RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy534
(145 letters)
>gnl|CDD|143309 cd05901, Ig_Versican, Immunoglobulin (Ig)-like domain of the
chondroitin sulfate proteoglycan core protein (CSPG),
versican. Ig_Versican: immunoglobulin (Ig)-like domain
of the chondroitin sulfate proteoglycan core protein
(CSPG), versican. 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, the CSPG aggrecan (not included in this
group) forms cartilage link protein stabilized
aggregates with HA. These aggregates contribute to the
tissue's load bearing properties. Like aggrecan,
versican has a wide distribution in connective tissue
and extracellular matrices. 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 = 117
Score = 40.3 bits (94), Expect = 4e-05
Identities = 17/40 (42%), Positives = 23/40 (57%)
Query: 40 EEYKGRISRVDKESPFGMASLNLTKIRESDQGWYECKVVF 79
+EY GR+S G ASL + K+R SD G Y C+V+
Sbjct: 61 QEYMGRVSVPSHPEDQGDASLTIVKLRASDAGVYRCEVMH 100
>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 = 36.4 bits (84), Expect = 0.001
Identities = 18/83 (21%), Positives = 28/83 (33%), Gaps = 17/83 (20%)
Query: 27 VYIWYDSYPTHEAEEYKGRISRVDKESPFGMASLNLTKIRESDQGWYECKVVFLNRSPNS 86
++ + +KGR+ + SL ++ +R SD G Y C V N
Sbjct: 49 IHYVTSTPNGKVGPRFKGRV-TLSGNGSKNDFSLTISNLRLSDSGTYTCAVSNPN----- 102
Query: 87 HKNGTWFHLDVHGVFNDGTELRI 109
VF GT L +
Sbjct: 103 -----------ELVFGAGTRLTV 114
Score = 29.1 bits (65), Expect = 0.46
Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 93 FHLDVHGVFNDGTELRISNIRSQDIGDYTC 122
L +G ND + L ISN+R D G YTC
Sbjct: 68 VTLSGNGSKNDFS-LTISNLRLSDSGTYTC 96
>gnl|CDD|143286 cd05878, Ig_Aggrecan_like, Immunoglobulin (Ig)-like domain of the
aggrecan-like chondroitin sulfate proteoglycan core
protein (CSPG). Ig_Aggrecan_like: immunoglobulin
(Ig)-like domain of the aggrecan-like chondroitin
sulfate proteoglycan core protein (CSPG)s. Included in
this group are the Ig domains of other CSPGs: 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. Members
of the vertebrate HPLN (hyaluronan/HA and proteoglycan
binding link) protein family are physically linked
adjacent to CSPG genes.
Length = 110
Score = 35.8 bits (83), Expect = 0.002
Identities = 16/41 (39%), Positives = 26/41 (63%)
Query: 39 AEEYKGRISRVDKESPFGMASLNLTKIRESDQGWYECKVVF 79
+EY+GR+S + G ASL ++++R SD G Y C+V+
Sbjct: 53 GQEYQGRVSLPNYPENRGDASLEISRLRSSDSGVYRCEVMH 93
>gnl|CDD|143195 cd05718, Ig1_PVR_like, First immunoglobulin (Ig) domain of
poliovirus receptor (PVR, also known as CD155) and
similar proteins. Ig1_PVR_like: domain similar to the
first immunoglobulin (Ig) domain of poliovirus receptor
(PVR, also known as CD155). Poliovirus (PV) binds to
its cellular receptor (PVR/CD155) to initiate
infection. CD155 is a membrane-anchored, single-span
glycoprotein; its extracellular region has three
Ig-like domains. There are four different isotypes of
CD155 (referred to as alpha, beta, gamma, and delta),
that result from alternate splicing of the CD155 mRNA,
and have identical extracellular domains. CD155-beta
and - gamma, are secreted, CD155-alpha and delta are
membrane-bound and function as PV receptors. The virus
recognition site is contained in the amino-terminal
domain, D1. Having the virus attachment site on the
receptor distal from the plasma membrane, may be
important for successful initiation of infection of
cells by the virus. CD155 binds in the poliovirus
"canyon" with a footprint similar to that of the
intercellular adhesion molecule-1 receptor on human
rhinoviruses. This group also includes the first
Ig-like domain of nectin-1 (also known as poliovirus
receptor related protein(PVRL)1; CD111), nectin-3 (also
known as PVRL 3), nectin-4 (also known as PVRL4; LNIR
receptor)and DNAX accessory molecule 1 (DNAM-1; CD226).
Length = 98
Score = 35.4 bits (82), Expect = 0.002
Identities = 12/46 (26%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 33 SYPTHEAEEYKGRISRVDKESPFGMASLNLTKIRESDQGWYECKVV 78
Y Y+GR+S ++ S A+++++ +R D+G Y C+
Sbjct: 39 QYGISIPPSYEGRVSFLN--SSLEDATISISNLRLEDEGNYICEFA 82
Score = 30.8 bits (70), Expect = 0.088
Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 20/59 (33%)
Query: 73 YECKVVFLNRSPNSHKNGTWFHLDVHGVFNDGTELRISNIRSQDIGDYTCLATHVLYPD 131
YE +V FLN S D T + ISN+R +D G+Y C +P
Sbjct: 48 YEGRVSFLNSSLE-----------------DAT-ISISNLRLEDEGNYICEF--ATFPQ 86
>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 = 34.8 bits (79), Expect = 0.002
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 79 FLNRSPNSHKNGTWFHLDVHGVFNDGTELRISNIRSQDIGDYTCLATH 126
N P T T L ISN+ +D G YTC+A++
Sbjct: 18 LKNGKPLPSSVLTRVRSSRGTSSGSST-LTISNVTLEDSGTYTCVASN 64
Score = 32.5 bits (73), Expect = 0.013
Identities = 11/58 (18%), Positives = 18/58 (31%), Gaps = 2/58 (3%)
Query: 20 ADDEDIPVYIWYDSYPTHEAEEYKGRISRVDKESPFGMASLNLTKIRESDQGWYECKV 77
A P W + + S S G ++L ++ + D G Y C
Sbjct: 7 ASGPPPPTITWLKNGKPLPSSVLTRVRSSRGTSS--GSSTLTISNVTLEDSGTYTCVA 62
>gnl|CDD|191810 pfam07679, I-set, Immunoglobulin I-set domain.
Length = 90
Score = 33.8 bits (78), Expect = 0.006
Identities = 13/42 (30%), Positives = 17/42 (40%), Gaps = 3/42 (7%)
Query: 87 HKNGTWFHLDVHGVF---NDGTELRISNIRSQDIGDYTCLAT 125
K+G L ISN++ D G YTC+AT
Sbjct: 35 FKDGQPLRSSDRFKVTYEGGTYTLTISNVQPDDEGKYTCVAT 76
>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 = 33.4 bits (76), Expect = 0.007
Identities = 13/22 (59%), Positives = 18/22 (81%)
Query: 103 DGTELRISNIRSQDIGDYTCLA 124
+G+EL ISN+R +D G YTC+A
Sbjct: 37 NGSELHISNVRYEDTGAYTCIA 58
>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 = 32.8 bits (75), Expect = 0.009
Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 103 DGTELRISNIRSQDIGDYTCLATHVL 128
DG+ L I N+ D G YTC A +
Sbjct: 38 DGS-LEILNVTKSDEGKYTCFAENFF 62
>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 = 0.013
Identities = 16/61 (26%), Positives = 23/61 (37%), Gaps = 15/61 (24%)
Query: 75 CKVVFLNRSPNSHKNGTWFHLDVHGVFNDG----------TELRISNIRSQDIGDYTCLA 124
C+ S + TW+ + G + L ISN+ +D G YTC A
Sbjct: 16 CEA-----SGSPPPEVTWYKQGGKLLAESGRFSVSRSGSTSTLTISNVTPEDSGTYTCAA 70
Query: 125 T 125
T
Sbjct: 71 T 71
Score = 30.6 bits (69), Expect = 0.074
Identities = 13/52 (25%), Positives = 17/52 (32%), Gaps = 5/52 (9%)
Query: 26 PVYIWYDSYPTHEAEEYKGRISRVDKESPFGMASLNLTKIRESDQGWYECKV 77
P WY A GR S S +L ++ + D G Y C
Sbjct: 24 PEVTWYKQGGKLLA--ESGRFSVSRSGSTS---TLTISNVTPEDSGTYTCAA 70
>gnl|CDD|214652 smart00409, IG, Immunoglobulin.
Length = 85
Score = 32.9 bits (75), Expect = 0.013
Identities = 16/61 (26%), Positives = 23/61 (37%), Gaps = 15/61 (24%)
Query: 75 CKVVFLNRSPNSHKNGTWFHLDVHGVFNDG----------TELRISNIRSQDIGDYTCLA 124
C+ S + TW+ + G + L ISN+ +D G YTC A
Sbjct: 16 CEA-----SGSPPPEVTWYKQGGKLLAESGRFSVSRSGSTSTLTISNVTPEDSGTYTCAA 70
Query: 125 T 125
T
Sbjct: 71 T 71
Score = 30.6 bits (69), Expect = 0.074
Identities = 13/52 (25%), Positives = 17/52 (32%), Gaps = 5/52 (9%)
Query: 26 PVYIWYDSYPTHEAEEYKGRISRVDKESPFGMASLNLTKIRESDQGWYECKV 77
P WY A GR S S +L ++ + D G Y C
Sbjct: 24 PEVTWYKQGGKLLA--ESGRFSVSRSGSTS---TLTISNVTPEDSGTYTCAA 70
>gnl|CDD|197706 smart00408, IGc2, Immunoglobulin C-2 Type.
Length = 63
Score = 31.2 bits (71), Expect = 0.036
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 88 KNGTWFHLDVHGVFNDGTELRISNIRSQDIGDYTCLATH 126
K+G V + T L I ++ +D G YTC+A +
Sbjct: 23 KDGKPLPESNRFVASGST-LTIKSVSLEDSGLYTCVAEN 60
Score = 24.7 bits (54), Expect = 8.5
Identities = 5/19 (26%), Positives = 8/19 (42%)
Query: 59 SLNLTKIRESDQGWYECKV 77
+L + + D G Y C
Sbjct: 40 TLTIKSVSLEDSGLYTCVA 58
>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 = 31.3 bits (71), Expect = 0.064
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 38 EAEEYKGRISRVDKESPFGMASLNLTKIRESDQGWYEC 75
+Y+GR+S D G+ ++ L ++R+ D GWY C
Sbjct: 45 VQSQYEGRVSLTDDPDN-GVFTVTLNQLRKEDAGWYWC 81
>gnl|CDD|214650 smart00406, IGv, Immunoglobulin V-Type.
Length = 81
Score = 30.4 bits (69), Expect = 0.083
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 27 VYIWYDSYPTHEAEEYKGRISRVDKESPFGMASLNLTKIRESDQGWYECKV 77
+ + ++ E YKGR + + K++ SL ++ +R D G Y C V
Sbjct: 32 LGYIGSNGSSYYQESYKGRFT-ISKDTSKNDVSLTISNLRVEDTGTYYCAV 81
>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 = 29.7 bits (67), Expect = 0.11
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 107 LRISNIRSQDIGDYTCLA 124
L+I N+ + D G YTC A
Sbjct: 37 LKIRNVTAGDEGSYTCEA 54
>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 = 30.2 bits (69), Expect = 0.12
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 107 LRISNIRSQDIGDYTCL 123
LRI N+R+ D G YTC
Sbjct: 67 LRIHNVRASDEGLYTCF 83
Score = 27.5 bits (62), Expect = 1.0
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 38 EAEEYKGRISRVDKESPFGMASLNLTKIRESDQGWYEC 75
+ EY+GR + G +L + +R SD+G Y C
Sbjct: 45 QMPEYRGRTELLKDAIAEGSVALRIHNVRASDEGLYTC 82
>gnl|CDD|143310 cd05902, Ig_Neurocan, Immunoglobulin (Ig)-like domain of the
chondroitin sulfate proteoglycan core protein (CSPG),
neurocan. Ig_Neurocan: immunoglobulin (Ig)-like domain
of the chondroitin sulfate proteoglycan core protein
(CSPG), neurocan. 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, the CSPG aggrecan (not included in this
group) forms cartilage link protein stabilized
aggregates with HA. These aggregates contribute to the
tissue's load bearing properties. Unlike aggrecan which
is widely distributed 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. Members
of the vertebrate HPLN (hyaluronan/HA and proteoglycan
binding link) protein family are physically linked
adjacent to CSPG genes.
Length = 110
Score = 30.2 bits (68), Expect = 0.17
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 39 AEEYKGRISRVDKESPFGMASLNLTKIRESDQGWYECKVVF 79
A+ ++GR+S ASL L+++R SD G Y C+VV
Sbjct: 53 AKAFQGRVSLPGYPKNRYNASLVLSRLRYSDSGTYRCEVVL 93
>gnl|CDD|143234 cd05757, Ig2_IL1R_like, Second immunoglobulin (Ig)-like domain of
interleukin-1 receptor (IL1R) and similar proteins.
Ig2_IL1R_like: domain similar to the second
immunoglobulin (Ig)-like domain of interleukin-1
receptor (IL1R). IL-1 alpha and IL-1 beta are cytokines
which participate in the regulation of inflammation,
immune responses, and hematopoiesis. These cytokines
bind to the IL-1 receptor type 1 (IL1R1), which is
activated on additional association with an accessory
protein, IL1RAP. IL-1 also binds a second receptor
designated type II (IL1R2). Mature IL1R1 consists of
three IG-like domains, a transmembrane domain, and a
large cytoplasmic domain. Mature IL1R2 is organized
similarly except that it has a short cytoplasmic domain.
The latter does not initiate signal transduction. A
naturally occurring cytokine IL-1RA (IL-1 receptor
antagonist) is widely expressed and binds to IL-1
receptors, inhibiting the binding of IL-1 alpha and IL-1
beta. This group also contains ILIR-like 1 (IL1R1L)
which maps to the same chromosomal location as IL1R1 and
IL1R2.
Length = 92
Score = 30.0 bits (68), Expect = 0.17
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 104 GTELRISNIRSQDIGDYTCLATH 126
G++L I N+ +D G+YTC T
Sbjct: 51 GSKLLIQNVTEEDAGNYTCKLTF 73
Score = 28.1 bits (63), Expect = 0.80
Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 10/62 (16%)
Query: 18 DFADDEDIPVYIWYDSYPTHEAEEYKGRISRVDKESPFGMASLNLTKIRESDQGWYECKV 77
DF ++ +P WY + + +G R K S L + + E D G Y CK+
Sbjct: 22 DFKNENTLPPVQWY-----KDCKLLEGDRKRFVKGS-----KLLIQNVTEEDAGNYTCKL 71
Query: 78 VF 79
F
Sbjct: 72 TF 73
>gnl|CDD|143207 cd05730, Ig3_NCAM-1_like, Third immunoglobulin (Ig)-like domain of
Neural Cell Adhesion Molecule NCAM-1 (NCAM).
Ig3_NCAM-1_like: domain similar to the third
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.
Length = 95
Score = 29.9 bits (67), Expect = 0.19
Identities = 11/25 (44%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 101 FN-DGTELRISNIRSQDIGDYTCLA 124
FN DG+E+ I ++ D +YTC+A
Sbjct: 53 FNEDGSEMTILDVDKLDEAEYTCIA 77
>gnl|CDD|222457 pfam13927, Ig_3, Immunoglobulin domain. This family contains
immunoglobulin-like domains.
Length = 74
Score = 29.3 bits (65), Expect = 0.20
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 75 CKVVFLNRSPN-SHKNGTWFHLDVHGVFNDGTELRISNIRSQDIGDYTCLATH 126
C P S G+ + G+ L +S++ S+D G YTC+A++
Sbjct: 22 CSAEGGPPPPTISWYRNGSISGGSGGLGSSGSTLTLSSVTSEDSGTYTCVASN 74
>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 = 29.2 bits (66), Expect = 0.29
Identities = 12/65 (18%), Positives = 26/65 (40%), Gaps = 5/65 (7%)
Query: 78 VFLNRSPNSHKNGTWFHLDVHGVFNDGTELRISNIRSQDIGDYTCLATHVLYPDLLVVLG 137
+ + NS G + ++ +G+ L I N+ +D G YT ++ + +
Sbjct: 32 IASYIATNSTVFGP-AYSGRETIYPNGS-LLIQNLTKEDSGTYT---LQIISTNGVTENA 86
Query: 138 SFHIH 142
F +
Sbjct: 87 KFFLR 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 = 29.1 bits (66), Expect = 0.36
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 58 ASLNLTKIRESDQGWYECKVVF 79
ASL +T +R D G Y C+V+
Sbjct: 68 ASLVITDLRLEDSGRYRCEVID 89
Score = 26.1 bits (58), Expect = 3.9
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 107 LRISNIRSQDIGDYTC 122
L I+++R +D G Y C
Sbjct: 70 LVITDLRLEDSGRYRC 85
>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 = 28.9 bits (65), Expect = 0.38
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 103 DGTELRISNIRSQDIGDYTCLATHV 127
D L I+ R D G Y C+AT++
Sbjct: 49 DDGNLLIAEARKSDEGTYKCVATNM 73
>gnl|CDD|143227 cd05750, Ig_Pro_neuregulin, Immunoglobulin (Ig)-like domain in
neuregulins (NRGs). Ig_Pro_neuregulin: immunoglobulin
(Ig)-like domain in neuregulins (NRGs). NRGs are
signaling molecules, which participate in cell-cell
interactions in the nervous system, breast, heart, and
other organ systems, and are implicated in the pathology
of diseases including schizophrenia, multiple sclerosis,
and breast cancer. There are four members of the
neuregulin gene family (NRG1, -2, -3, and -4). The NRG-1
protein, binds to and activates the tyrosine kinases
receptors ErbB3 and ErbB4, initiating signaling
cascades. The other NRGs proteins bind one or the other
or both of these ErbBs. NRG-1 has multiple functions;
for example, in the brain it regulates various processes
such as radial glia formation and neuronal migration,
dendritic development, and expression of
neurotransmitters receptors; in the peripheral nervous
system NRG-1 regulates processes such as target cell
differentiation, and Schwann cell survival. There are
many NRG-1 isoforms, which arise from the alternative
splicing of mRNA. Less is known of the functions of the
other NRGs. NRG-2 and -3 are expressed predominantly in
the nervous system. NRG-2 is expressed by motor neurons
and terminal Schwann cells, and is concentrated near
synaptic sites and may be a signal that regulates
synaptic differentiation. NRG-4 has been shown to direct
pancreatic islet cell development towards the delta-cell
lineage.
Length = 75
Score = 28.3 bits (63), Expect = 0.42
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 105 TELRISNIRSQDIGDYTCLATHVLYPD 131
+EL+I+ + D G+YTC+ ++L D
Sbjct: 43 SELQINKAKLADSGEYTCVVENILGND 69
>gnl|CDD|143183 cd04982, IgV_TCR_gamma, Immunoglobulin (Ig) variable (V) domain of
T-cell receptor (TCR) gamma chain. IgV_TCR_gamma:
immunoglobulin (Ig) variable (V) domain of the gamma
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 = 28.5 bits (64), Expect = 0.62
Identities = 15/81 (18%), Positives = 28/81 (34%), Gaps = 13/81 (16%)
Query: 27 VYIWYDSYPTHEAEEYKGRISRVDKESPFGMASLNLTKIRESDQGWYECKVVFLNRSPNS 86
+Y+ S + K + K+ ++L + + + D Y C + + S
Sbjct: 47 LYVSSTSTQRKLSGGTKNKFE-ARKDVGKSTSTLTIQNLEKEDSATYYC-AYWESGSSYY 104
Query: 87 HKNGTWFHLDVHGVFNDGTEL 107
K VF GT+L
Sbjct: 105 IK-----------VFGSGTKL 114
>gnl|CDD|143208 cd05731, Ig3_L1-CAM_like, Third immunoglobulin (Ig)-like domain of
the L1 cell adhesion molecule (CAM). Ig3_L1-CAM_like:
domain similar to the third immunoglobulin (Ig)-like
domain of the L1 cell adhesion molecule (CAM). L1
belongs to the L1 subfamily of cell adhesion molecules
(CAMs) and is comprised of an extracellular region
having six Ig-like domains and five fibronectin type III
domains, a transmembrane region and an intracellular
domain. L1 is primarily expressed in the nervous system
and is involved in its development and function. 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. This
group also contains the chicken neuron-glia cell
adhesion molecule, Ng-CAM and human neurofascin.
Length = 71
Score = 27.7 bits (62), Expect = 0.73
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 102 NDGTELRISNIRSQDIGDYTCLA 124
N L+I N+ +D G+Y C A
Sbjct: 33 NFNKTLKIDNVSEEDDGEYRCTA 55
>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 = 27.5 bits (61), Expect = 0.89
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 48 RVDKESPFGMASLNLTKIRESDQGWYECKVV 78
RV S G +L + ++ESDQG Y C+ +
Sbjct: 32 RVSITSEGGYGTLTIRDVKESDQGAYTCEAI 62
Score = 27.1 bits (60), Expect = 1.3
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 6/38 (15%)
Query: 104 GTELRISNIRSQDIGDYTCLA-----THVLYPDLLVVL 136
GT L I +++ D G YTC A PD ++ +
Sbjct: 42 GT-LTIRDVKESDQGAYTCEAINTRGMVFGIPDGILTV 78
>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 = 27.9 bits (62), Expect = 0.92
Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 20 ADDEDIPVYIWYDSYPTHEAEEYKGRISRVDKESPFGMASLNLTKIRESDQGWYEC 75
A+ + IP W + + K R+ ++SL L ++ +D G Y+C
Sbjct: 25 AEGDPIPEITWRRATRNFSEGD-KSLDGRIVVRGHARVSSLTLKDVQLTDAGRYDC 79
>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 = 27.2 bits (60), Expect = 1.1
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 88 KNGTWFHLDV-HGVFNDGTELRISNIRSQDIGDYTCLATHVL 128
K G+ +D H V + GT LRIS + D G Y C A +++
Sbjct: 23 KGGSQLSVDRRHLVLSSGT-LRISRVALHDQGQYECQAVNIV 63
>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 = 27.6 bits (61), Expect = 1.6
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 41 EYKGRISRVDKESPFGMASLNLTKIRESDQGWYECKVVF 79
EY R+S + + A+L +T++R +D G Y C+V+
Sbjct: 57 EYLDRVSLPNYPAIPSDATLEITELRSNDSGTYRCEVMH 95
>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 = 26.3 bits (58), Expect = 1.6
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 2/45 (4%)
Query: 78 VFLNRSPNSHKNGTWFHLDVHGVFNDGTELRISNIRSQDIGDYTC 122
V + + T D + V + L ISN+ +D G YTC
Sbjct: 18 VTWFKEGKGLEESTTVGTDENRVSS--ITLTISNVTPEDSGTYTC 60
>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 = 27.0 bits (60), Expect = 2.0
Identities = 16/65 (24%), Positives = 20/65 (30%), Gaps = 16/65 (24%)
Query: 61 NLTKIRESDQGWYECKVVFLNRSPNSHKNGTWFHLDVHGVFNDGTELRISNIRSQDIGDY 120
NL + W P K L V DG L I ++ D G Y
Sbjct: 23 NLASVV-----WL------FQGGPLQRKEEPEERLLV---TEDG--LLIRSVSPADAGVY 66
Query: 121 TCLAT 125
TC +
Sbjct: 67 TCQSV 71
>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 = 26.9 bits (59), Expect = 2.2
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 20 ADDEDIPVYIWYDSYPTHE-AEEYKGRISRVDKESPFGMASLNLTKIRESDQGWYECK 76
A+ E IP W + H +E K R++ + G +SL++ ++ SD G Y+C+
Sbjct: 25 AEGEPIPEITWKRASDGHTFSEGDKSPDGRIEVKGQHGESSLHIKDVKLSDSGRYDCE 82
>gnl|CDD|143181 cd04980, IgV_L_kappa, Immunoglobulin (Ig) light chain, kappa type,
variable (V) domain. IgV_L_kappa: Immunoglobulin (Ig)
light chain, kappa type, variable (V) domain. 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. There are five types of heavy chains (alpha,
gamma, delta, epsilon, and mu), which determine the type
of immunoglobulin: IgA, IgG, IgD, IgE, and IgM,
respectively. In higher vertebrates, there are two types
of light chain, designated kappa and lambda, which seem
to be functionally identical, and can associate with any
of the heavy chains.
Length = 106
Score = 26.7 bits (59), Expect = 2.5
Identities = 6/24 (25%), Positives = 8/24 (33%)
Query: 107 LRISNIRSQDIGDYTCLATHVLYP 130
L IS + +D Y C
Sbjct: 73 LTISRVEPEDAAVYYCQQYGTFPY 96
>gnl|CDD|220790 pfam10510, PIG-S, Phosphatidylinositol-glycan biosynthesis class S
protein. PIG-S is one of several key, core, components
of the glycosylphosphatidylinositol (GPI) trans-amidase
complex that mediates GPI anchoring in the endoplasmic
reticulum. Anchoring occurs when a protein's C-terminal
GPI attachment signal peptide is replaced with a
pre-assembled GPI. Mammalian GPITransamidase consists of
at least five components: Gaa1, Gpi8, PIG-S, PIG-T, and
PIG-U, all five of which are required for function. It
is possible that Gaa1, Gpi8, PIG-S, and PIG-T form a
tightly associated core that is only weakly associated
with PIG-U. The exact function of PIG-S is unclear.
Length = 502
Score = 27.7 bits (62), Expect = 2.6
Identities = 20/120 (16%), Positives = 35/120 (29%), Gaps = 16/120 (13%)
Query: 25 IPVYIWYDSYPTHEAEEYKGRISRV--DKESPFGMASLNLTKIRESDQGWYECKVVFLNR 82
+PVYI DS +AE + + + D SL L +RE+
Sbjct: 46 VPVYIVSDSLFPDDAEALQREVQHLLDDLAQTQVAWSLQLKVLRETVD------------ 93
Query: 83 SPNSHKNGTWFHLDVHGVFNDGTELRISNIRSQDIGDYTCLATHVLYPDLLVVLGSFHIH 142
+ V ++ + + D + V PDL + +
Sbjct: 94 EEEELSPSSTEVRVVPEEEDESSSSELQAG--GKETDVVYPDSSVPSPDLPSSYLAQFVA 151
>gnl|CDD|143296 cd05888, Ig1_Nectin-4_like, Frst immunoglobulin (Ig) domain of
nectin-4 (also known as poliovirus receptor related
protein 4, or as LNIR receptor) and similar proteins.
Ig1_Nectin-4_like: domain similar to the first
immunoglobulin (Ig) domain of nectin-4 (also known as
poliovirus receptor related protein 4, or as LNIR
receptor). Nectin-4 belongs to the nectin family, which
is comprised of four transmembrane glycoproteins
(nectins-1 through -4). Nectins are synaptic cell
adhesion molecules (CAMs) which participate in adhesion
and signaling at various intracellular junctions.
Nectins form homophilic cis-dimers, followed by
homophilic and heterophilic trans-dimers involved in
cell-cell adhesion. For example nectin-4
trans-interacts with nectin-1. Nectin-4 has also been
shown to interact with the actin filament-binding
protein, afadin. Unlike the other nectins, which are
widely expressed in adult tissues, nectin-4 is mainly
expressed during embryogenesis, and is not detected in
normal adult tissue or in serum. Nectin-4 is
re-expressed in breast carcinoma, and patients having
metastatic breast cancer have a circulating form of
nectin-4 formed from the ectodomain.
Length = 100
Score = 26.4 bits (58), Expect = 2.8
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 34 YPTHEAEEYKGRISRVDKESPFGMASLNLTKIRESDQGWYECKV 77
Y E Y+GR+ R + +P +L L ++D+G Y+C+V
Sbjct: 41 YGQTEFHAYEGRV-RFETPNPIADGALILRNAVQADEGKYKCRV 83
>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 = 26.2 bits (57), Expect = 2.8
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 6/32 (18%)
Query: 44 GRISRVDKESPFGMASLNLTKIRESDQGWYEC 75
GRI ++ + S ESDQG YEC
Sbjct: 30 GRIKQLRSGALQIENS------EESDQGKYEC 55
>gnl|CDD|152583 pfam12148, DUF3590, Protein of unknown function (DUF3590). This
domain is found in eukaryotes, and is typically between
83 and 97 amino acids in length. It is found in
association with pfam00097, pfam02182, pfam00628,
pfam00240. There are two conserved sequence motifs: RAR
and NYN. The domain is part of the protein NIRF which
has zinc finger and ubiquitinating domains. The
function of this domain is likely to be mainly
structural, however this has not been confirmed.
Length = 85
Score = 26.2 bits (58), Expect = 2.9
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 17 GDFADDEDIPVYIWYDSYPTHEAEEYKGRISR 48
A+DED+ ++ YD YP + + G+ R
Sbjct: 23 KALAEDEDVIYHVKYDDYPENGVVQMTGKDVR 54
>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 = 26.5 bits (59), Expect = 3.1
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 107 LRISNIRSQDIGDYTCLATHVLYPDLLVV 135
L I+++R +D G Y C L + +VV
Sbjct: 70 LVITDLRLEDYGRYRCEVIDGLEDESVVV 98
Score = 26.1 bits (58), Expect = 3.7
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 41 EYKGRISRVDKESPFGMASLNLTKIRESDQGWYECKVV 78
Y+GR+ + + ASL +T +R D G Y C+V+
Sbjct: 53 SYQGRVFL--RRAHDLDASLVITDLRLEDYGRYRCEVI 88
>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 = 25.8 bits (56), Expect = 3.4
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 100 VFNDGTELRISNIRSQDIGDYTCLA 124
+++DG+ L I NI D G YTC A
Sbjct: 35 IWDDGS-LEILNITKLDEGSYTCFA 58
>gnl|CDD|143182 cd04981, IgV_H, Immunoglobulin (Ig) heavy chain (H), variable (V)
domain. IgV_H: Immunoglobulin (Ig) heavy chain (H),
variable (V) domain. 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. There are
five types of heavy chains (alpha, gamma, delta,
epsilon, and mu), which determine the type of
immunoglobulin: IgA, IgG, IgD, IgE, and IgM,
respectively. In higher vertebrates, there are two
types of light chain, designated kappa and lambda,
which can associate with any of the heavy chains. This
family includes alpha, gamma, delta, epsilon, and mu
heavy chains.
Length = 117
Score = 25.8 bits (57), Expect = 5.4
Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 5/49 (10%)
Query: 29 IWYDSYPTHEAEEYKGR--ISRVDKESPFGMASLNLTKIRESDQGWYEC 75
I T+ A+ KGR I+R +S L L + D Y C
Sbjct: 48 INPGGGETYYADSVKGRFTITRDTSKS---TVYLQLNSLTPEDTAVYYC 93
>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 = 5.4
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 103 DGTELRISNIRSQDIGDYTCLATHVLYPDLLVVLGSFHIH 142
DG L +SN++ D Y C A++V +L + +H
Sbjct: 39 DGGTLILSNVQPNDTAVYQCNASNVHGY----LLANAFVH 74
>gnl|CDD|143178 cd04977, Ig1_NCAM-1_like, First immunoglobulin (Ig)-like domain of
neural cell adhesion molecule NCAM-1 and similar
proteins. Ig1_NCAM-1 like: first immunoglobulin
(Ig)-like domain of neural cell adhesion molecule
NCAM-1. NCAM-1 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-nonNCAM), 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 the Ig1, Ig2, and Ig3
domains. 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 = 92
Score = 25.6 bits (56), Expect = 6.0
Identities = 15/43 (34%), Positives = 20/43 (46%)
Query: 83 SPNSHKNGTWFHLDVHGVFNDGTELRISNIRSQDIGDYTCLAT 125
SPN K T + V + + L I N +D G Y C+AT
Sbjct: 35 SPNGEKLVTQQQISVVQNDDVRSTLTIYNANIEDAGIYKCVAT 77
>gnl|CDD|218049 pfam04373, DUF511, Protein of unknown function (DUF511). Bacterial
protein of unknown function.
Length = 310
Score = 26.5 bits (59), Expect = 6.2
Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 62 LTKIRESDQGWYECKVVFLNRSPNSHKNGT-WFHLDVHGV 100
L K + +Y CK + RS N G W H D+ GV
Sbjct: 119 LVKYLYENLNFY-CKTIDHERSSNKRGGGNKWLHPDIVGV 157
>gnl|CDD|238766 cd01489, Uba2_SUMO, Ubiquitin activating enzyme (E1) subunit UBA2.
UBA2 is part of the heterodimeric activating enzyme
(E1), specific for the SUMO family of ubiquitin-like
proteins (Ubls). E1 enzymes are part of a conjugation
cascade to attach Ub or Ubls, covalently to substrate
proteins consisting of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and Ubls C-terminus. The E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Post-translational
modification by SUMO family of ubiquitin-like proteins
(Ublps) is involved in cell division, nuclear transport,
the stress response and signal transduction. UBA2
contains both the nucleotide-binding motif involved in
adenylation and the catalytic cysteine involved in the
thioester intermediate and Ublp transfer to E2.
Length = 312
Score = 26.2 bits (58), Expect = 6.5
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 56 GMASLNLTKIRESDQGWYECKVVFLNRSPNSHK 88
G+ L K+ D +C+ VFLN PN K
Sbjct: 264 GLIVLEALKVLSGD--KEQCRTVFLNLQPNRRK 294
>gnl|CDD|223996 COG1070, XylB, Sugar (pentulose and hexulose) kinases [Carbohydrate
transport and metabolism].
Length = 502
Score = 26.2 bits (58), Expect = 6.9
Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 6/52 (11%)
Query: 21 DDEDIPVY---IWYDSYPTHEAEEYKGRISRVDKESPFG---MASLNLTKIR 66
D P+ +W D+ E EE + R+ + G M K+
Sbjct: 91 DANGEPLRPAILWNDTRAAEEVEELEERLGGEALYARTGLQAMPGFTAPKLL 142
>gnl|CDD|224153 COG1232, HemY, Protoporphyrinogen oxidase [Coenzyme metabolism].
Length = 444
Score = 26.1 bits (58), Expect = 7.1
Identities = 7/59 (11%), Positives = 18/59 (30%), Gaps = 3/59 (5%)
Query: 5 FAVKSIFQMLSVGDFADDEDIPVYIWYDSYPTHEAEEYKGRISRVDKESPFGMASLNLT 63
+ + ++ G D + V W + P +E + R+ + +
Sbjct: 364 AVLDDLKKLG--GINGDPVFVEVTRWKYAMPQYEV-GHLDRLEPIRAALKGAYPGIKSV 419
>gnl|CDD|239091 cd02407, PTH2_family, Peptidyl-tRNA hydrolase, type 2 (PTH2)_like
. Peptidyl-tRNA hydrolase activity releases tRNA from
the premature translation termination product
peptidyl-tRNA. Two structurally different enzymes have
been reported to encode such activity, Pth present in
bacteria and eukaryotes and Pth2 present in archaea and
eukaryotes.
Length = 115
Score = 25.6 bits (57), Expect = 7.8
Identities = 7/34 (20%), Positives = 14/34 (41%)
Query: 7 VKSIFQMLSVGDFADDEDIPVYIWYDSYPTHEAE 40
V S ++L + A + +P + D+ T
Sbjct: 56 VPSEEELLELAKKAKELGLPHSLIQDAGRTQIPP 89
>gnl|CDD|143270 cd05862, Ig1_VEGFR, First immunoglobulin (Ig)-like domain of
vascular endothelial growth factor (VEGF) receptor(R).
IG1_VEGFR: first immunoglobulin (Ig)-like domain of
vascular endothelial growth factor (VEGF) receptor(R).
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). VEGF_A interacts with both VEGFR-1 and
VEGFR-2. VEGFR-1 binds strongest to VEGF, VEGF-2 binds
more weakly. VEGFR-3 appears not to bind VEGF, but binds
other members of the VEGF family (VEGF-C and -D). VEGFRs
bind VEGFs with high affinity with 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 = 86
Score = 25.2 bits (55), Expect = 7.9
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 107 LRISNIRSQDIGDYTCLAT 125
L I N+ D+G YTC A+
Sbjct: 52 LTIENVTLSDLGRYTCTAS 70
>gnl|CDD|143219 cd05742, Ig1_VEGFR_like, First immunoglobulin (Ig)-like domain of
vascular endothelial growth factor (VEGF) receptor (R)
and similar proteins. Ig1_VEGFR_like: first
immunoglobulin (Ig)-like domain of vascular endothelial
growth factor (VEGF) receptor(R) related proteins. 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). VEGF-A interacts with both VEGFR-1 and
VEGFR-2. VEGFR-1 binds strongest to VEGF, VEGF-2 binds
more weakly. VEGFR-3 appears not to bind VEGF, but binds
other members of the VEGF family (VEGF-C and -D). VEGFRs
bind VEGFs with high affinity with 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. This group also contains
alpha-type platelet-derived growth factor receptor
precursor (PDGFR)-alpha (CD140a), and PDGFR-beta
(CD140b). PDGFRs alpha and beta have an extracellular
component with five Ig-like domains, a transmembrane
segment, and a cytoplasmic portion that has protein
tyrosine kinase activity.
Length = 84
Score = 25.0 bits (55), Expect = 8.0
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 107 LRISNIRSQDIGDYTCLATH 126
L I N +D G YTC A+
Sbjct: 51 LTIPNATLKDSGTYTCAASS 70
>gnl|CDD|143266 cd05858, Ig3_FGFR-2, Third immunoglobulin (Ig)-like domain of
fibroblast growth factor receptor 2 (FGFR2).
Ig3_FGFR-2-like; domain similar to the third
immunoglobulin (Ig)-like domain of human fibroblast
growth factor receptor 2 (FGFR2). Fibroblast growth
factors (FGFs) participate in morphogenesis,
development, angiogenesis, and wound healing. These
FGF-stimulated processes are mediated by four FGFR
tyrosine kinases (FGRF1-4). FGFRs are comprised of an
extracellular portion consisting of three Ig-like
domains, a transmembrane helix, and a cytoplasmic
portion having protein tyrosine kinase activity. The
highly conserved Ig-like domains 2 and 3, and the linker
region between D2 and D3 define a general binding site
for FGFs. FGFR2 is required for male sex determination.
Length = 90
Score = 25.3 bits (55), Expect = 8.1
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 107 LRISNIRSQDIGDYTCLA 124
L + N+ +D G+YTCLA
Sbjct: 57 LYLRNVTFEDAGEYTCLA 74
>gnl|CDD|239041 cd02126, PA_EDEM3_like, PA_EDEM3_like: protease associated domain
(PA) domain-containing EDEM3-like proteins. This group
contains various PA domain-containing proteins similar
to mouse EDEM3 (ER-degradation-enhancing
mannosidase-like 3 protein). EDEM3 contains a region,
similar to Class I alpha-mannosidases (gylcosyl
hydrolase family 47), N-terminal to the PA domain. EDEM3
accelerates glycoprotein ERAD (ER-associated
degradation). In transfected mammalian cells,
overexpression of EDEM3 enhances the mannose trimming
from the N-glycans, of a model misfolded protein
[alpha1-antitrypsin null (Hong Kong)] as well as, from
total glycoproteins. Mannose trimming appears to be
involved in the selection of ERAD substrates. EDEM3 has
a different specificity of trimming than ER
alpha-mannosidase 1. The significance of the PA domain
to EDEM3 has not been ascertained. It may be a
protein-protein interaction domain. At peptidase active
sites, the PA domain may participate in substrate
binding and/or promoting conformational changes, which
influence the stability and accessibility of the site to
substrate.
Length = 126
Score = 25.4 bits (56), Expect = 8.8
Identities = 10/24 (41%), Positives = 11/24 (45%)
Query: 4 SFAVKSIFQMLSVGDFADDEDIPV 27
S +F M GD DD IPV
Sbjct: 78 SSDTAPMFAMSGDGDSTDDVTIPV 101
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 0.137 0.430
Gapped
Lambda K H
0.267 0.0832 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,340,834
Number of extensions: 632581
Number of successful extensions: 611
Number of sequences better than 10.0: 1
Number of HSP's gapped: 610
Number of HSP's successfully gapped: 68
Length of query: 145
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 57
Effective length of database: 7,034,450
Effective search space: 400963650
Effective search space used: 400963650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (24.4 bits)