RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6536
(67 letters)
>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 = 64.0 bits (156), Expect = 9e-16
Identities = 25/50 (50%), Positives = 32/50 (64%), Gaps = 2/50 (4%)
Query: 20 GATFVITCETVGVPTPLVSWRLNWNHIPAKC--TTTSEDGVGTLTCPDIQ 67
G T TC GVPTP+++WRLNW H+P + TSE G GTLT D++
Sbjct: 1 GETVEFTCVATGVPTPIINWRLNWGHVPDSARVSITSEGGYGTLTIRDVK 50
>gnl|CDD|191810 pfam07679, I-set, Immunoglobulin I-set domain.
Length = 90
Score = 35.7 bits (83), Expect = 1e-04
Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 2/59 (3%)
Query: 11 PPPKVTLDIGATFVITCETVGVPTPLVSWRLNWNHIPA--KCTTTSEDGVGTLTCPDIQ 67
P V + G + TC G P P VSW + + + + T E G TLT ++Q
Sbjct: 6 KPKDVEVQEGESARFTCTVTGDPDPTVSWFKDGQPLRSSDRFKVTYEGGTYTLTISNVQ 64
>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 = 34.3 bits (79), Expect = 4e-04
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 20 GATFVITCETVGVPTPLVSWRLNWNHI 46
G T + CE G+P P ++WRLN I
Sbjct: 1 GETGRLDCEAEGIPQPTITWRLNGVPI 27
>gnl|CDD|214653 smart00410, IG_like, Immunoglobulin like. IG domains that cannot
be classified into one of IGv1, IGc1, IGc2, IG.
Length = 85
Score = 32.5 bits (74), Expect = 0.003
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 12 PPKVTLDIGATFVITCETVGVPTPLVSWR---LNWNHIPAKCTTTSEDGVGTLT 62
PP VT+ G + ++CE G P P V+W + + + TLT
Sbjct: 1 PPSVTVKEGESVTLSCEASGSPPPEVTWYKQGGKLLAESGRFSVSRSGSTSTLT 54
>gnl|CDD|214652 smart00409, IG, Immunoglobulin.
Length = 85
Score = 32.5 bits (74), Expect = 0.003
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 12 PPKVTLDIGATFVITCETVGVPTPLVSWR---LNWNHIPAKCTTTSEDGVGTLT 62
PP VT+ G + ++CE G P P V+W + + + TLT
Sbjct: 1 PPSVTVKEGESVTLSCEASGSPPPEVTWYKQGGKLLAESGRFSVSRSGSTSTLT 54
>gnl|CDD|216971 pfam02317, Octopine_DH, NAD/NADP octopine/nopaline dehydrogenase,
alpha-helical domain. This group of enzymes act on the
CH-NH substrate bond using NAD(+) or NADP(+) as an
acceptor. The Pfam family consists mainly of octopine
and nopaline dehydrogenases from Ti plasmids.
Length = 152
Score = 31.1 bits (71), Expect = 0.018
Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 9/51 (17%)
Query: 2 TSPAYIKTNPPPK------VTLDIGATFVITC---ETVGVPTPLVSWRLNW 43
T+ AY PPK +T D+ V E GVPTPL+ + W
Sbjct: 95 TNAAYNGLPAPPKSLDHRYITEDVPFGLVPLKALAELAGVPTPLIDSIIAW 145
>gnl|CDD|206066 pfam13895, Ig_2, Immunoglobulin domain. This domain contains
immunoglobulin-like domains.
Length = 80
Score = 30.1 bits (68), Expect = 0.023
Identities = 13/57 (22%), Positives = 20/57 (35%), Gaps = 5/57 (8%)
Query: 12 PPKVTLDIGATFVITCETVGVPTPLVSWRLNWNHIPAKC-----TTTSEDGVGTLTC 63
P + G +TC G P P +W + + + S + GT TC
Sbjct: 6 PSPTVVFEGEDVTLTCSAPGNPPPNYTWYKDGVPLSSSQNGFFTPNVSAEDSGTYTC 62
>gnl|CDD|197706 smart00408, IGc2, Immunoglobulin C-2 Type.
Length = 63
Score = 28.5 bits (64), Expect = 0.062
Identities = 11/49 (22%), Positives = 19/49 (38%), Gaps = 2/49 (4%)
Query: 19 IGATFVITCETVGVPTPLVSWRLNWNHIPAKCTTTSEDGVGTLTCPDIQ 67
G + +TC G P P ++W + +P + TLT +
Sbjct: 1 EGQSVTLTCPAEGNPVPNITWLKDGKPLPESNRFVA--SGSTLTIKSVS 47
>gnl|CDD|143173 cd04972, Ig_TrkABC_d4, Fourth domain (immunoglobulin-like) of Trk
receptors TrkA, TrkB and TrkC. TrkABC_d4: the fourth
domain of Trk receptors TrkA, TrkB and TrkC, this is an
immunoglobulin (Ig)-like domain which binds to
neurotrophin. The Trk family of receptors are tyrosine
kinase receptors. They are activated by dimerization,
leading to autophosphorylation of intracellular
tyrosine residues, and triggering the signal
transduction pathway. TrkA, TrkB, and TrkC share
significant sequence homology and domain organization.
The first three domains are leucine-rich domains. The
fourth and fifth domains are Ig-like domains playing a
part in ligand binding. TrkA, Band C mediate the
trophic effects of the neurotrophin Nerve growth factor
(NGF) family. TrkA is recognized by NGF. TrKB is
recognized by brain-derived neurotrophic factor (BDNF)
and neurotrophin (NT)-4. TrkC is recognized by NT-3.
NT-3 is promiscuous as in some cell systems it
activates TrkA and TrkB receptors. TrkA is a receptor
found in all major NGF targets, including the
sympathetic, trigeminal, and dorsal root ganglia,
cholinergic neurons of the basal forebrain and the
striatum. TrKB transcripts are found throughout
multiple structures of the central and peripheral
nervous systems. The TrkC gene is expressed throughout
the mammalian nervous system.
Length = 90
Score = 27.9 bits (62), Expect = 0.19
Identities = 15/57 (26%), Positives = 19/57 (33%)
Query: 6 YIKTNPPPKVTLDIGATFVITCETVGVPTPLVSWRLNWNHIPAKCTTTSEDGVGTLT 62
I + P + G T I C G P P V W + + T T E V
Sbjct: 1 TIPVDGPNATVVYEGGTATIRCTAEGSPLPKVEWIIAGLIVIQTRTDTLETTVDIYN 57
>gnl|CDD|143275 cd05867, Ig4_L1-CAM_like, Fourth immunoglobulin (Ig)-like domain
of the L1 cell adhesion molecule (CAM).
Ig4_L1-CAM_like: fourth immunoglobulin (Ig)-like
domain of the L1 cell adhesion molecule (CAM). L1 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.
Length = 76
Score = 27.5 bits (61), Expect = 0.23
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 20 GATFVITCETVGVPTPLVSWRLN 42
G T + C+ G+PTP ++W +N
Sbjct: 1 GETARLDCQVEGIPTPNITWSIN 23
>gnl|CDD|143214 cd05737, Ig_Myomesin_like_C, C-temrinal immunoglobulin (Ig)-like
domain of myomesin and M-protein. Ig_Myomesin_like_C:
domain similar to the C-temrinal immunoglobulin
(Ig)-like domain of myomesin and M-protein. Myomesin
and M-protein are both structural proteins localized to
the M-band, a transverse structure in the center of the
sarcomere, and are candidates for M-band bridges. Both
proteins are modular, consisting mainly of repetitive
Ig-like and fibronectin type III (FnIII) domains.
Myomesin is expressed in all types of vertebrate
striated muscle; M-protein has a muscle-type specific
expression pattern. Myomesin is present in both slow
and fast fibers; M-protein is present only in fast
fibers. It has been suggested that myomesin acts as a
molecular spring with alternative splicing as a means
of modifying its elasticity.
Length = 92
Score = 27.5 bits (61), Expect = 0.24
Identities = 14/31 (45%), Positives = 16/31 (51%)
Query: 12 PPKVTLDIGATFVITCETVGVPTPLVSWRLN 42
P VT+ G T +TC G P P VSW N
Sbjct: 8 PDVVTIMEGKTLNLTCTVFGDPDPEVSWLKN 38
>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 = 27.2 bits (60), Expect = 0.40
Identities = 7/27 (25%), Positives = 15/27 (55%)
Query: 16 TLDIGATFVITCETVGVPTPLVSWRLN 42
T ++G + + C+ G P P ++W +
Sbjct: 14 TANLGQSVTLACDADGFPEPTMTWTKD 40
>gnl|CDD|143277 cd05869, Ig5_NCAM-1, Fifth immunoglobulin (Ig)-like domain of
Neural Cell Adhesion Molecule NCAM-1 (NCAM).
Ig5_NCAM-1: 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.
Length = 97
Score = 26.9 bits (59), Expect = 0.40
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 14 KVTLDIGATFVITCETVGVPTPLVSWRLNWNHIPAKCTT-------TSEDGVGTLTCPDI 66
+ +++ +TCE G P P ++WR + +I ++ T S V +LT I
Sbjct: 11 QTAMELEEQITLTCEASGDPIPSITWRTSTRNISSEEKTLDGHIVVRSHARVSSLTLKYI 70
Query: 67 Q 67
Q
Sbjct: 71 Q 71
>gnl|CDD|143299 cd05891, Ig_M-protein_C, C-terminal immunoglobulin (Ig)-like
domain of M-protein (also known as myomesin-2).
Ig_M-protein_C: the C-terminal immunoglobulin (Ig)-like
domain of M-protein (also known as myomesin-2).
M-protein is a structural protein localized to the
M-band, a transverse structure in the center of the
sarcomere, and is a candidate for M-band bridges.
M-protein is modular consisting mainly of repetitive
IG-like and fibronectin type III (FnIII) domains, and
has a muscle-type specific expression pattern.
M-protein is present in fast fibers.
Length = 92
Score = 26.8 bits (59), Expect = 0.47
Identities = 13/31 (41%), Positives = 15/31 (48%)
Query: 12 PPKVTLDIGATFVITCETVGVPTPLVSWRLN 42
P VT+ G T +TC G P P V W N
Sbjct: 8 PDVVTIMEGKTLNLTCTVFGNPDPEVIWFKN 38
>gnl|CDD|143224 cd05747, Ig5_Titin_like, M5, fifth immunoglobulin (Ig)-like
domain of human titin C terminus and similar proteins.
Ig5_Titin_like: domain similar to the M5, fifth
immunoglobulin (Ig)-like domain from the human titin C
terminus. Titin (also called connectin) is a fibrous
sarcomeric protein specifically found in vertebrate
striated muscle. Titin is gigantic; depending on
isoform composition it ranges from 2970 to 3700 kDa,
and is of a length that spans half a sarcomere. Titin
largely consists of multiple repeats of Ig-like and
fibronectin type 3 (FN-III)-like domains. Titin
connects the ends of myosin thick filaments to Z disks
and extends along the thick filament to the H zone, and
appears to function similar to an elastic band, keeping
the myosin filaments centered in the sarcomere during
muscle contraction or stretching.
Length = 92
Score = 26.5 bits (58), Expect = 0.64
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 2 TSPAYIKTNPPPKVTLDIGATFVITCETVGVPTPLVSW 39
T PA I T P +T+ G + +C+ G P P V+W
Sbjct: 1 TLPATILTKPR-SLTVSEGESARFSCDVDGEPAPTVTW 37
>gnl|CDD|143282 cd05874, Ig6_NrCAM, Sixth immunoglobulin (Ig)-like domain of
NrCAM (Ng (neuronglia) CAM-related cell adhesion
molecule). Ig6_NrCAM: sixth immunoglobulin (Ig)-like
domain of NrCAM (Ng (neuronglia) CAM-related cell
adhesion molecule). NrCAM 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. NrCAM is primarily
expressed in the nervous system.
Length = 77
Score = 26.1 bits (57), Expect = 0.73
Identities = 16/40 (40%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 24 VITCETVGVPTPLVSWRLNWNH--IPAKCTTTSEDGVGTL 61
VI CE G P P SW N H I T + GTL
Sbjct: 2 VIQCEAKGKPPPSFSWTRNGTHFDIDKDPKVTMKPNTGTL 41
>gnl|CDD|240270 PTZ00107, PTZ00107, hexokinase; Provisional.
Length = 464
Score = 26.6 bits (59), Expect = 0.96
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 41 LNWNHIPAKCTTTSEDGVGTL 61
N++PA D VGTL
Sbjct: 204 FKRNNVPANVVAVLNDTVGTL 224
>gnl|CDD|143283 cd05875, Ig6_hNeurofascin_like, Sixth immunoglobulin (Ig)-like
domain of human neurofascin (NF).
Ig6_hNeurofascin_like: the sixth immunoglobulin
(Ig)-like domain of human neurofascin (NF). NF 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 a cytoplasmic domain. NF
has many alternatively spliced isoforms having
different temporal expression patterns during
development. NF participates in axon subcellular
targeting and synapse formation, however little is
known of the functions of the different isoforms.
Length = 77
Score = 25.3 bits (55), Expect = 1.4
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 24 VITCETVGVPTPLVSWRLN 42
+I CE G P P W N
Sbjct: 2 IIECEAKGNPVPTFQWTRN 20
>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 = 25.4 bits (56), Expect = 1.5
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 12 PPKVTLDIGATFVITCET-VGVPTPLVSWRLN 42
P + +G V+ C G P P VSWR +
Sbjct: 3 PSDTQVAVGEMAVLECSPPRGHPEPTVSWRKD 34
>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 = 25.6 bits (56), Expect = 1.6
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 25 ITCETVGVPTPLVSWR 40
+TCE G P P ++WR
Sbjct: 21 LTCEAEGDPIPEITWR 36
>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 = 25.3 bits (55), Expect = 1.6
Identities = 10/19 (52%), Positives = 10/19 (52%)
Query: 24 VITCETVGVPTPLVSWRLN 42
V CE G PTP V W N
Sbjct: 3 VFECEVTGKPTPTVKWVKN 21
>gnl|CDD|236493 PRK09389, PRK09389, (R)-citramalate synthase; Provisional.
Length = 488
Score = 25.7 bits (57), Expect = 1.9
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 14 KVTLDIGATFVITCETVGVPTPLVSWRL 41
K ++ GA + C+TVG+ TP ++ L
Sbjct: 150 KAGIEAGADRICFCDTVGILTPEKTYEL 177
>gnl|CDD|176160 cd08471, PBP2_CrgA_like_2, The C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator CrgA-like, contains the type 2 periplasmic
binding fold. This CD represents the substrate binding
domain of an uncharacterized LysR-type transcriptional
regulator (LTTR) CrgA-like 2. The LTTRs are acting as
both auto-repressors and activators of target promoters,
controlling operons involved in a wide variety of
cellular processes such as amino acid biosynthesis, CO2
fixation, antibiotic resistance, degradation of aromatic
compounds, nodule formation of nitrogen-fixing bacteria,
and synthesis of virulence factors, to name a few. In
contrast to the tetrameric form of other LTTRs, CrgA
from Neisseria meningitides assembles into an octameric
ring, which can bind up to four 63-bp DNA
oligonucleotides. Phylogenetic cluster analysis showed
that the CrgA-like regulators form a subclass of the
LTTRs that function as octamers. The CrgA is an
auto-repressor of its own gene and activates the
expression of the mdaB gene which coding for an
NADPH-quinone reductase and that its action is increased
by MBL (alpha-methylene-gamma-butyrolactone), an inducer
of NADPH-quinone oxidoreductase. The structural
topology of this substrate-binding domain is most
similar to that of the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake of
a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 201
Score = 25.6 bits (57), Expect = 2.0
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 3/38 (7%)
Query: 3 SPAYIKTNPPPKVTLDIGATFVITCETVGVPTPLVSWR 40
SPAY+ + PK D+ I + P WR
Sbjct: 77 SPAYLARHGTPKHPDDLADHDCIAFTGLS---PAPEWR 111
>gnl|CDD|143210 cd05733, Ig6_L1-CAM_like, Sixth immunoglobulin (Ig)-like domain
of the L1 cell adhesion molecule (CAM) and similar
proteins. Ig6_L1-CAM_like: domain similar to the sixth
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 NrCAM [Ng(neuronglia)CAM-related cell
adhesion molecule], which is primarily expressed in the
nervous system, and human neurofascin.
Length = 77
Score = 24.7 bits (54), Expect = 2.2
Identities = 11/23 (47%), Positives = 11/23 (47%)
Query: 23 FVITCETVGVPTPLVSWRLNWNH 45
VI CE G P P SW N H
Sbjct: 1 IVIKCEAKGNPPPTFSWTRNGTH 23
>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 = 24.4 bits (52), Expect = 2.8
Identities = 11/37 (29%), Positives = 16/37 (43%)
Query: 24 VITCETVGVPTPLVSWRLNWNHIPAKCTTTSEDGVGT 60
+TC G P P ++W N +P+ T GT
Sbjct: 2 TLTCLASGPPPPTITWLKNGKPLPSSVLTRVRSSRGT 38
>gnl|CDD|132848 cd07209, Pat_hypo_Ecoli_Z1214_like, Hypothetical patatin similar to
Z1214 protein of Escherichia coli. Patatin-like
phospholipase similar to Z1214 protein of Escherichia
coli. This family predominantly consists of bacterial
patatin glycoproteins and some representatives from
eukaryotes and archaea. The patatin protein accounts for
up to 40% of the total soluble protein in potato tubers.
Patatin is a storage protein, but it also has the
enzymatic activity of a lipid acyl hydrolase, catalyzing
the cleavage of fatty acids from membrane lipids.
Members of this family have also been found in
vertebrates.
Length = 215
Score = 24.9 bits (55), Expect = 3.7
Identities = 6/33 (18%), Positives = 9/33 (27%)
Query: 10 NPPPKVTLDIGATFVITCETVGVPTPLVSWRLN 42
N P +D+GA +I
Sbjct: 146 NTPLSPAIDLGADEIIVVSLSDKGRDDRKGTPP 178
>gnl|CDD|143317 cd07693, Ig1_Robo, First immunoglobulin (Ig)-like domain in Robo
(roundabout) receptors and similar proteins. Ig1_Robo:
domain similar to the first 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 = 100
Score = 24.4 bits (53), Expect = 3.8
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 12 PPKVTLDIGATFVITCETVGVPTPLVSW 39
P + + G + C+ G PTP + W
Sbjct: 8 PSDLIVSKGDPATLNCKAEGRPTPTIQW 35
>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 = 24.1 bits (52), Expect = 4.0
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 20 GATFVITCETVGVPTPLVSWR 40
G T CE G P P + W+
Sbjct: 1 GRTVTFQCEATGNPQPAIFWQ 21
>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 = 23.9 bits (52), Expect = 5.7
Identities = 6/18 (33%), Positives = 8/18 (44%)
Query: 25 ITCETVGVPTPLVSWRLN 42
+ C G P P W +N
Sbjct: 24 LNCRARGSPPPTYRWLMN 41
>gnl|CDD|143169 cd04968, Ig3_Contactin_like, Third Ig domain of contactin.
Ig3_Contactin_like: Third 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 = 88
Score = 23.6 bits (51), Expect = 6.8
Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 4/49 (8%)
Query: 20 GATFVITCETVGVPTPLVSWR-LNWNHIPAKCTTTSEDGVGTLTCPDIQ 67
G + C +G P P + WR ++ + + + S L P+IQ
Sbjct: 16 GQNVTLECFALGNPVPQIKWRKVDGSMPSSAEISMSG---AVLKIPNIQ 61
>gnl|CDD|143216 cd05739, Ig3_RPTP_IIa_LAR_like, Third immunoglobulin (Ig)-like
domain of the receptor protein tyrosine phosphatase
(RPTP)-F, also known as LAR. Ig3_RPTP_IIa_LAR_like:
domain similar to the third 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. Included in this group is
Drosophila LAR (DLAR).
Length = 69
Score = 23.3 bits (50), Expect = 8.0
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 20 GATFVITCETVGVPTPLVSW 39
G + +TC VG P P V W
Sbjct: 1 GGSVNLTCVAVGAPMPYVKW 20
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
0.317 0.134 0.443
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: 3,333,455
Number of extensions: 230560
Number of successful extensions: 215
Number of sequences better than 10.0: 1
Number of HSP's gapped: 214
Number of HSP's successfully gapped: 32
Length of query: 67
Length of database: 10,937,602
Length adjustment: 38
Effective length of query: 29
Effective length of database: 9,252,150
Effective search space: 268312350
Effective search space used: 268312350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.4 bits)