RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3125
(163 letters)
>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 = 36.8 bits (85), Expect = 9e-04
Identities = 12/84 (14%), Positives = 29/84 (34%), Gaps = 12/84 (14%)
Query: 3 CTVMGL--GRPVSWMRKRDLHILTTNIYTYTGDA----------RFSVIHPQNSDEWNMK 50
C+ V W ++ I+ T R ++ + +++++
Sbjct: 23 CSFSSSSGSTSVYWYKQPLGKGPELIIHYVTSTPNGKVGPRFKGRVTLSGNGSKNDFSLT 82
Query: 51 IDYAQKRDAGIYECQVNTEPKMNM 74
I + D+G Y C V+ ++
Sbjct: 83 ISNLRLSDSGTYTCAVSNPNELVF 106
Score = 31.8 bits (72), Expect = 0.057
Identities = 7/40 (17%), Positives = 20/40 (50%)
Query: 115 RFSVIHPQNSDEWNMKIDYAQKRDAGIYECQVNTEPKMNM 154
R ++ + +++++ I + D+G Y C V+ ++
Sbjct: 67 RVTLSGNGSKNDFSLTISNLRLSDSGTYTCAVSNPNELVF 106
>gnl|CDD|214653 smart00410, IG_like, Immunoglobulin like. IG domains that cannot
be classified into one of IGv1, IGc1, IGc2, IG.
Length = 85
Score = 35.6 bits (82), Expect = 0.002
Identities = 14/71 (19%), Positives = 21/71 (29%), Gaps = 11/71 (15%)
Query: 3 CTVMGLGRP-VSWMRKRDLHILTTNIYTYTGDARFSVIHPQNSDEWNMKIDYAQKRDAGI 61
C G P V+W ++ + RFSV + + I D+G
Sbjct: 16 CEASGSPPPEVTWYKQGGKLLAE--------SGRFSVSR--SGSTSTLTISNVTPEDSGT 65
Query: 62 YECQVNTEPKM 72
Y C
Sbjct: 66 YTCAATNSSGS 76
Score = 30.6 bits (69), Expect = 0.092
Identities = 9/40 (22%), Positives = 12/40 (30%), Gaps = 2/40 (5%)
Query: 113 DARFSVIHPQNSDEWNMKIDYAQKRDAGIYECQVNTEPKM 152
RFSV + + I D+G Y C
Sbjct: 39 SGRFSVSR--SGSTSTLTISNVTPEDSGTYTCAATNSSGS 76
>gnl|CDD|214652 smart00409, IG, Immunoglobulin.
Length = 85
Score = 35.6 bits (82), Expect = 0.002
Identities = 14/71 (19%), Positives = 21/71 (29%), Gaps = 11/71 (15%)
Query: 3 CTVMGLGRP-VSWMRKRDLHILTTNIYTYTGDARFSVIHPQNSDEWNMKIDYAQKRDAGI 61
C G P V+W ++ + RFSV + + I D+G
Sbjct: 16 CEASGSPPPEVTWYKQGGKLLAE--------SGRFSVSR--SGSTSTLTISNVTPEDSGT 65
Query: 62 YECQVNTEPKM 72
Y C
Sbjct: 66 YTCAATNSSGS 76
Score = 30.6 bits (69), Expect = 0.092
Identities = 9/40 (22%), Positives = 12/40 (30%), Gaps = 2/40 (5%)
Query: 113 DARFSVIHPQNSDEWNMKIDYAQKRDAGIYECQVNTEPKM 152
RFSV + + I D+G Y C
Sbjct: 39 SGRFSVSR--SGSTSTLTISNVTPEDSGTYTCAATNSSGS 76
>gnl|CDD|191810 pfam07679, I-set, Immunoglobulin I-set domain.
Length = 90
Score = 35.3 bits (82), Expect = 0.002
Identities = 18/65 (27%), Positives = 22/65 (33%), Gaps = 12/65 (18%)
Query: 3 CTVMGLGRP-VSWMRKRDLHILTTNIYTYTGDARFSVIHPQNSDEWNMKIDYAQKRDAGI 61
CTV G P VSW K + RF V + + + I Q D G
Sbjct: 22 CTVTGDPDPTVSW-FKDGQPL--------RSSDRFKVTYEGGTYT--LTISNVQPDDEGK 70
Query: 62 YECQV 66
Y C
Sbjct: 71 YTCVA 75
Score = 29.1 bits (66), Expect = 0.35
Identities = 9/34 (26%), Positives = 12/34 (35%), Gaps = 2/34 (5%)
Query: 113 DARFSVIHPQNSDEWNMKIDYAQKRDAGIYECQV 146
RF V + + + I Q D G Y C
Sbjct: 44 SDRFKVTYEGGTYT--LTISNVQPDDEGKYTCVA 75
>gnl|CDD|143167 cd00099, IgV, Immunoglobulin variable domain (IgV). IgV:
Immunoglobulin variable domain (IgV). Members of the
IgV family are components of immunoglobulin (Ig) and T
cell receptors. The basic structure of Ig molecules is
a tetramer of two light chains and two heavy chains
linked by disulfide bonds. In Ig, each chain is
composed of one variable domain (IgV) and one or more
constant domains (IgC); these names reflect the fact
that the variability in sequences is higher in the
variable domain than in the constant domain. Within the
variable domain, there are regions of even more
variability called the hypervariable or
complementarity-determining regions (CDRs) which are
responsible for antigen binding. A predominant feature
of most Ig domains is the disulfide bridge connecting 2
beta-sheets with a tryptophan residue packed against
the disulfide bond.
Length = 105
Score = 31.9 bits (73), Expect = 0.038
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 8/63 (12%)
Query: 12 VSWMRKRD------LHILTTNIYTYTGD--ARFSVIHPQNSDEWNMKIDYAQKRDAGIYE 63
+ W R++ L +++N Y G RFS + + + I Q D+ +Y
Sbjct: 24 IFWYRQKPGKGPELLIYISSNGSQYAGGVKGRFSGTRDSSKSSFTLTISSLQPEDSAVYY 83
Query: 64 CQV 66
C V
Sbjct: 84 CAV 86
Score = 30.7 bits (70), Expect = 0.13
Identities = 9/32 (28%), Positives = 14/32 (43%)
Query: 115 RFSVIHPQNSDEWNMKIDYAQKRDAGIYECQV 146
RFS + + + I Q D+ +Y C V
Sbjct: 55 RFSGTRDSSKSSFTLTISSLQPEDSAVYYCAV 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 = 31.3 bits (70), Expect = 0.041
Identities = 10/69 (14%), Positives = 19/69 (27%), Gaps = 8/69 (11%)
Query: 3 CTVMGLGRP-VSWMRKRDLHILTTNIYTYTGDARFSVIHPQNSDEWNMKIDYAQKRDAGI 61
C G P ++W++ + + S + I D+G
Sbjct: 5 CLASGPPPPTITWLKNGKPLPSSVLTRVRSSRGTSSGSS-------TLTISNVTLEDSGT 57
Query: 62 YECQVNTEP 70
Y C +
Sbjct: 58 YTCVASNSA 66
Score = 25.5 bits (55), Expect = 4.9
Identities = 6/28 (21%), Positives = 10/28 (35%)
Query: 123 NSDEWNMKIDYAQKRDAGIYECQVNTEP 150
+S + I D+G Y C +
Sbjct: 39 SSGSSTLTISNVTLEDSGTYTCVASNSA 66
>gnl|CDD|197706 smart00408, IGc2, Immunoglobulin C-2 Type.
Length = 63
Score = 27.8 bits (62), Expect = 0.58
Identities = 10/67 (14%), Positives = 20/67 (29%), Gaps = 16/67 (23%)
Query: 1 MACTVMGLGRP-VSWMRKRDLHILTTNIYTYTGDARFSVIHPQNSDEWNMKIDYAQKRDA 59
+ C G P ++W +D L + + ++ D+
Sbjct: 7 LTCPAEGNPVPNITW--LKDGKPLPESNRFVASGSTLTIKS-------------VSLEDS 51
Query: 60 GIYECQV 66
G+Y C
Sbjct: 52 GLYTCVA 58
>gnl|CDD|225428 COG2873, MET17, O-acetylhomoserine sulfhydrylase [Amino acid
transport and metabolism].
Length = 426
Score = 29.6 bits (67), Expect = 0.64
Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 6/44 (13%)
Query: 20 LHILTTNIYTYTGDARFSVIHPQNSDEWNMKIDYAQKRDAGIYE 63
L NI GDAR VIHP ++ + ++ AG+
Sbjct: 363 LFSHLANI----GDARSLVIHPASTTHRQL--SEEEQAAAGVTP 400
Score = 27.6 bits (62), Expect = 3.2
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 6/42 (14%)
Query: 102 LLTTNIYTYTGDARFSVIHPQNSDEWNMKIDYAQKRDAGIYE 143
NI GDAR VIHP ++ + ++ AG+
Sbjct: 365 SHLANI----GDARSLVIHPASTTHRQL--SEEEQAAAGVTP 400
>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 = 27.5 bits (61), Expect = 1.6
Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 9/67 (13%)
Query: 3 CTVMGLGRPVSWMRKRDLHILTTNIYTYTGDARFSVIHPQNSDEWNMKIDYAQKRDAGIY 62
C V+G + +SW ++T + SV+ + + I A DAGIY
Sbjct: 22 CQVIGEPKDISWFSPNGEKLVT--------QQQISVVQ-NDDVRSTLTIYNANIEDAGIY 72
Query: 63 ECQVNTE 69
+C
Sbjct: 73 KCVATDA 79
>gnl|CDD|236159 PRK08134, PRK08134, O-acetylhomoserine
aminocarboxypropyltransferase; Validated.
Length = 433
Score = 28.6 bits (64), Expect = 1.7
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 13/64 (20%)
Query: 32 GDARFSVIHPQNSDEWNMKIDYAQKRDAGIYECQVNTEPKMNMAIMLN-----VDDRGRG 86
GDAR VIHP ++ + M D A AGI E + ++I L +DD R
Sbjct: 373 GDARSLVIHPASTTHFRM--DAAALAAAGI------GEGTIRLSIGLEDADDLIDDLKRA 424
Query: 87 ARLS 90
+ +
Sbjct: 425 LKAA 428
Score = 27.8 bits (62), Expect = 2.6
Identities = 15/32 (46%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 112 GDARFSVIHPQNSDEWNMKIDYAQKRDAGIYE 143
GDAR VIHP ++ + M D A AGI E
Sbjct: 373 GDARSLVIHPASTTHFRM--DAAALAAAGIGE 402
>gnl|CDD|176521 cd08579, GDPD_memb_like, Glycerophosphodiester phosphodiesterase
domain of uncharacterized bacterial
glycerophosphodiester phosphodiesterases. This
subfamily corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in
uncharacterized bacterial glycerophosphodiester
phosphodiesterases. In addition to a C-terminal GDPD
domain, most members in this family have an N-terminus
that functions as a membrane anchor.
Length = 220
Score = 27.9 bits (63), Expect = 2.1
Identities = 9/32 (28%), Positives = 13/32 (40%)
Query: 131 IDYAQKRDAGIYECQVNTEPKMNMAIMLNVDG 162
I A + +Y VN M + + VDG
Sbjct: 183 IRQAHQNGKKVYVWTVNDPDDMQRYLAMGVDG 214
>gnl|CDD|197311 cd09077, R1-I-EN, Endonuclease domain encoded by various R1- and
I-clade non-long terminal repeat retrotransposons. This
family contains the endonuclease (EN) domain of various
non-long terminal repeat (non-LTR) retrotransposons,
long interspersed nuclear elements (LINEs) which belong
to the subtype 2, R1- and I-clade. LINES can be
classified into two subtypes. Subtype 2 has two ORFs:
the second (ORF2) encodes a modular protein consisting
of an N-terminal apurine/apyrimidine endonuclease domain
(EN), a central reverse transcriptase, and a
zinc-finger-like domain at the C-terminus. Most non-LTR
retrotransposons are inserted throughout the host
genome; however, many retrotransposons of the R1 clade
exhibit target-specific retrotransposition. This family
includes the endonucleases of SART1 and R1bm, from the
silkworm Bombyx mori, which belong to the R1-clade. It
also includes the endonuclease of snail (Biomphalaria
glabrata) Nimbus/Bgl and mosquito Aedes aegypti
(MosquI), both which belong to the I-clade. This family
belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 205
Score = 27.3 bits (61), Expect = 3.3
Identities = 7/27 (25%), Positives = 11/27 (40%), Gaps = 1/27 (3%)
Query: 14 WMRKRDLHIL-TTNIYTYTGDARFSVI 39
W+ L +L N T+ S+I
Sbjct: 145 WIANLGLVLLNDGNSPTFVRPRGTSII 171
>gnl|CDD|219034 pfam06448, DUF1081, Domain of Unknown Function (DUF1081). This
region is found in Apolipophorin proteins.
Length = 114
Score = 26.5 bits (59), Expect = 3.9
Identities = 12/56 (21%), Positives = 21/56 (37%), Gaps = 2/56 (3%)
Query: 96 NFAFPDLLTTNIYTYTGDARFSV-IHPQNS-DEWNMKIDYAQKRDAGIYECQVNTE 149
+ +PD+ TN G A F + + + K +Y R + +V E
Sbjct: 24 DMNYPDVFRTNALPLGGPASFKLELEKTPEVRGYTAKANYKLDRGDKSIKLKVEAE 79
>gnl|CDD|143252 cd05775, Ig_SLAM-CD84_like_N, N-terminal immunoglobulin (Ig)-like
domain of the signaling lymphocyte activation molecule
(SLAM) family, CD84_like. Ig_SLAM-CD84_like_N: The
N-terminal immunoglobulin (Ig)-like domain of the
signaling lymphocyte activation molecule (SLAM) family,
CD84_like. The SLAM family is a group of immune-cell
specific receptors that can regulate both adaptive and
innate immune responses. Members of this group include
proteins such as CD84, SLAM (CD150), Ly-9 (CD229),
NTB-A (ly-108, SLAM6), 19A (CRACC), and SLAMF9. The
genes coding for the SLAM family are nested on
chromosome 1, in humans at 1q23, and in mice at 1H2.
The SLAM family is a subset of the CD2 family, which
also includes CD2 and CD58 located on chromosome 1 at
1p13 in humans. In mice, CD2 is located on chromosome
3, and there is no CD58 homolog. The SLAM family
proteins are organized as an extracellular domain with
either two or four Ig-like domains, a single
transmembrane segment, and a cytoplasmic region having
Tyr-based motifs. The extracellular domain is organized
as a membrane-distal Ig variable (IgV) domain that is
responsible for ligand recognition and a
membrane-proximal truncated Ig constant-2 (IgC2)
domain.
Length = 97
Score = 26.1 bits (58), Expect = 4.7
Identities = 14/67 (20%), Positives = 24/67 (35%), Gaps = 10/67 (14%)
Query: 12 VSWMRKRDLHILTTNIYTYTGDARFSVIHPQNSDEWN-------MKIDYAQKRDAGIYEC 64
++W L I+T V P + N ++I + DAG Y
Sbjct: 22 ITWSFNTSLAIITP---GEETAPEIIVTDPSYKERVNFSQNDYSLQISNLKMEDAGSYRA 78
Query: 65 QVNTEPK 71
++NT+
Sbjct: 79 EINTKNG 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 = 25.0 bits (55), Expect = 7.9
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 5/28 (17%)
Query: 48 NMKIDYAQKRDAGIYECQVNTEPKMNMA 75
N+ I A+K D G Y+C NM
Sbjct: 52 NLLIAEARKSDEGTYKCVAT-----NMV 74
Score = 25.0 bits (55), Expect = 7.9
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 5/28 (17%)
Query: 128 NMKIDYAQKRDAGIYECQVNTEPKMNMA 155
N+ I A+K D G Y+C NM
Sbjct: 52 NLLIAEARKSDEGTYKCVAT-----NMV 74
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 0.416
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: 8,117,224
Number of extensions: 701701
Number of successful extensions: 444
Number of sequences better than 10.0: 1
Number of HSP's gapped: 444
Number of HSP's successfully gapped: 32
Length of query: 163
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 74
Effective length of database: 6,990,096
Effective search space: 517267104
Effective search space used: 517267104
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: 55 (25.2 bits)