RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5694
(129 letters)
>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 = 33.1 bits (76), Expect = 0.008
Identities = 24/89 (26%), Positives = 38/89 (42%), Gaps = 11/89 (12%)
Query: 31 VILGNTAVLRCQIPSYMSEYIIVTSWIQDDVNIYLNTDTGGKYVVLSSGDLYVFNATPND 90
V +G AVL C P E + SW +D + + ++ G+L + A +D
Sbjct: 8 VAVGEMAVLECSPPRGHPEPTV--SWRKDGQPL---NLDNERVRIVDDGNLLIAEARKSD 62
Query: 91 GYKSYRCRTVNKI-TGESQASVFQTRLSI 118
Y+C N + ES A+ RLS+
Sbjct: 63 EGT-YKCVATNMVGERESAAA----RLSV 86
>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 = 31.0 bits (70), Expect = 0.033
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 4/66 (6%)
Query: 34 GNTAVLRCQIPSYMSEYIIVTSWIQDDVNIYLNTDTGGKYVVLSSGDLYVFNATPNDGYK 93
G++ L C + + +W ++ + +T G +SS L + N TP D
Sbjct: 1 GSSVTLTCSVSGPPQVDV---TWFKEGKGLEESTTVGTDENRVSSITLTISNVTPEDSG- 56
Query: 94 SYRCRT 99
+Y C
Sbjct: 57 TYTCVV 62
>gnl|CDD|143281 cd05873, Ig_Sema4D_like, Immunoglobulin (Ig)-like domain of the
class IV semaphorin Sema4D. Ig_Sema4D_like;
Immunoglobulin (Ig)-like domain of Sema4D. Sema4D is a
Class IV semaphorin. Semaphorins are classified based on
structural features additional to the Sema domain.
Sema4D has extracellular Sema and Ig domains, a
transmembrane domain, and a short cytoplasmic domain.
Sema4D plays a part in the development of GABAergic
synapses. Sema4D in addition is an immune semaphorin. It
is abundant on resting T cells; its expression is weak
on resting B cells and antigen presenting cells (APCs),
but is upregulated by various stimuli. The receptor used
by Sema4D in the immune system is CD72. Sem4D enhances
the activation of B cells and DCs through binding CD72,
perhaps by reducing CD72s inhibitory signals. The
receptor used by Sema4D in the non-lymphatic tissues is
plexin-B1. Sem4D is anchored to the cell surface but its
extracellular domain can be released from the cell
surface by a metalloprotease-dependent process. Sem4D
may mediate its effects in its membrane bound form,
and/or its cleaved form.
Length = 87
Score = 29.8 bits (67), Expect = 0.14
Identities = 24/87 (27%), Positives = 37/87 (42%), Gaps = 12/87 (13%)
Query: 28 EHNVILGNTAVLRCQIPSYMSEYIIVTSWIQDDVNIYLNTDTGGKYVVLSSGDLYVFNAT 87
+ LGN A L+C S ++ W D + T KY++ G L +FNA+
Sbjct: 5 QRTFKLGNNAELKCSPKSNLAR----VVWKFDGKVL---TPESAKYLLYRDG-LLIFNAS 56
Query: 88 PNDGYKSYRCRTVNKITGESQASVFQT 114
D + Y+C +V K + QT
Sbjct: 57 EADAGR-YQCLSVEKSKAK---LFTQT 79
>gnl|CDD|214653 smart00410, IG_like, Immunoglobulin like. IG domains that cannot
be classified into one of IGv1, IGc1, IGc2, IG.
Length = 85
Score = 28.6 bits (64), Expect = 0.35
Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 11/85 (12%)
Query: 31 VILGNTAVLRCQIPSYMSEYIIVTSWIQDDVNIYLNTDTGGKYVVLSSGD---LYVFNAT 87
V G + L C+ + +W + + G++ V SG L + N T
Sbjct: 6 VKEGESVTLSCEASGSPPPEV---TWYKQGGKLLA---ESGRFSVSRSGSTSTLTISNVT 59
Query: 88 PNDGYKSYRCR-TVNKITGESQASV 111
P D +Y C T + + S ++
Sbjct: 60 PED-SGTYTCAATNSSGSASSGTTL 83
>gnl|CDD|214652 smart00409, IG, Immunoglobulin.
Length = 85
Score = 28.6 bits (64), Expect = 0.35
Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 11/85 (12%)
Query: 31 VILGNTAVLRCQIPSYMSEYIIVTSWIQDDVNIYLNTDTGGKYVVLSSGD---LYVFNAT 87
V G + L C+ + +W + + G++ V SG L + N T
Sbjct: 6 VKEGESVTLSCEASGSPPPEV---TWYKQGGKLLA---ESGRFSVSRSGSTSTLTISNVT 59
Query: 88 PNDGYKSYRCR-TVNKITGESQASV 111
P D +Y C T + + S ++
Sbjct: 60 PED-SGTYTCAATNSSGSASSGTTL 83
>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 = 1.3
Identities = 18/89 (20%), Positives = 33/89 (37%), Gaps = 11/89 (12%)
Query: 31 VILGNTAVLRCQIPSYMSEYIIVTSWIQDDVNIYLNTDTGGKYVVLSSGDLYVFNATPND 90
V+ GN+ L C S ++ V W+ + + + +V G L + + +P D
Sbjct: 8 VVEGNSVFLECSPKSNLAS---VV-WLFQGGPLQRKEEPEERLLVTEDGLL-IRSVSPAD 62
Query: 91 GYKSYRCRTVNKITGESQASVFQTRLSIT 119
Y C++V E S+
Sbjct: 63 A-GVYTCQSV-----EHGFKQTLATYSLN 85
>gnl|CDD|236315 PRK08633, PRK08633, 2-acyl-glycerophospho-ethanolamine
acyltransferase; Validated.
Length = 1146
Score = 28.0 bits (63), Expect = 1.5
Identities = 7/30 (23%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 2 KMKDTFLLFFPMLPVVKQKYEINVNYEHNV 31
+ D+ L F +L ++ +Y + V N+
Sbjct: 409 LLPDSLLRFL-LLLLMHTRYRLRVEGRENI 437
>gnl|CDD|215246 PLN02447, PLN02447, 1,4-alpha-glucan-branching enzyme.
Length = 758
Score = 27.7 bits (62), Expect = 1.8
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 66 NTDTGGKYVVLSSGDL-YVFNATPNDGYKSYR 96
D G K +V GDL +VFN P + Y YR
Sbjct: 639 RKDEGDKVIVFERGDLVFVFNFHPTNSYSDYR 670
>gnl|CDD|237466 PRK13674, PRK13674, putative GTP cyclohydrolase; Provisional.
Length = 271
Score = 27.5 bits (62), Expect = 1.8
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 91 GYKSYRCRTVNKITGESQASVFQTRLSITGKLKSLC 126
G+K Y + E + VF+ L + + SLC
Sbjct: 123 GWKDYPVT----LEAELRDGVFRLELKVEVPVSSLC 154
>gnl|CDD|139606 PRK13486, PRK13486, bifunctional enterobactin receptor/adhesin
protein; Provisional.
Length = 696
Score = 27.7 bits (61), Expect = 2.3
Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 20 KYEINVNYEHNVILGNTAVLRCQIPSYMSEYI--IVTSWIQDDVNIYLNT 67
K E +V+YE V N A L + +M+++ IV+ I D+ N Y+N+
Sbjct: 471 KPEESVSYEAGVYYDNPAGLNANVTGFMTDFSNKIVSYSINDNTNSYVNS 520
>gnl|CDD|100063 cd05825, LbH_wcaF_like, wcaF-like: This group is composed of the
protein product of the E. coli wcaF gene and similar
proteins. WcaF is part of the gene cluster responsible
for the biosynthesis of the extracellular
polysaccharide colanic acid. The wcaF protein is
predicted to contain a left-handed parallel beta-helix
(LbH) domain encoded by imperfect tandem repeats of a
hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X).
Proteins containing hexapeptide repeats are often
enzymes showing acyltransferase activity. Many are
trimeric in their active forms.
Length = 107
Score = 25.6 bits (57), Expect = 4.4
Identities = 11/26 (42%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 55 SWIQDDVNIY-LNTDTGGKYVVLSSG 79
SWI + V IY L T G +S G
Sbjct: 10 SWIGEGVWIYNLAPVTIGSDACISQG 35
>gnl|CDD|233071 TIGR00649, MG423, conserved hypothetical protein. Contains an
ATP-binding domain at the N-terminal end of the protein.
Possibly part of a superfamily of beta-lactmases
[Hypothetical proteins, Conserved].
Length = 422
Score = 26.5 bits (59), Expect = 5.0
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 43 IPSYMSEYIIVTSWIQDDVNIYLNTDTGGKYVVLSSGDLYVFNATPNDG 91
+ E+ +T I D V L+T G ++ +GD + F+ TP G
Sbjct: 124 GENTAIEFFRITHSIPDSVGFALHTPLG---YIVYTGD-FKFDNTPVIG 168
>gnl|CDD|143256 cd05848, Ig1_Contactin-5, First Ig domain of contactin-5.
Ig1_Contactin-5: First Ig domain of the neural cell
adhesion molecule contactin-5. Contactins are comprised
of six Ig domains followed by four fibronectin type III
(FnIII) domains, anchored to the membrane by
glycosylphosphatidylinositol. The different contactins
show different expression patterns in the central
nervous system. In rats, a lack of contactin-5 (NB-2)
results in an impairment of the neuronal activity in the
auditory system. Contactin-5 is expressed specifically
in the postnatal nervous system, peaking at about 3
weeks postnatal. Contactin-5 is highly expressed in the
adult human brain in the occipital lobe and in the
amygdala; lower levels of expression have been detected
in the corpus callosum, caudate nucleus, and spinal
cord.
Length = 94
Score = 25.3 bits (55), Expect = 6.0
Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 16/71 (22%)
Query: 38 VLRCQ-----IPSYMSEYIIVTSWIQDDVNIYLNTDTGGKYVVLSSGDLYVFNATPNDGY 92
+L C+ +P+Y W+++ I +D +Y L G+L + N +
Sbjct: 23 ILNCEARGNPVPTY--------RWLRNGTEIDTESDY--RYS-LIDGNLIISNPSEVKDS 71
Query: 93 KSYRCRTVNKI 103
Y+C N I
Sbjct: 72 GRYQCLATNSI 82
>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 = 25.2 bits (55), Expect = 7.0
Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 69 TGGKYVVLSSGD----LYVFNATPNDGYKSYRCRTVNKITGESQASV 111
T + V+ + D L ++NA D Y+C + ES+A+V
Sbjct: 43 TQQQISVVQNDDVRSTLTIYNANIEDA-GIYKCVATDAKGTESEATV 88
>gnl|CDD|236703 PRK10502, PRK10502, putative acyl transferase; Provisional.
Length = 182
Score = 25.7 bits (57), Expect = 7.7
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 55 SWIQDDVNIY-LNTDTGGKYVVLSSG 79
+WI DDV +Y L T G + V+S
Sbjct: 78 AWIGDDVWLYNLGEITIGAHCVISQK 103
>gnl|CDD|241300 cd01270, PTB_CAPON-like, Carboxyl-terminal PDZ ligand of neuronal
nitric oxide synthase protein (CAPON)
Phosphotyrosine-binding (PTB) domain. CAPON (also known
as Nitric oxide synthase 1 adaptor protein, NOS1AP,
encodes a cytosolic protein that binds to the signaling
molecule, neuronal NOS (nNOS). It contains a N-terminal
PTB domain that binds to the small monomeric G protein,
Dexras1 and a C-terminal PDZ-binding domain that
mediates interactions with nNOS. Included in this cd
are C. elegan proteins dystrobrevin, DYB-1, which
controls neurotransmitter release and muscle Ca(2+)
transients by localizing BK channels and DYstrophin-like
phenotype and CAPON related,DYC-1, which is functionally
related to dystrophin homolog, DYS-1. Mutations in the
dystrophin gene causes Duchenne muscular dystrophy.
DYS-1 shares sequence similarity, including key motifs,
with their mammalian counterparts. These CAPON-like
proteins all have a single PTB domain. PTB domains have
a common PH-like fold and are found in various
eukaryotic signaling molecules. This domain was
initially shown to binds peptides with a NPXY motif with
differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 179
Score = 25.7 bits (57), Expect = 7.9
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 73 YVVLSSGDLYVFNATPNDGYKS-YRCRTVNKITGESQA 109
YV S DL +F+ DG + ++C V K +SQA
Sbjct: 112 YVSHDSQDLKIFSYIARDGSSNVFKC-NVFKSKKKSQA 148
>gnl|CDD|204339 pfam09922, DUF2154, Cell wall-active antibiotics response protein
(DUF2154).
Length = 115
Score = 24.9 bits (55), Expect = 9.6
Identities = 10/55 (18%), Positives = 20/55 (36%), Gaps = 4/55 (7%)
Query: 21 YEINVNYEHNVILGNTAVLRCQIPSYMSEYIIVTSWIQDD----VNIYLNTDTGG 71
++ V+ +H+ I G + +E I S D+ + I + G
Sbjct: 58 SDVEVSLDHSAIYGGVDFFDEEEYGLRNESIRYRSENYDEAERRLKIITSLFIGD 112
>gnl|CDD|177369 PHA02528, 43, DNA polymerase; Provisional.
Length = 881
Score = 25.8 bits (57), Expect = 9.8
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 4/32 (12%)
Query: 56 WIQDDVNIYLNT---DTGGKYVVLSSGD-LYV 83
WI+ +N YLN YV+ D +YV
Sbjct: 582 WIERKMNEYLNKLCKTEDEDYVIYGDTDSIYV 613
>gnl|CDD|215067 PLN00129, PLN00129, succinate dehydrogenase [ubiquinone]
iron-sulfur subunit.
Length = 276
Score = 25.5 bits (56), Expect = 10.0
Identities = 6/12 (50%), Positives = 9/12 (75%)
Query: 89 NDGYKSYRCRTV 100
+D +K YRC T+
Sbjct: 238 DDEFKLYRCHTI 249
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
0.320 0.135 0.400
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: 6,265,370
Number of extensions: 527110
Number of successful extensions: 398
Number of sequences better than 10.0: 1
Number of HSP's gapped: 397
Number of HSP's successfully gapped: 27
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
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: 53 (24.4 bits)