region containing three Ig-like
domains, a transmembrane region, and a 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 has
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.
Length = 95
Score = 28.5 bits (63), Expect = 0.17
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 26 GSTKVTPDKRIQLVDG----YNLQITDLQTTDAGSYQCQIGTL 64
G + D RIQLV + I+++Q +D G Y C I T+
Sbjct: 42 GEKRALRDNRIQLVKSTPTELIISISNVQLSDEGEYTCSIFTM 84
>gnl|CDD|143223 cd05746, Ig4_Peroxidasin, Fourth immunoglobulin (Ig)-like domain
of peroxidasin. Ig4_Peroxidasin: the fourth
immunoglobulin (Ig)-like domain in peroxidasin.
Peroxidasin has a peroxidase domain and interacting
extracellular motifs containing four Ig-like domains.
It has been suggested that peroxidasin is secreted, and
has functions related to the stabilization of the
extracellular matrix. It may play a part in various
other important processes such as removal and
destruction of cells, which have undergone programmed
cell death, and protection of the organism against
non-self.
Length = 69
Score = 27.9 bits (62), Expect = 0.20
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 9/48 (18%)
Query: 13 VLAW-KRGIAILTAGSTKVTPDKRIQLVDGYNLQITDLQTTDAGSYQC 59
+ W K G+ + +G ++P+ GY L I D+ D G Y+C
Sbjct: 14 TITWNKDGVQVTESGKFHISPE-------GY-LAIRDVGVADQGRYEC 53
>gnl|CDD|143260 cd05852, Ig5_Contactin-1, Fifth Ig domain of contactin-1.
Ig5_Contactin-1: fifth Ig domain of the neural cell
adhesion molecule contactin-1. Contactins are comprised
of six Ig domains followed by four fibronectin type III
(FnIII) domains anchored to the membrane by
glycosylphosphatidylinositol. Contactin-1 is
differentially expressed in tumor tissues and may
through a RhoA mechanism, facilitate invasion and
metastasis of human lung adenocarcinoma.
Length = 73
Score = 27.7 bits (61), Expect = 0.26
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 7/46 (15%)
Query: 14 LAWKRGIAILTAGSTKVTPDKRIQLVDGYNLQITDLQTTDAGSYQC 59
+W +G +L S RI + D +L+I ++ D GSY C
Sbjct: 18 FSWSKGTELLVNNS-------RISIWDDGSLEILNITKLDEGSYTC 56
>gnl|CDD|143177 cd04976, Ig2_VEGFR, Second immunoglobulin (Ig)-like domain of
vascular endothelial growth factor receptor (VEGFR).
Ig2_VEGFR: Second immunoglobulin (Ig)-like domain of
vascular endothelial growth factor receptor (VEGFR).
The VEGFRs have an extracellular component with seven
Ig-like domains, a transmembrane segment, and an
intracellular tyrosine kinase domain interrupted by a
kinase-insert domain. The VEGFR family consists of
three members, VEGFR-1 (Flt-1), VEGFR-2 (KDR/Flk-1) and
VEGFR-3 (Flt-4). VEGFRs bind VEGFs with high affinity
at the Ig-like domains. VEGF-A is important to the
growth and maintenance of vascular endothelial cells
and to the development of new blood- and
lymphatic-vessels in physiological and pathological
states. VEGFR-2 is a major mediator of the mitogenic,
angiogenic and microvascular permeability-enhancing
effects of VEGF-A. VEGFR-1 may play an inhibitory part
in these processes by binding VEGF and interfering with
its interaction with VEGFR-2. VEGFR-1 has a signaling
role in mediating monocyte chemotaxis. VEGFR-2 and -1
may mediate a chemotactic and a survival signal in
hematopoietic stem cells or leukemia cells. VEGFR-3 has
been shown to be involved in tumor angiogenesis and
growth.
Length = 71
Score = 26.6 bits (59), Expect = 0.56
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 29 KVTPDKRIQLVDGYNLQITDLQTTDAGSY 57
K+ +K G++L I D+ DAG+Y
Sbjct: 22 KLISEKNRTKKSGHSLTIKDVTEEDAGNY 50
>gnl|CDD|143279 cd05871, Ig_Semaphorin_classIII, Immunoglobulin (Ig)-like domain
of class III semaphorin. Ig_Semaphorin_class III;
Immunoglobulin (Ig)-like domain of class III
semaphorins. Semaphorins are classified into various
classes on the basis of structural features additional
to the Sema domain. Class III semaphorins are a
vertebrate class having a Sema domain, an Ig domain, a
short basic domain, and are secreted. They have been
shown to be axonal guidance cues and have a part in the
regulation of the cardiovascular, immune and
respiratory systems. Sema3A, the prototype member of
this class III subfamily, induces growth cone collapse
and is an inhibitor of axonal sprouting. In perinatal
rat cortex as a chemoattractant, it functions to
direct, for pyramidal neurons, the orientated extension
of apical dendrites. It may play a role, prior to the
development of apical dendrites, in signaling the
radial migration of newborn cortical neurons towards
the upper layers. Sema3A selectively inhibits vascular
endothelial growth factor receptor (VEGF)-induced
angiogenesis and induces microvascular permeability.
This group also includes Sema3B, -C, -D, -E, -G.
Length = 91
Score = 26.6 bits (59), Expect = 0.84
Identities = 10/35 (28%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 26 GSTKVTPDKRIQLVDGYNLQITDLQTTDAGSYQCQ 60
+V ++R+ + L + LQ +DAG Y C
Sbjct: 38 RKEEVKTEERL-IHTERGLLLRSLQRSDAGVYTCT 71
>gnl|CDD|143204 cd05727, Ig2_Contactin-2-like, Second Ig domain of the neural
cell adhesion molecule contactin-2 and similar
proteins. Ig2_Contactin-2-like: second Ig domain of
the neural cell adhesion molecule contactin-2.
Contactins are comprised of six Ig domains followed by
four fibronectin type III (FnIII) domains anchored to
the membrane by glycosylphosphatidylinositol.
Contactin-2 (aliases TAG-1, axonin-1) facilitates cell
adhesion by homophilic binding between molecules in
apposed membranes. The first four Ig domains form the
intermolecular binding fragment which arranges as a
compact U-shaped module by contacts between Ig domains
1 and 4, and domains 2 and 3. It has been proposed that
a linear zipper-like array forms, from contactin-2
molecules alternatively provided by the two apposed
membranes.
Length = 96
Score = 26.4 bits (58), Expect = 0.92
Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 30 VTPDKR--IQLVDGYNLQITDLQTTDAGSYQCQIGTL 64
+ D R + +G NL I ++ +D G+Y C + +
Sbjct: 47 IPEDGRRFVSQTNG-NLYIAKVEASDRGNYSCFVSSP 82
>gnl|CDD|143190 cd05713, Ig_MOG_like, Immunoglobulin (Ig)-like domain of myelin
oligodendrocyte glycoprotein (MOG). Ig_MOG_like:
immunoglobulin (Ig)-like domain of myelin
oligodendrocyte glycoprotein (MOG). MOG, a minor
component of the myelin sheath, is an important
CNS-specific autoantigen, linked to the pathogenesis of
multiple sclerosis (MS) and experimental autoimmune
encephalomyelitis (EAE). It is a transmembrane protein
having an extracellular Ig domain. MOG is expressed in
the CNS on the outermost lamellae of the myelin sheath,
and on the surface of oligodendrocytes, and may
participate in the completion, compaction, and/or
maintenance of myelin. This group also includes
butyrophilin (BTN). BTN is the most abundant protein in
bovine milk-fat globule membrane (MFGM).
Length = 100
Score = 26.4 bits (59), Expect = 0.99
Identities = 6/16 (37%), Positives = 11/16 (68%)
Query: 44 LQITDLQTTDAGSYQC 59
L+I +++ +D G Y C
Sbjct: 67 LRIHNVRASDEGLYTC 82
>gnl|CDD|143193 cd05716, Ig_pIgR, Immunoglobulin (Ig)-like domain in the
polymeric Ig receptor (pIgR). Ig_pIgR: Immunoglobulin
(Ig)-like domain in the polymeric Ig receptor (pIgR).
pIgR delivers dimeric IgA and pentameric IgM to mucosal
secretions. Polymeric immunoglobulin (pIgs) are the
first defense against pathogens and toxins. IgA and IgM
can form polymers via an 18-residue extension at their
c-termini referred to as the tailpiece. pIgR transports
pIgs across mucosal epithelia into mucosal secretions.
Human pIgR is a glycosylated type I transmembrane
protein, comprised of a 620 residue extracellular
region, a 23 residue transmembrane region, and a 103
residue cytoplasmic tail. The extracellular region
contains five domains that share sequence similarity
with Ig variable (v) regions.
Length = 98
Score = 26.3 bits (58), Expect = 1.0
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 46 ITDLQTTDAGSYQCQIGT 63
+ L+ DAG Y C +G
Sbjct: 68 LNQLRKEDAGWYWCGVGD 85
>gnl|CDD|215677 pfam00047, ig, Immunoglobulin domain. Members of the
immunoglobulin superfamily are found in hundreds of
proteins of different functions. Examples include
antibodies, the giant muscle kinase titin and receptor
tyrosine kinases. Immunoglobulin-like domains may be
involved in protein-protein and protein-ligand
interactions. The Pfam alignments do not include the
first and last strand of the immunoglobulin-like
domain.
Length = 62
Score = 25.6 bits (56), Expect = 1.1
Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 16 WKRGIAILTAGSTKVTPDKRIQLVDGYNLQITDLQTTDAGSYQCQ 60
W + L +T T + R+ L I+++ D+G+Y C
Sbjct: 20 WFKEGKGLEESTTVGTDENRVS---SITLTISNVTPEDSGTYTCV 61
>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 = 26.2 bits (58), Expect = 1.1
Identities = 12/45 (26%), Positives = 16/45 (35%), Gaps = 4/45 (8%)
Query: 16 WKRGIAILTAGSTKVTPDKRIQLVDGYNLQITDLQTTDAGSYQCQ 60
W L ++ + DG L I + DAG Y CQ
Sbjct: 29 WLFQGGPLQRKE--EPEERLLVTEDG--LLIRSVSPADAGVYTCQ 69
>gnl|CDD|237960 PRK15407, PRK15407, lipopolysaccharide biosynthesis protein RfbH;
Provisional.
Length = 438
Score = 26.8 bits (60), Expect = 1.2
Identities = 8/10 (80%), Positives = 10/10 (100%)
Query: 41 GYNLQITDLQ 50
GYNL+ITD+Q
Sbjct: 287 GYNLKITDMQ 296
>gnl|CDD|143325 cd07701, Ig1_Necl-3, First (N-terminal) immunoglobulin (Ig)-like
domain of nectin-like molecule-3 (Necl-3, also known as
cell adhesion molecule 2 (CADM2)). Ig1_Necl-3: domain
similar to the N-terminal immunoglobulin (Ig)-like
domain of nectin-like molecule-3, Necl-3 (also known as
cell adhesion molecule 2 (CADM2), SynCAM2, IGSF4D).
Nectin-like molecules have similar domain structures to
those of nectins. At least five nectin-like molecules
have been identified (Necl-1 - Necl-5). They all have
an extracellular region containing three Ig-like
domains, a transmembrane region, and a 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-3 accumulates
in central and peripheral nervous system tissue, and
has been shown to selectively interact with
oligodendrocytes.
Length = 95
Score = 26.2 bits (57), Expect = 1.2
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 26 GSTKVTPDKRIQLVDG----YNLQITDLQTTDAGSYQCQIGTLEPK 67
K D RI+LV ++ I+D+ +D G Y C + T+ K
Sbjct: 42 DDKKALRDNRIELVRASWHELSISISDVSLSDEGQYTCSLFTMPVK 87
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 26.5 bits (59), Expect = 1.3
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 17 KRGIAILTAGSTKVTPDKRIQLVD 40
+RGI I T P +RI +D
Sbjct: 45 ERGITIKTGVVEFEWPKRRINFID 68
>gnl|CDD|143203 cd05726, Ig4_Robo, Third immunoglobulin (Ig)-like domain in Robo
(roundabout) receptors. Ig4_Robo: domain similar to
the third immunoglobulin (Ig)-like domain in Robo
(roundabout) receptors. Robo receptors play a role in
the development of the central nervous system (CNS),
and are receptors of Slit protein. Slit is a repellant
secreted by the neural cells in the midline. Slit acts
through Robo to prevent most neurons from crossing the
midline from either side. Three mammalian Robo homologs
(robo1, -2, and -3), and three mammalian Slit homologs
(Slit-1,-2, -3), have been identified. Commissural
axons, which cross the midline, express low levels of
Robo; longitudinal axons, which avoid the midline,
express high levels of Robo. robo1, -2, and -3 are
expressed by commissural neurons in the vertebrate
spinal cord and Slits 1, -2, -3 are expressed at the
ventral midline. Robo-3 is a divergent member of the
Robo family which instead of being a positive regulator
of slit responsiveness, antagonizes slit responsiveness
in precrossing axons. The Slit-Robo interaction is
mediated by the second leucine-rich repeat (LRR) domain
of Slit and the two N-terminal Ig domains of Robo, Ig1
and Ig2. The primary Robo binding site for Slit2 has
been shown by surface plasmon resonance experiments and
mutational analysis to be is the Ig1 domain, while the
Ig2 domain has been proposed to harbor a weak secondary
binding site.
Length = 90
Score = 26.1 bits (57), Expect = 1.3
Identities = 13/44 (29%), Positives = 18/44 (40%)
Query: 17 KRGIAILTAGSTKVTPDKRIQLVDGYNLQITDLQTTDAGSYQCQ 60
K G L R + +L IT++Q +D G Y CQ
Sbjct: 22 KEGSQNLLFSYQPPQSSSRFSVSQTGDLTITNVQRSDVGYYICQ 65
>gnl|CDD|143179 cd04978, Ig4_L1-NrCAM_like, Fourth immunoglobulin (Ig)-like
domain of L1, Ng-CAM (Neuron-glia CAM cell adhesion
molecule), and NrCAM (Ng-CAM-related).
Ig4_L1-NrCAM_like: fourth immunoglobulin (Ig)-like
domain of L1, Ng-CAM (Neuron-glia CAM cell adhesion
molecule), and NrCAM (Ng-CAM-related). These proteins
belong to the L1 subfamily of cell adhesion molecules
(CAMs) and are comprised of an extracellular region
having six Ig-like domains and five fibronectin type
III domains, a transmembrane region and an
intracellular domain. These molecules are primarily
expressed in the nervous system. L1 is associated with
an X-linked recessive disorder, X-linked hydrocephalus,
MASA syndrome, or spastic paraplegia type 1, that
involves abnormalities of axonal growth.
Length = 76
Score = 25.4 bits (56), Expect = 1.5
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 31 TPDKRIQLVDGYNLQITDLQTTDAGSYQC 59
P + VDG L ++++Q D YQC
Sbjct: 30 LPPDPRRRVDGGTLILSNVQPNDTAVYQC 58
>gnl|CDD|143205 cd05728, Ig4_Contactin-2-like, Fourth Ig domain of the neural
cell adhesion molecule contactin-2 and similar
proteins. Ig4_Contactin-2-like: fourth Ig domain of
the neural cell adhesion molecule contactin-2.
Contactins are comprised of six Ig domains followed by
four fibronectin type III (FnIII) domains anchored to
the membrane by glycosylphosphatidylinositol.
Contactin-2 (aliases TAG-1, axonin-1) facilitates cell
adhesion by homophilic binding between molecules in
apposed membranes. The first four Ig domains form the
intermolecular binding fragment which arranges as a
compact U-shaped module by contacts between Ig domains
1 and 4, and domains 2 and 3. It has been proposed that
a linear zipper-like array forms, from contactin-2
molecules alternatively provided by the two apposed
membranes.
Length = 85
Score = 25.6 bits (56), Expect = 1.6
Identities = 12/25 (48%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 35 RIQLVDGYNLQITDLQTTDAGSYQC 59
RI++ G +L+IT L +D+G YQC
Sbjct: 45 RIEVEAG-DLRITKLSLSDSGMYQC 68
>gnl|CDD|143215 cd05738, Ig2_RPTP_IIa_LAR_like, Second immunoglobulin (Ig)-like
domain of the receptor protein tyrosine phosphatase
(RPTP)-F, also known as LAR. Ig2_RPTP_IIa_LAR_like:
domain similar to the second immunoglobulin (Ig)-like
domain found in the receptor protein tyrosine
phosphatase (RPTP)-F, also known as LAR. LAR belongs to
the RPTP type IIa subfamily. Members of this subfamily
are cell adhesion molecule-like proteins involved in
central nervous system (CNS) development. They have
large extracellular portions, comprised of multiple
Ig-like domains and two to nine fibronectin type III
(FNIII) domains, and a cytoplasmic portion having two
tandem phosphatase domains.
Length = 74
Score = 25.4 bits (55), Expect = 1.6
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 30 VTPDKRIQLVDGYNLQITDLQTTDAGSYQC 59
T + RI+ + LQI + + +D G Y+C
Sbjct: 26 TTSNGRIKQLRSGALQIENSEESDQGKYEC 55
>gnl|CDD|215595 PLN03130, PLN03130, ABC transporter C family member; Provisional.
Length = 1622
Score = 26.2 bits (58), Expect = 1.9
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 5/36 (13%)
Query: 27 STKVTPDKRIQLVDGYNLQITDLQTTDAGSYQ--CQ 60
S ++T + R + G +IT+L TTDA + Q CQ
Sbjct: 384 SLRLTHEGRKKFTSG---KITNLMTTDAEALQQICQ 416
>gnl|CDD|143326 cd07702, Ig2_VEGFR-1, Second immunoglobulin (Ig)-like domain of
vascular endothelial growth factor receptor 1
(VEGFR-1). Ig2_VEGFR-1: Second immunoglobulin
(Ig)-like domain of vascular endothelial growth factor
receptor 1 (VEGFR-1). VEGFRs have an extracellular
component with seven Ig-like domains, a transmembrane
segment, and an intracellular tyrosine kinase domain
interrupted by a kinase-insert domain. VEGFRs bind
VEGFs with high affinity at the Ig-like domains.
VEGFR-1 binds VEGF-A strongly; VEGF-A is important to
the growth and maintenance of vascular endothelial
cells and to the development of new blood- and
lymphatic-vessels in physiological and pathological
states. VEGFR-1 may play an inhibitory rolet in the
function of VEGFR-2 by binding VEGF-A and interfering
with its interaction with VEGFR-2. VEGFR-1 has a
signaling role in mediating monocyte chemotaxis and may
mediate a chemotactic and a survival signal in
hematopoietic stem cells or leukemia cells.
Length = 72
Score = 25.2 bits (55), Expect = 1.9
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 38 LVDGYNLQITDLQTTDAGSY 57
VDGY+L I D+ DAG Y
Sbjct: 32 HVDGYSLVIKDVTEEDAGIY 51
>gnl|CDD|237383 PRK13421, PRK13421, F0F1 ATP synthase subunit A; Provisional.
Length = 223
Score = 25.8 bits (57), Expect = 2.0
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 10/55 (18%)
Query: 20 IAILTAGSTKVT-----PDKRIQ-----LVDGYNLQITDLQTTDAGSYQCQIGTL 64
+A+L AGS T R+Q +V + QI D TD Y+ IGTL
Sbjct: 30 MAVLAAGSALATRRLSLAPGRLQSVLELVVTTIDAQIRDTMQTDPAPYRALIGTL 84
>gnl|CDD|143281 cd05873, Ig_Sema4D_like, Immunoglobulin (Ig)-like domain of the
class IV semaphorin Sema4D. Ig_Sema4D_like;
Immunoglobulin (Ig)-like domain of Sema4D. Sema4D is a
Class IV semaphorin. Semaphorins are classified based
on structural features additional to the Sema domain.
Sema4D has extracellular Sema and Ig domains, a
transmembrane domain, and a short cytoplasmic domain.
Sema4D plays a part in the development of GABAergic
synapses. Sema4D in addition is an immune semaphorin.
It is abundant on resting T cells; its expression is
weak on resting B cells and antigen presenting cells
(APCs), but is upregulated by various stimuli. The
receptor used by Sema4D in the immune system is CD72.
Sem4D enhances the activation of B cells and DCs
through binding CD72, perhaps by reducing CD72s
inhibitory signals. The receptor used by Sema4D in the
non-lymphatic tissues is plexin-B1. Sem4D is anchored
to the cell surface but its extracellular domain can be
released from the cell surface by a
metalloprotease-dependent process. Sem4D may mediate
its effects in its membrane bound form, and/or its
cleaved form.
Length = 87
Score = 25.2 bits (55), Expect = 2.2
Identities = 10/35 (28%), Positives = 12/35 (34%), Gaps = 1/35 (2%)
Query: 25 AGSTKVTPDKRIQLVDGYNLQITDLQTTDAGSYQC 59
G + L L I + DAG YQC
Sbjct: 32 DGKVLTPESAKYLLYRD-GLLIFNASEADAGRYQC 65
>gnl|CDD|143213 cd05736, Ig2_Follistatin_like, Second immunoglobulin (Ig)-like
domain of a follistatin-like molecule encoded by the
Mahya gene and similar proteins. Ig2_Follistatin_like:
domain similar to the second immunoglobulin (Ig)-like
domain found in a follistatin-like molecule encoded by
the CNS-related Mahya gene. Mahya genes have been
retained in certain Bilaterian branches during
evolution. They are conserved in Hymenoptera and
Deuterostomes, but are absent from other metazoan
species such as fruit fly and nematode. Mahya proteins
are secretory, with a follistatin-like domain
(Kazal-type serine/threonine protease inhibitor domain
and EF-hand calcium-binding domain), two Ig-like
domains, and a novel C-terminal domain. Mahya may be
involved in learning and memory and in processing of
sensory information in Hymenoptera and vertebrates.
Follistatin is a secreted, multidomain protein that
binds activins with high affinity and antagonizes their
signaling.
Length = 76
Score = 25.3 bits (55), Expect = 2.3
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 3 YLSGLPDKNYVLAW-KRGIAILTAGSTKVTPDKRIQLVDGYNLQITDLQTTDAGSYQCQ 60
+ G+P L W K G+ I S ++T + +G L I++++ D G+Y C
Sbjct: 6 HAEGIPLPR--LTWLKNGMDITPKLSKQLT-----LIANGSELHISNVRYEDTGAYTCI 57
>gnl|CDD|185758 cd09219, TLP-F, thaumatin-like proteins: basidiomycete homologs.
This subfamily is represented by Lentinula edodes TLG1,
a thaumatin-like protein (TLP), as well as, other
basidiomycete homologs. In general, TLPs are involved
in host defense and a wide range of developmental
processes in fungi, plants, and animals. TLG1 TLP is
involved in lentinan degradation and fruiting body
senescence. TLG1 expressed in Escherichia coli and
Aspergillus oryzae exhibited beta-1,3-glucanase activity
and demonstrated lentinan degrading activity. TLG1 is
proposed to be involved in lentinan and cell wall
degradation during senescence following harvest and
spore diffusion. TLPs are three-domain, crescent-fold
structures with either an electronegative,
electropositive, or neutral cleft occurring between
domains I and II. TLG1 from Lentinula edodes contains
the required acidic amino acids conserved in the
appropriate positions to possess an electronegative
cleft. TLPs within this subfamily contain 13 conserved
Cys residues; the number of total Cys residues in these
TLPs varies from 16 in L. edodes TLG1 to 18 in other
basidiomycete homologs.
Length = 229
Score = 25.7 bits (56), Expect = 2.3
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 2/45 (4%)
Query: 36 IQLVDGYN--LQITDLQTTDAGSYQCQIGTLEPKEITHTLEILGF 78
I LVDG+N L IT+ T Q + L P + L+ G
Sbjct: 106 ISLVDGFNIPLNITNNITCPQPQCQVDLNVLCPALLRGPLDQKGV 150
>gnl|CDD|220574 pfam10106, DUF2345, Uncharacterized protein conserved in bacteria
(DUF2345). Members of this family are found in various
bacterial hypothetical proteins, as well as Rhs element
Vgr proteins.
Length = 156
Score = 25.6 bits (57), Expect = 2.4
Identities = 9/35 (25%), Positives = 17/35 (48%)
Query: 13 VLAWKRGIAILTAGSTKVTPDKRIQLVDGYNLQIT 47
+L+ GIA+ T S + + + L G + Q+
Sbjct: 19 LLSAPAGIALTTPQSLHLAAGEHLALTAGQDTQLA 53
>gnl|CDD|236745 PRK10722, PRK10722, hypothetical protein; Provisional.
Length = 247
Score = 25.7 bits (57), Expect = 2.6
Identities = 17/44 (38%), Positives = 27/44 (61%), Gaps = 6/44 (13%)
Query: 6 GLPDKNYVLAWKRGIAILTAGSTKVTPDKRIQLV---DGYNLQI 46
LPD ++ A+K+GI + K+TP +R Q+V + Y+LQI
Sbjct: 99 RLPDDSWQNAFKQGILL---ADAKITPAERRQIVERLNAYSLQI 139
>gnl|CDD|143184 cd04983, IgV_TCR_alpha_like, Immunoglobulin (Ig) variable (V)
domain of T-cell receptor (TCR) alpha chain and similar
proteins. IgV_TCR_alpha: immunoglobulin (Ig) variable
domain of the alpha 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 represents the
variable domain of the alpha chain of TCRs and also
includes the variable domain of delta chains of TCRs.
Alpha/beta TCRs recognize antigen as peptide fragments
presented by major histocompatibility complex (MHC)
molecules. The variable domain of TCRs is responsible
for antigen recognition, and is located at the
N-terminus of the receptor. Gamma/delta TCRs recognize
intact protein antigens; they recognize proteins
antigens directly and without antigen processing, and
MHC independently of the bound peptide.
Length = 109
Score = 25.3 bits (56), Expect = 2.8
Identities = 6/16 (37%), Positives = 9/16 (56%)
Query: 44 LQITDLQTTDAGSYQC 59
L I+ Q +D+ Y C
Sbjct: 72 LHISAAQLSDSAVYFC 87
>gnl|CDD|143167 cd00099, IgV, Immunoglobulin variable domain (IgV). IgV:
Immunoglobulin variable domain (IgV). Members of the
IgV family are components of immunoglobulin (Ig) and T
cell receptors. The basic structure of Ig molecules is
a tetramer of two light chains and two heavy chains
linked by disulfide bonds. In Ig, each chain is
composed of one variable domain (IgV) and one or more
constant domains (IgC); these names reflect the fact
that the variability in sequences is higher in the
variable domain than in the constant domain. Within the
variable domain, there are regions of even more
variability called the hypervariable or
complementarity-determining regions (CDRs) which are
responsible for antigen binding. A predominant feature
of most Ig domains is the disulfide bridge connecting 2
beta-sheets with a tryptophan residue packed against
the disulfide bond.
Length = 105
Score = 25.0 bits (55), Expect = 2.9
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 44 LQITDLQTTDAGSYQCQIG 62
L I+ LQ D+ Y C +
Sbjct: 69 LTISSLQPEDSAVYYCAVS 87
>gnl|CDD|214650 smart00406, IGv, Immunoglobulin V-Type.
Length = 81
Score = 25.0 bits (55), Expect = 3.0
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 42 YNLQITDLQTTDAGSYQCQI 61
+L I++L+ D G+Y C +
Sbjct: 62 VSLTISNLRVEDTGTYYCAV 81
>gnl|CDD|220642 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein
3. This is a family of conserved proteins which were
originally described as death-associated-protein-3
(DAP-3). The proteins carry a P-loop DNA-binding motif,
and induce apoptosis. DAP3 has been shown to be a
pro-apoptotic factor in the mitochondrial matrix and to
be crucial for mitochondrial biogenesis and so has also
been designated as MRP-S29 (mitochondrial ribosomal
protein subunit 29).
Length = 274
Score = 24.9 bits (55), Expect = 4.1
Identities = 6/30 (20%), Positives = 11/30 (36%)
Query: 14 LAWKRGIAILTAGSTKVTPDKRIQLVDGYN 43
+ G + +T V+ R V G +
Sbjct: 201 NDFPNGGVVTALAATGVSNTPRPIRVPGLS 230
>gnl|CDD|143192 cd05715, Ig_P0-like, Immunoglobulin (Ig)-like domain of Protein
zero (P0) and similar proteins. Ig_P0ex-like: domain
similar to the immunoglobulin (Ig) domain of Protein
zero (P0). P0 accounts for over 50% of the total
protein in peripheral nervous system (PNS) myelin. P0
is a single-pass transmembrane glycoprotein with a
highly basic intracellular domain and an extracellular
Ig domain. The extracellular domain of P0 (P0-ED) is
similar to the Ig variable domain, carrying one
acceptor sequence for N-linked glycosylation. P0 plays
a role in membrane adhesion in the spiral wraps of the
myelin sheath. The intracellular domain is thought to
mediate membrane apposition of the cytoplasmic faces
and may, through electrostatic interactions, interact
directly with lipid headgroups. It is thought that
homophilic interactions of the P0 extracellular domain
mediate membrane juxtaposition in the extracellular
space of PNS myelin. This group also contains the Ig
domain of Sodium channel subunit beta-2 (SCN2B), and of
epithelial V-like antigen 1 (EVA). EVA, also known as
myelin protein zero-like 2, is an adhesion molecule,
which may play a role in structural organization of the
thymus and early lymphocyte development. SCN2B subunits
play a role in determining sodium channel density and
function in neurons,and in control of electrical
excitability in the brain.
Length = 116
Score = 24.2 bits (53), Expect = 5.9
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 46 ITDLQTTDAGSYQCQI 61
I +LQ TD G+Y C +
Sbjct: 84 IHNLQFTDNGTYTCDV 99
>gnl|CDD|143308 cd05900, Ig_Aggrecan, Immunoglobulin (Ig)-like domain of the
chondroitin sulfate proteoglycan core protein (CSPG),
aggrecan. Ig_Aggrecan: immunoglobulin (Ig)-like domain
of the chondroitin sulfate proteoglycan core protein
(CSPG), aggrecan. These aggregates contribute to the
tissue's load bearing properties. In CSPGs, the Ig-like
domain is followed by hyaluronan (HA)-binding tandem
repeats, and a C-terminal region with epidermal growth
factor-like, lectin-like, and complement regulatory
protein-like domains. Separating these N- and
C-terminal regions is a nonhomologous glycosaminoglycan
attachment region. In cartilage, aggrecan forms
cartilage link protein stabilized aggregates with HA.
These aggregates contribute to the tissue's load
bearing properties. Aggrecan has a wide distribution in
connective tissue and extracellular matrices. Members
of the vertebrate HPLN (hyaluronan/HA and proteoglycan
binding link) protein family are physically linked
adjacent to CSPG genes.
Length = 112
Score = 24.1 bits (52), Expect = 6.6
Identities = 8/18 (44%), Positives = 17/18 (94%)
Query: 44 LQITDLQTTDAGSYQCQI 61
L+IT+L++ D+G+Y+C++
Sbjct: 76 LEITELRSNDSGTYRCEV 93
>gnl|CDD|143220 cd05743, Ig_Perlecan_D2_like, Immunoglobulin (Ig)-like domain II
(D2) of the human basement membrane heparan sulfate
proteoglycan perlecan, also known as HSPG2.
Ig_Perlecan_D2_like: the immunoglobulin (Ig)-like
domain II (D2) of the human basement membrane heparan
sulfate proteoglycan perlecan, also known as HSPG2.
Perlecan consists of five domains. Domain I has three
putative heparan sulfate attachment sites; domain II
has four LDL receptor-like repeats, and one Ig-like
repeat; domain III resembles the short arm of laminin
chains; domain IV has multiple Ig-like repeats (21
repeats in human perlecan); and domain V resembles the
globular G domain of the laminin A chain and internal
repeats of EGF. Perlecan may participate in a variety
of biological functions including cell binding,
LDL-metabolism, basement membrane assembly and
selective permeability, calcium binding, and growth-
and neurite-promoting activities.
Length = 78
Score = 24.0 bits (52), Expect = 7.2
Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 4/34 (11%)
Query: 32 PDKRIQLVDGYN----LQITDLQTTDAGSYQCQI 61
PD + L I D++ +D G+Y C+
Sbjct: 28 PDSARVSITSEGGYGTLTIRDVKESDQGAYTCEA 61
>gnl|CDD|143330 cd07706, IgV_TCR_delta, Immunoglobulin (Ig) variable (V) domain
of T-cell receptor (TCR) delta chain. IgV_TCR_delta:
immunoglobulin (Ig) variable (V) domain of the delta
chain of gamma/delta T-cell receptors (TCRs). TCRs
mediate antigen recognition by T lymphocytes, and are
heterodimers consisting of alpha and beta chains or
gamma and delta chains. Each chain contains a variable
(V) and a constant (C) region. The majority of T cells
contain alpha/beta TCRs but a small subset contain
gamma/delta TCRs. Alpha/beta TCRs recognize antigen as
peptide fragments presented by major histocompatibility
complex (MHC) molecules. Gamma/delta TCRs recognize
intact protein antigens; they recognize protein
antigens directly and without antigen processing, and
MHC independently of the bound peptide. Gamma/delta T
cells can also be stimulated by non-peptide antigens
such as small phosphate- or amine-containing compounds.
The variable domain of gamma/delta TCRs is responsible
for antigen recognition and is located at the
N-terminus of the receptor.
Length = 116
Score = 24.0 bits (52), Expect = 7.9
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 43 NLQITDLQTTDAGSYQCQIGTLEP 66
+L I+ LQ D+ Y C + TL
Sbjct: 73 SLTISALQLEDSAKYFCALSTLGM 96
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
0.318 0.137 0.402
Gapped
Lambda K H
0.267 0.0637 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,893,019
Number of extensions: 290101
Number of successful extensions: 309
Number of sequences better than 10.0: 1
Number of HSP's gapped: 309
Number of HSP's successfully gapped: 56
Length of query: 78
Length of database: 10,937,602
Length adjustment: 47
Effective length of query: 31
Effective length of database: 8,852,964
Effective search space: 274441884
Effective search space used: 274441884
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 (21.7 bits)
S2: 53 (24.4 bits)