RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10361
(236 letters)
>gnl|CDD|214653 smart00410, IG_like, Immunoglobulin like. IG domains that cannot
be classified into one of IGv1, IGc1, IGc2, IG.
Length = 85
Score = 47.1 bits (112), Expect = 2e-07
Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 10/84 (11%)
Query: 154 GSTINLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLIQKARPS 213
G ++ L+C S PP + W + +S R + + S L I P
Sbjct: 9 GESVTLSC--EASGSPPPEVTWYKQGGKLLAESGR-----FSVSRSGSTSTLTISNVTPE 61
Query: 214 DNGKYQC---NPANSQAKSVMVNV 234
D+G Y C N + S + + V
Sbjct: 62 DSGTYTCAATNSSGSASSGTTLTV 85
Score = 36.7 bits (85), Expect = 0.001
Identities = 16/72 (22%), Positives = 27/72 (37%), Gaps = 3/72 (4%)
Query: 53 CQVSFVRHRDIHLLTTGRYTYTNDQRFRVINNPTSDDWTLQLKYPQHKDTGIYECQVSTT 112
C+ S ++ G RF V + ++ TL + +D+G Y C + +
Sbjct: 16 CEASGSPPPEVTWYKQGGKLLAESGRFSVSRSGST--STLTISNVTPEDSGTYTCAATNS 73
Query: 113 PHQAH-YIYLTV 123
A LTV
Sbjct: 74 SGSASSGTTLTV 85
Score = 29.0 bits (65), Expect = 0.62
Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 2/48 (4%)
Query: 9 IHLLTTGRYTYTNDQRFRVINNPTSDDWTLQLKYPQHKDTGIYECQVS 56
+ G RF V + ++ TL + +D+G Y C +
Sbjct: 26 VTWYKQGGKLLAESGRFSVSRSGST--STLTISNVTPEDSGTYTCAAT 71
>gnl|CDD|214652 smart00409, IG, Immunoglobulin.
Length = 85
Score = 47.1 bits (112), Expect = 2e-07
Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 10/84 (11%)
Query: 154 GSTINLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLIQKARPS 213
G ++ L+C S PP + W + +S R + + S L I P
Sbjct: 9 GESVTLSC--EASGSPPPEVTWYKQGGKLLAESGR-----FSVSRSGSTSTLTISNVTPE 61
Query: 214 DNGKYQC---NPANSQAKSVMVNV 234
D+G Y C N + S + + V
Sbjct: 62 DSGTYTCAATNSSGSASSGTTLTV 85
Score = 36.7 bits (85), Expect = 0.001
Identities = 16/72 (22%), Positives = 27/72 (37%), Gaps = 3/72 (4%)
Query: 53 CQVSFVRHRDIHLLTTGRYTYTNDQRFRVINNPTSDDWTLQLKYPQHKDTGIYECQVSTT 112
C+ S ++ G RF V + ++ TL + +D+G Y C + +
Sbjct: 16 CEASGSPPPEVTWYKQGGKLLAESGRFSVSRSGST--STLTISNVTPEDSGTYTCAATNS 73
Query: 113 PHQAH-YIYLTV 123
A LTV
Sbjct: 74 SGSASSGTTLTV 85
Score = 29.0 bits (65), Expect = 0.62
Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 2/48 (4%)
Query: 9 IHLLTTGRYTYTNDQRFRVINNPTSDDWTLQLKYPQHKDTGIYECQVS 56
+ G RF V + ++ TL + +D+G Y C +
Sbjct: 26 VTWYKQGGKLLAESGRFSVSRSGST--STLTISNVTPEDSGTYTCAAT 71
>gnl|CDD|197706 smart00408, IGc2, Immunoglobulin C-2 Type.
Length = 63
Score = 43.9 bits (104), Expect = 2e-06
Identities = 19/72 (26%), Positives = 26/72 (36%), Gaps = 12/72 (16%)
Query: 154 GSTINLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLIQKARPS 213
G ++ LTC +P P I W + + N G S L I+
Sbjct: 2 GQSVTLTCPAEGNPVPN--ITWLKDGKPLP------ESNRFVASG----STLTIKSVSLE 49
Query: 214 DNGKYQCNPANS 225
D+G Y C NS
Sbjct: 50 DSGLYTCVAENS 61
Score = 27.4 bits (61), Expect = 1.6
Identities = 8/38 (21%), Positives = 15/38 (39%)
Query: 19 YTNDQRFRVINNPTSDDWTLQLKYPQHKDTGIYECQVS 56
+ + N + TL +K +D+G+Y C
Sbjct: 22 LKDGKPLPESNRFVASGSTLTIKSVSLEDSGLYTCVAE 59
Score = 27.4 bits (61), Expect = 1.6
Identities = 8/38 (21%), Positives = 15/38 (39%)
Query: 73 YTNDQRFRVINNPTSDDWTLQLKYPQHKDTGIYECQVS 110
+ + N + TL +K +D+G+Y C
Sbjct: 22 LKDGKPLPESNRFVASGSTLTIKSVSLEDSGLYTCVAE 59
>gnl|CDD|191810 pfam07679, I-set, Immunoglobulin I-set domain.
Length = 90
Score = 40.3 bits (95), Expect = 5e-05
Identities = 25/84 (29%), Positives = 32/84 (38%), Gaps = 11/84 (13%)
Query: 154 GSTINLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLIQKARPS 213
G + TC V P+P + W + + S R V E G T L I +P
Sbjct: 15 GESARFTCTVTGDPDPT--VSWFKDGQPLR-SSDR--FKVTYEGGTYT---LTISNVQPD 66
Query: 214 DNGKYQC---NPANSQAKSVMVNV 234
D GKY C N A S + V
Sbjct: 67 DEGKYTCVATNSAGEAEASAELTV 90
>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 = 39.0 bits (90), Expect = 1e-04
Identities = 21/77 (27%), Positives = 28/77 (36%), Gaps = 7/77 (9%)
Query: 157 INLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLIQKARPSDNG 216
+ LTC S PP I W N + S + + S L I D+G
Sbjct: 1 VTLTC--LASGPPPPTITWLKNGKPLP--SSVLTRVRSSRGTSSGSSTLTISNVTLEDSG 56
Query: 217 KYQC---NPANSQAKSV 230
Y C N A + + SV
Sbjct: 57 TYTCVASNSAGTVSASV 73
Score = 29.0 bits (64), Expect = 0.52
Identities = 10/33 (30%), Positives = 14/33 (42%)
Query: 24 RFRVINNPTSDDWTLQLKYPQHKDTGIYECQVS 56
R R +S TL + +D+G Y C S
Sbjct: 31 RVRSSRGTSSGSSTLTISNVTLEDSGTYTCVAS 63
Score = 29.0 bits (64), Expect = 0.52
Identities = 10/33 (30%), Positives = 14/33 (42%)
Query: 78 RFRVINNPTSDDWTLQLKYPQHKDTGIYECQVS 110
R R +S TL + +D+G Y C S
Sbjct: 31 RVRSSRGTSSGSSTLTISNVTLEDSGTYTCVAS 63
>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 = 37.9 bits (88), Expect = 4e-04
Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 8/73 (10%)
Query: 154 GSTINLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLIQKARPS 213
G T+ TCV P P I W N + DS R V++ +E G T L I+ + S
Sbjct: 1 GETVEFTCVATGVPTP--IINWRLNWGHVP-DSAR--VSITSEGGYGT---LTIRDVKES 52
Query: 214 DNGKYQCNPANSQ 226
D G Y C N++
Sbjct: 53 DQGAYTCEAINTR 65
>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 = 36.3 bits (84), Expect = 0.002
Identities = 29/97 (29%), Positives = 45/97 (46%), Gaps = 12/97 (12%)
Query: 143 IIGG-PEVF-IENGSTINLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGET 200
++GG P+V I G T+NLTC V +P + W N+ ++ NV E+G+
Sbjct: 3 VVGGLPDVVTIMEGKTLNLTCTV--FGDPDPEVSWLKNDQALALSDH---YNVKVEQGKY 57
Query: 201 TVSYLLIQKARPSDNGKYQCNPAN---SQAKSVMVNV 234
+ L I+ D+GKY N + V V+V
Sbjct: 58 --ASLTIKGVSSEDSGKYGIVVKNKYGGETVDVTVSV 92
>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 = 0.003
Identities = 14/83 (16%), Positives = 26/83 (31%), Gaps = 4/83 (4%)
Query: 33 SDDWTLQLKYPQHKDTGIYECQVSFVRHRDIHLLTTGRYTYTNDQRFRVINNPTSDDWTL 92
S Y + G + + R+ R + N + +D++L
Sbjct: 26 SSSSGSTSVYWYKQPLGKGPELIIHYVTSTPNGKVGPRF----KGRVTLSGNGSKNDFSL 81
Query: 93 QLKYPQHKDTGIYECQVSTTPHQ 115
+ + D+G Y C VS
Sbjct: 82 TISNLRLSDSGTYTCAVSNPNEL 104
Score = 36.0 bits (83), Expect = 0.004
Identities = 23/89 (25%), Positives = 31/89 (34%), Gaps = 16/89 (17%)
Query: 147 PEVFIENGSTINLTCVVRFSPEPPAYIFW------NHNEAIISYDSQRGGVNVITE-KGE 199
V + G ++ L C S ++W E II Y + V KG
Sbjct: 9 RPVTVAEGGSVTLPCSFS-SSSGSTSVYWYKQPLGKGPELIIHYVTSTPNGKVGPRFKGR 67
Query: 200 TTVS--------YLLIQKARPSDNGKYQC 220
T+S L I R SD+G Y C
Sbjct: 68 VTLSGNGSKNDFSLTISNLRLSDSGTYTC 96
Score = 33.7 bits (77), Expect = 0.021
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 24 RFRVINNPTSDDWTLQLKYPQHKDTGIYECQVSF 57
R + N + +D++L + + D+G Y C VS
Sbjct: 67 RVTLSGNGSKNDFSLTISNLRLSDSGTYTCAVSN 100
>gnl|CDD|222457 pfam13927, Ig_3, Immunoglobulin domain. This family contains
immunoglobulin-like domains.
Length = 74
Score = 33.9 bits (77), Expect = 0.009
Identities = 19/78 (24%), Positives = 25/78 (32%), Gaps = 11/78 (14%)
Query: 143 IIGGPEVFIENGSTINLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTV 202
I P + +G + LTC P PP W N +I G
Sbjct: 4 ITVSPSPSVTSGGGVTLTCSAEGGPPPPTI-SWYRNGSISGGSGGLGSSG---------- 52
Query: 203 SYLLIQKARPSDNGKYQC 220
S L + D+G Y C
Sbjct: 53 STLTLSSVTSEDSGTYTC 70
>gnl|CDD|143223 cd05746, Ig4_Peroxidasin, Fourth immunoglobulin (Ig)-like domain of
peroxidasin. Ig4_Peroxidasin: the fourth immunoglobulin
(Ig)-like domain in peroxidasin. Peroxidasin has a
peroxidase domain and interacting extracellular motifs
containing four Ig-like domains. It has been suggested
that peroxidasin is secreted, and has functions related
to the stabilization of the extracellular matrix. It may
play a part in various other important processes such as
removal and destruction of cells, which have undergone
programmed cell death, and protection of the organism
against non-self.
Length = 69
Score = 33.3 bits (76), Expect = 0.012
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 17/72 (23%)
Query: 157 INLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVS---YLLIQKARPS 213
+ + C + PEP I WN + GV +TE G+ +S YL I+ +
Sbjct: 1 VQIPCSAQGDPEP--TITWN-----------KDGVQ-VTESGKFHISPEGYLAIRDVGVA 46
Query: 214 DNGKYQCNPANS 225
D G+Y+C N+
Sbjct: 47 DQGRYECVARNT 58
>gnl|CDD|206066 pfam13895, Ig_2, Immunoglobulin domain. This domain contains
immunoglobulin-like domains.
Length = 80
Score = 33.2 bits (76), Expect = 0.016
Identities = 13/73 (17%), Positives = 18/73 (24%), Gaps = 18/73 (24%)
Query: 154 GSTINLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLIQKARPS 213
G + LTC PP W + +S
Sbjct: 14 GEDVTLTC--SAPGNPPPNYTWYKDGVPLSSSQNG----------------FFTPNVSAE 55
Query: 214 DNGKYQCNPANSQ 226
D+G Y C +N
Sbjct: 56 DSGTYTCVASNGG 68
>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 = 33.1 bits (76), Expect = 0.027
Identities = 17/80 (21%), Positives = 24/80 (30%), Gaps = 14/80 (17%)
Query: 154 GSTINLTCVVRFSPEPPAYIFW------NHNEAIISYDSQRGGVNV-------ITEKGET 200
G ++ L+C YIFW E +I S T
Sbjct: 6 GESVTLSCTYS-GSFSSYYIFWYRQKPGKGPELLIYISSNGSQYAGGVKGRFSGTRDSSK 64
Query: 201 TVSYLLIQKARPSDNGKYQC 220
+ L I +P D+ Y C
Sbjct: 65 SSFTLTISSLQPEDSAVYYC 84
Score = 30.4 bits (69), Expect = 0.23
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 7/68 (10%)
Query: 63 IHLLTTGRYTYTNDQ--RFRVINNPTSDDWTLQLKYPQHKDTGIYECQVSTTPHQAHYIY 120
+ +++ Y RF + + +TL + Q +D+ +Y C VS + +
Sbjct: 38 LIYISSNGSQYAGGVKGRFSGTRDSSKSSFTLTISSLQPEDSAVYYCAVSLSGGTYKLYF 97
Query: 121 -----LTV 123
LTV
Sbjct: 98 GQGTRLTV 105
Score = 29.2 bits (66), Expect = 0.72
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 9 IHLLTTGRYTYTNDQ--RFRVINNPTSDDWTLQLKYPQHKDTGIYECQVS 56
+ +++ Y RF + + +TL + Q +D+ +Y C VS
Sbjct: 38 LIYISSNGSQYAGGVKGRFSGTRDSSKSSFTLTISSLQPEDSAVYYCAVS 87
>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 = 32.6 bits (74), Expect = 0.035
Identities = 29/84 (34%), Positives = 42/84 (50%), Gaps = 9/84 (10%)
Query: 143 IIGG-PEVF-IENGSTINLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGET 200
+IGG P+V I G T+NLTC V +P+P + W N+ I +V E+G+
Sbjct: 3 VIGGLPDVVTIMEGKTLNLTCTVFGNPDPE--VIWFKNDQDIELSEH---YSVKLEQGK- 56
Query: 201 TVSYLLIQKARPSDNGKYQCNPAN 224
+ L I+ D+GKY N N
Sbjct: 57 -YASLTIKGVTSEDSGKYSINVKN 79
>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 = 31.7 bits (72), Expect = 0.036
Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 7/67 (10%)
Query: 154 GSTINLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLIQKARPS 213
GS++ LTC V S P + W + + V T++ + L I P
Sbjct: 1 GSSVTLTCSV--SGPPQVDVTWFKEGKGLEESTT-----VGTDENRVSSITLTISNVTPE 53
Query: 214 DNGKYQC 220
D+G Y C
Sbjct: 54 DSGTYTC 60
>gnl|CDD|143184 cd04983, IgV_TCR_alpha_like, Immunoglobulin (Ig) variable (V)
domain of T-cell receptor (TCR) alpha chain and similar
proteins. IgV_TCR_alpha: immunoglobulin (Ig) variable
domain of the alpha chain of alpha/beta T-cell antigen
receptors (TCRs). TCRs mediate antigen recognition by T
lymphocytes, and are composed of alpha and beta, or
gamma and delta, polypeptide chains with variable (V)
and constant (C) regions. This group represents the
variable domain of the alpha chain of TCRs and also
includes the variable domain of delta chains of TCRs.
Alpha/beta TCRs recognize antigen as peptide fragments
presented by major histocompatibility complex (MHC)
molecules. The variable domain of TCRs is responsible
for antigen recognition, and is located at the
N-terminus of the receptor. Gamma/delta TCRs recognize
intact protein antigens; they recognize proteins
antigens directly and without antigen processing, and
MHC independently of the bound peptide.
Length = 109
Score = 32.2 bits (74), Expect = 0.057
Identities = 19/85 (22%), Positives = 33/85 (38%), Gaps = 14/85 (16%)
Query: 147 PEVFIENGSTINLTCVVRFSPEPPAYIFW---NHNEA---IISYDS-----QRGGVNVIT 195
+ ++ G + L C +S Y+FW + +I S ++G +
Sbjct: 6 QSLSVQEGENVTLNC--NYSTSTFYYLFWYRQYPGQGPQFLIYISSNGEEKEKGRFSATL 63
Query: 196 EKGETTVSYLLIQKARPSDNGKYQC 220
+K S L I A+ SD+ Y C
Sbjct: 64 DK-SRKSSSLHISAAQLSDSAVYFC 87
>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 = 31.3 bits (71), Expect = 0.082
Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 12/71 (16%)
Query: 150 FIENGSTINLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLIQK 209
+ G+ L C A + W + +++ +S + ++ G LLI
Sbjct: 7 TFKLGNNAELKCS---PKSNLARVVWKFDGKVLTPESAKY---LLYRDG------LLIFN 54
Query: 210 ARPSDNGKYQC 220
A +D G+YQC
Sbjct: 55 ASEADAGRYQC 65
>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 = 31.2 bits (71), Expect = 0.084
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 205 LLIQKARPSDNGKYQCNPANS 225
LLI +AR SD G Y+C N
Sbjct: 53 LLIAEARKSDEGTYKCVATNM 73
>gnl|CDD|143194 cd05717, Ig1_Necl-1-3_like, First (N-terminal) immunoglobulin
(Ig)-like domain of the nectin-like molecules Necl-1 -
Necl-3 (also known as cell adhesion molecules CADM3,
CADM1, and CADM2 respectively). Ig1_Necl-1-3_like:
N-terminal immunoglobulin (Ig)-like domain of the
nectin-like molecules Necl-1 (also known as cell
adhesion molecule 3 (CADM3)), Necl-2 (CADM1), and Necl-3
(CADM2). At least five nectin-like molecules have been
identified (Necl-1 - Necl-5). They all have an
extracellular region containing three Ig-like domains, a
transmembrane region, and a cytoplasmic region. The
N-terminal Ig-like domain of the extracellular region
belongs to the V-type subfamily of Ig domains, is
essential to cell-cell adhesion, and plays a part in the
interaction with the envelope glycoprotein D of various
viruses. Necl-1, Necl-2, and Necl-3 have
Ca(2+)-independent homophilic and heterophilic cell-cell
adhesion activity. Necl-1 is specifically expressed in
neural tissue, and is important to the formation of
synapses, axon bundles, and myelinated axons. Necl-2 is
expressed in a wide variety of tissues, and is a
putative tumour suppressor gene, which is downregulated
in aggressive neuroblastoma. Necl-3 accumulates in
central and peripheral nervous system tissue, and has
been shown to selectively interact with
oligodendrocytes. This group also contains Class-I
MHC-restricted T-cell-associated molecule (CRTAM), whose
expression pattern is consistent with its expression in
Class-I MHC-restricted T-cells.
Length = 95
Score = 31.2 bits (71), Expect = 0.12
Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 8/84 (9%)
Query: 47 DTGIYECQVSFVRHRDIHLLTTGRYT-YTN------DQRFRVINNPTSDDWTLQLKYPQH 99
T +C+V + + + T Y N D R +++N ++++ ++ +
Sbjct: 13 GTATLKCRVKNNDNSSLQWSNPNQQTLYFNDKRALRDNRIQLVNF-SANELSISISNVSL 71
Query: 100 KDTGIYECQVSTTPHQAHYIYLTV 123
D G Y C + T P Q +TV
Sbjct: 72 SDEGRYTCSLYTMPVQTAKATVTV 95
>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 = 30.8 bits (70), Expect = 0.14
Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 9/73 (12%)
Query: 148 EVFIENGSTINLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLI 207
V + G+++ L C + S A + W + + ++TE G LLI
Sbjct: 5 VVTVVEGNSVFLECSPK-SNL--ASVVWLFQGGPLQRKEEPEERLLVTEDG------LLI 55
Query: 208 QKARPSDNGKYQC 220
+ P+D G Y C
Sbjct: 56 RSVSPADAGVYTC 68
>gnl|CDD|143289 cd05881, Ig1_Necl-2, First (N-terminal) immunoglobulin (Ig)-like
domain of nectin-like molecule 2 (also known as cell
adhesion molecule 1 (CADM1)). Ig1_Necl-2: domain
similar to the N-terminal immunoglobulin (Ig)-like
domain of nectin-like molecule-2, Necl-2 (also known as
cell adhesion molecule 1 (CADM1), SynCAM1, IGSF4A,
Tslc1, sgIGSF, and RA175). Nectin-like molecules have
similar domain structures to those of nectins. At least
five nectin-like molecules have been identified (Necl-1
- Necl-5). They all have an extracellular region
containing three Ig-like domains, a transmembrane
region, and a cytoplasmic region. The N-terminal Ig-like
domain of the extracellular region, belongs to the
V-type subfamily of Ig domains, is essential to
cell-cell adhesion, and plays a part in the interaction
with the envelope glycoprotein D of various viruses.
Necl-2 has Ca(2+)-independent homophilic and
heterophilic cell-cell adhesion activity. Necl-2 is
expressed in a wide variety of tissues, and is a
putative tumour suppressor gene, which is downregulated
in aggressive neuroblastoma.
Length = 95
Score = 30.8 bits (69), Expect = 0.15
Identities = 25/84 (29%), Positives = 36/84 (42%), Gaps = 8/84 (9%)
Query: 47 DTGIYECQVSFVRHRDIHLLTTGRYTY-------TNDQRFRVINNPTSDDWTLQLKYPQH 99
+ I C+V I LL R T D RF+++N +S++ + L
Sbjct: 13 EVAIISCRVKNNDDSVIQLLNPNRQTIYFRDVRPLKDSRFQLVNF-SSNELRVSLSNVSL 71
Query: 100 KDTGIYECQVSTTPHQAHYIYLTV 123
D G Y CQ+ T P Q Y +TV
Sbjct: 72 SDEGRYFCQLYTDPPQEAYTTITV 95
>gnl|CDD|143166 cd00098, IgC, Immunoglobulin Constant domain. IgC: Immunoglobulin
constant domain (IgC). Members of the IgC family are
components of immunoglobulin, T-cell receptors, CD1 cell
surface glycoproteins, secretory glycoproteins A/C, and
Major Histocompatibility Complex (MHC) class I/II
molecules. In immunoglobulins, each chain is composed of
one variable domain (IgV) and one or more IgC domains.
These names reflect the fact that the variability in
sequences is higher in the variable domain than in the
constant domain. The IgV domain is responsible for
antigen binding, and the IgC domain is involved in
oligomerization and molecular interactions.
Length = 95
Score = 30.9 bits (70), Expect = 0.17
Identities = 13/70 (18%), Positives = 25/70 (35%), Gaps = 2/70 (2%)
Query: 152 ENGSTINLTCVV-RFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLIQKA 210
G ++ LTC+ F P P + W N ++ ++ + S L + +
Sbjct: 11 LLGGSVTLTCLATGFYP-PDITVTWLKNGKELTSGVTTTPPVPNSDGTYSVSSQLTVSPS 69
Query: 211 RPSDNGKYQC 220
+ Y C
Sbjct: 70 DWNSGDTYTC 79
>gnl|CDD|143242 cd05765, Ig_3, Subgroup of the immunoglobulin (Ig) superfamily.
Ig_3: subgroup of the 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
the Ig superfamily 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 = 81
Score = 29.8 bits (67), Expect = 0.31
Identities = 24/77 (31%), Positives = 31/77 (40%), Gaps = 13/77 (16%)
Query: 154 GSTINLTCVVRFSPEPPAYIFWNHN-----EAIISYDSQRGGVNVITEKGETTVSYLLIQ 208
G T + C V + PP I W I+ + RG V V T + L+I
Sbjct: 1 GETASFHCDV--TGRPPPEITWEKQVHGKENLIMRPNHVRGNVVV------TNIGQLVIY 52
Query: 209 KARPSDNGKYQCNPANS 225
A+P D G Y C NS
Sbjct: 53 NAQPQDAGLYTCTARNS 69
>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 = 30.0 bits (68), Expect = 0.31
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 73 YTNDQRFRV-INNPTSDDWTLQLKYPQHKDTGIYECQVSTTP 113
RV N + +D T+ + + +D G Y C+ +T P
Sbjct: 44 IPPSYEGRVSFLNSSLEDATISISNLRLEDEGNYICEFATFP 85
>gnl|CDD|214650 smart00406, IGv, Immunoglobulin V-Type.
Length = 81
Score = 29.7 bits (67), Expect = 0.34
Identities = 18/79 (22%), Positives = 25/79 (31%), Gaps = 14/79 (17%)
Query: 156 TINLTCVVRFSPEPPAYIFW------NHNEAIISYDSQRGGVNVITEKGETTVS------ 203
++ L+C S Y+ W E + S + KG T+S
Sbjct: 1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSNGSSYYQESYKGRFTISKDTSKN 60
Query: 204 --YLLIQKARPSDNGKYQC 220
L I R D G Y C
Sbjct: 61 DVSLTISNLRVEDTGTYYC 79
Score = 27.7 bits (62), Expect = 1.4
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 24 RFRVINNPTSDDWTLQLKYPQHKDTGIYECQV 55
RF + + + +D +L + + +DTG Y C V
Sbjct: 50 RFTISKDTSKNDVSLTISNLRVEDTGTYYCAV 81
Score = 27.7 bits (62), Expect = 1.4
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 78 RFRVINNPTSDDWTLQLKYPQHKDTGIYECQV 109
RF + + + +D +L + + +DTG Y C V
Sbjct: 50 RFTISKDTSKNDVSLTISNLRVEDTGTYYCAV 81
>gnl|CDD|143303 cd05895, Ig_Pro_neuregulin-1, Immunoglobulin (Ig)-like domain found
in neuregulin (NRG)-1. Ig_Pro_neuregulin-1:
immunoglobulin (Ig)-like domain found in neuregulin
(NRG)-1. There are many NRG-1 isoforms which arise from
the alternative splicing of mRNA. NRG-1 belongs to the
neuregulin gene family, which is comprised of four
genes. This group represents NRG-1. NRGs are signaling
molecules, which participate in cell-cell interactions
in the nervous system, breast, and heart, and other
organ systems, and are implicated in the pathology of
diseases including schizophrenia, multiple sclerosis,
and breast cancer. The NRG-1 protein binds to and
activates the tyrosine kinases receptors ErbB3 and
ErbB4, initiating signaling cascades. 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.
Length = 76
Score = 29.2 bits (65), Expect = 0.37
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 192 NVITEKGETTVSYLLIQKARPSDNGKYQCNPANSQAK-SVMVNV 234
N I + + S L I KA +DNG+Y+C ++ SV NV
Sbjct: 33 NKIKIRKKKKSSELQISKASLADNGEYKCMVSSKLGNDSVTANV 76
>gnl|CDD|143235 cd05758, Ig5_KIRREL3-like, Fifth immunoglobulin (Ig)-like domain of
Kirrel (kin of irregular chiasm-like) 3 (also known as
Neph2) and similar proteins. Ig5_KIRREL3-like: domain
similar to the fifth immunoglobulin (Ig)-like domain of
Kirrel (kin of irregular chiasm-like) 3 (also known as
Neph2). This protein has five Ig-like domains, one
transmembrane domain, and a cytoplasmic tail. Included
in this group is mammalian Kirrel (Neph1), Kirrel2
(Neph3), and Drosophila RST (irregular chiasm
C-roughest) protein. These proteins contain multiple Ig
domains, have properties of cell adhesion molecules, and
are important in organ development.
Length = 98
Score = 29.7 bits (67), Expect = 0.38
Identities = 21/74 (28%), Positives = 27/74 (36%), Gaps = 4/74 (5%)
Query: 154 GSTINLTCVVRFSPEPPAYIFWNHNEAII-SYDSQRGGVNVITEKGETTVSYLLIQKARP 212
G + C + +P PP I W E + S S R V +S L I +
Sbjct: 16 GDKGRVECFIFSTP-PPDRIVWTWKENELESGSSGRYTVETDP-SPGGVLSTLTISNTQE 73
Query: 213 SD-NGKYQCNPANS 225
SD Y C NS
Sbjct: 74 SDFQTSYNCTAWNS 87
>gnl|CDD|143236 cd05759, Ig2_KIRREL3-like, Second immunoglobulin (Ig)-like domain
of Kirrel (kin of irregular chiasm-like) 3 (also known
as Neph2). Ig2_KIRREL3-like: domain similar to the
second immunoglobulin (Ig)-like domain of Kirrel (kin of
irregular chiasm-like) 3 (also known as Neph2). This
protein has five Ig-like domains, one transmembrane
domain, and a cytoplasmic tail. Included in this group
is mammalian Kirrel (Neph1), Kirrel2 (Neph3), and
Drosophila RST (irregular chiasm C-roughest) protein.
These proteins contain multiple Ig domains, have
properties of cell adhesion molecules, and are important
in organ development.
Length = 82
Score = 29.3 bits (66), Expect = 0.39
Identities = 30/90 (33%), Positives = 39/90 (43%), Gaps = 23/90 (25%)
Query: 158 NLTCVVRFSPEPPAYIFWNH-----NEAIISYDSQRGGVNVITEKGETTVSYLLIQKARP 212
NLTC R +P A I W + A S + + G K ETTVS L I P
Sbjct: 3 NLTCRAR-GAKPAAEIIWFRDGEVLDGATYSKELLKDG------KRETTVSTLPIT---P 52
Query: 213 S--DNGK-YQC---NPA--NSQAKSVMVNV 234
S D G+ + C N A + SV ++V
Sbjct: 53 SDHDTGRTFTCRARNEALPTGKETSVTLDV 82
>gnl|CDD|143264 cd05856, Ig2_FGFRL1-like, Second immunoglobulin (Ig)-like domain
of fibroblast growth factor (FGF)
receptor_like-1(FGFRL1). Ig2_FGFRL1-like: second
immunoglobulin (Ig)-like domain of fibroblast growth
factor (FGF) receptor_like-1(FGFRL1). FGFRL1 is
comprised of a signal peptide, three extracellular
Ig-like modules, a transmembrane segment, and a short
intracellular domain. FGFRL1 is expressed
preferentially in skeletal tissues. Similar to FGF
receptors, the expressed protein interacts specifically
with heparin and with FGF2. FGFRL1 does not have a
protein tyrosine kinase domain at its C terminus;
neither does its cytoplasmic domain appear to interact
with a signaling partner. It has been suggested that
FGFRL1 may not have any direct signaling function, but
instead acts as a decoy receptor trapping FGFs and
preventing them from binding other receptors.
Length = 82
Score = 29.4 bits (66), Expect = 0.41
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 18 TYTNDQRFRVINNPTSD---DWTLQLKYPQHKDTGIYECQVS 56
T+ D + WTL LK + +D+G Y C VS
Sbjct: 27 TWLKDNKPLTPTEIGESRKKKWTLSLKNLKPEDSGKYTCHVS 68
Score = 29.4 bits (66), Expect = 0.41
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 72 TYTNDQRFRVINNPTSD---DWTLQLKYPQHKDTGIYECQVS 110
T+ D + WTL LK + +D+G Y C VS
Sbjct: 27 TWLKDNKPLTPTEIGESRKKKWTLSLKNLKPEDSGKYTCHVS 68
Score = 25.9 bits (57), Expect = 6.3
Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 10/71 (14%)
Query: 154 GSTINLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLIQKARPS 213
GS++ L CV +P P + N+ + + K + T+S ++ +P
Sbjct: 9 GSSVRLKCVASGNPRP-DITWLKDNKPLTPTEIGES------RKKKWTLS---LKNLKPE 58
Query: 214 DNGKYQCNPAN 224
D+GKY C+ +N
Sbjct: 59 DSGKYTCHVSN 69
>gnl|CDD|143206 cd05729, Ig2_FGFR_like, Second immunoglobulin (Ig)-like domain of
fibroblast growth factor (FGF) receptor and similar
proteins. Ig2_FGFR_like: domain similar to the second
immunoglobulin (Ig)-like domain of fibroblast growth
factor (FGF) receptor. FGF receptors bind FGF signaling
polypeptides. FGFs participate in multiple processes
such as morphogenesis, development, and angiogenesis.
FGFs bind to four FGF receptor tyrosine kinases (FGFR1,
-2, -3, -4). Receptor diversity is controlled by
alternative splicing producing splice variants with
different ligand binding characteristics and different
expression patterns. FGFRs have an extracellular region
comprised of three Ig-like domains, a single
transmembrane helix, and an intracellular tyrosine
kinase domain. Ligand binding and specificity reside in
the Ig-like domains 2 and 3, and the linker region that
connects these two. FGFR activation and signaling depend
on FGF-induced dimerization, a process involving cell
surface heparin or heparin sulfate proteoglycans. This
group also contains fibroblast growth factor (FGF)
receptor_like-1(FGFRL1). FGFRL1 does not have a protein
tyrosine kinase domain at its C terminus; neither does
its cytoplasmic domain appear to interact with a
signaling partner. It has been suggested that FGFRL1 may
not have any direct signaling function, but instead acts
as a decoy receptor trapping FGFs and preventing them
from binding other receptors.
Length = 85
Score = 29.3 bits (66), Expect = 0.47
Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 7/67 (10%)
Query: 154 GSTINLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLIQKARPS 213
GST+ L C +P P + + G +K T L+++ PS
Sbjct: 9 GSTVRLKCPASGNP-RPTITWLKDGKPFKKEHRIGGYKV--RKKKWT----LILESVVPS 61
Query: 214 DNGKYQC 220
D+GKY C
Sbjct: 62 DSGKYTC 68
Score = 25.8 bits (57), Expect = 6.9
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 36 WTLQLKYPQHKDTGIYECQVS 56
WTL L+ D+G Y C V
Sbjct: 51 WTLILESVVPSDSGKYTCIVE 71
Score = 25.8 bits (57), Expect = 6.9
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 90 WTLQLKYPQHKDTGIYECQVS 110
WTL L+ D+G Y C V
Sbjct: 51 WTLILESVVPSDSGKYTCIVE 71
>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 = 29.5 bits (67), Expect = 0.50
Identities = 8/16 (50%), Positives = 8/16 (50%)
Query: 205 LLIQKARPSDNGKYQC 220
L I R SD G Y C
Sbjct: 67 LRIHNVRASDEGLYTC 82
>gnl|CDD|143273 cd05865, Ig1_NCAM-1, First immunoglobulin (Ig)-like domain of
neural cell adhesion molecule NCAM-1. Ig1_NCAM-1: 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.
Length = 96
Score = 29.2 bits (65), Expect = 0.52
Identities = 22/63 (34%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 53 CQVSF-VRHRDIHLLT-TGRYTYTNDQRFRVINNPTSDDW--TLQLKYPQHKDTGIYECQ 108
CQV+ + +DI + G N QR V+ N DD+ TL + D GIY+C
Sbjct: 22 CQVAGEAKDKDISWFSPNGEKLTPNQQRISVVRN---DDYSSTLTIYNANIDDAGIYKCV 78
Query: 109 VST 111
VS
Sbjct: 79 VSN 81
Score = 26.9 bits (59), Expect = 4.3
Identities = 17/45 (37%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 14 TGRYTYTNDQRFRVINNPTSDDW--TLQLKYPQHKDTGIYECQVS 56
G N QR V+ N DD+ TL + D GIY+C VS
Sbjct: 39 NGEKLTPNQQRISVVRN---DDYSSTLTIYNANIDDAGIYKCVVS 80
>gnl|CDD|143221 cd05744, Ig_Myotilin_C_like, Immunoglobulin (Ig)-like domain of
myotilin, palladin, and myopalladin.
Ig_Myotilin_like_C: immunoglobulin (Ig)-like domain in
myotilin, palladin, and myopalladin. Myotilin,
palladin, and myopalladin function as scaffolds that
regulate actin organization. Myotilin and myopalladin
are most abundant in skeletal and cardiac muscle;
palladin is ubiquitously expressed in the organs of
developing vertebrates and plays a key role in cellular
morphogenesis. The three family members each interact
with specific molecular partners: all three bind to
alpha-actinin; in addition, palladin also binds to
vasodilator-stimulated phosphoprotein (VASP) and ezrin,
myotilin binds to filamin and actin, and myopalladin
also binds to nebulin and cardiac ankyrin repeat protein
(CARP).
Length = 75
Score = 28.6 bits (64), Expect = 0.68
Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 6/68 (8%)
Query: 157 INLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLIQKARPSDNG 216
+ L C R S PP IFW N +++Y++ R + + LLIQ A D G
Sbjct: 1 VRLEC--RVSAIPPPQIFWKKNNEMLTYNTDR----ISLYQDNCGRICLLIQNANKEDAG 54
Query: 217 KYQCNPAN 224
Y + N
Sbjct: 55 WYTVSAVN 62
>gnl|CDD|143324 cd07700, IgV_CD8_beta, Immunoglobulin (Ig) like domain of CD8 beta
chain. IgV_CD8_beta: immunoglobulin (Ig)-like domain in
CD8 beta. The CD8 glycoprotein plays an essential role
in the control of T-cell selection, maturation and the
T-cell receptor (TCR)-mediated response to peptide
antigen. CD8 is comprised of alpha and beta subunits and
is expressed as either an alpha/alpha or alpha/beta
dimer. Both dimeric isoforms can serve as a coreceptor
for T cell activation and differentiation, however they
have distinct physiological roles, different cellular
distributions, unique binding partners etc. Each CD8
subunit is comprised of an extracellular domain
containing a V-type Ig-like domain, a single pass
transmembrane portion and a short intracellular domain.
Length = 107
Score = 28.7 bits (64), Expect = 1.2
Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 19/90 (21%)
Query: 149 VFIENGSTINLTCVVRFSPEPPAYIFW---------NHNEAIISYDSQRG---GVNVITE 196
+ ++ +T+ L+C + E I+W +H E + + G G V E
Sbjct: 1 ILVQTNNTVKLSCEAKGISENTR-IYWLRWRQAPKDSHFEFLALWSPLGGATYGEEVSQE 59
Query: 197 KGETTV-----SYLL-IQKARPSDNGKYQC 220
K V Y L I + +P D+G Y C
Sbjct: 60 KFSIRVTSDSSRYRLHINRVKPEDSGTYFC 89
>gnl|CDD|143212 cd05735, Ig8_DSCAM, Eight immunoglobulin (Ig) domain of Down
Syndrome Cell Adhesion molecule (DSCAM). Ig8_DSCAM:
the eight immunoglobulin (Ig) domain of Down Syndrome
Cell Adhesion molecule (DSCAM). DSCAM is a cell adhesion
molecule expressed largely in the developing nervous
system. The gene encoding DSCAM is located at human
chromosome 21q22, the locus associated with the mental
retardation phenotype of Down Syndrome. DSCAM is
predicted to be the largest member of the IG
superfamily. It has been demonstrated that DSCAM can
mediate cation-independent homophilic intercellular
adhesion.
Length = 88
Score = 28.1 bits (62), Expect = 1.3
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 168 EPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLIQKARPSDNGKYQCNPANS 225
E P + W + II+ + R V+ E G+ +S L I D+G + C+ NS
Sbjct: 13 EKPIIVRWEKEDRIINPEMSRYLVST-KEVGDEVISTLQILPTVREDSGFFSCHAINS 69
>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 = 27.8 bits (62), Expect = 1.5
Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 10/57 (17%)
Query: 24 RFRVINNPTSDDWTLQ-----LKYP--QHKDTGIYECQVSFVRHRDIHLLTTGRYTY 73
++R ++ + LK P Q +D G YEC+ ++ +D H GR
Sbjct: 34 KWRKVDGSMPSSAEISMSGAVLKIPNIQFEDEGTYECEAENIKGKDTH---QGRIYV 87
>gnl|CDD|239523 cd03431, DNA_Glycosylase_C, DNA glycosylase (MutY in bacteria and
hMYH in humans) is responsible for repairing misread
A*oxoG residues to C*G by removing the inappropriately
paired adenine base from the DNA backbone. It belongs to
the Nudix hydrolase superfamily and is important for the
repair of various genotoxic lesions. Enzymes belonging
to this superfamily requires a divalent cation, such as
Mg2+ or Mn2+ for their activity. They are also
recognized by a highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V). However, DNA
glycosylase does not seem to contain this signature
motif. DNA glycosylase consists of 2 domains: the
N-terminal domain contains the catalytic properties of
the enzyme and the C-terminal domain affects substrate
(oxoG) binding and enzymatic turnover. The C-terminal
domain is highly similar to MutT, based on secondary
structure and topology, despite low sequence identity.
MutT sanitizes the nucleotide precursor pool by
hydrolyzing oxo-dGTP to oxo-dGMO and inorganic
pyrophosphate. The similarity strongly suggests that the
two proteins share a common evolutionary origin.
Length = 118
Score = 28.5 bits (64), Expect = 1.5
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 122 TVVVLVINDGKYLLVPEPETDIIGG 146
VV++ NDG+ LL PE ++ G
Sbjct: 5 IAVVVIRNDGRVLLEKRPEKGLLAG 29
>gnl|CDD|143301 cd05893, Ig_Palladin_C, C-terminal immunoglobulin (Ig)-like domain
of palladin. Ig_Palladin_C: C-terminal immunoglobulin
(Ig)-like domain of palladin. Palladin belongs to the
palladin-myotilin-myopalladin family. Proteins belonging
to this family contain multiple Ig-like domains and
function as scaffolds, modulating actin cytoskeleton.
Palladin binds to alpha-actinin ezrin,
vasodilator-stimulated phosphoprotein VASP, SPIN90 (DIP,
mDia interacting protein), and Src. Palladin also binds
F-actin directly, via its Ig3 domain. Palladin is
expressed as several alternatively spliced isoforms,
having various combinations of Ig-like domains, in a
cell-type-specific manner. It has been suggested that
palladin's different Ig-like domains may be specialized
for distinct functions.
Length = 75
Score = 27.7 bits (61), Expect = 1.6
Identities = 19/68 (27%), Positives = 27/68 (39%), Gaps = 6/68 (8%)
Query: 157 INLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLIQKARPSDNG 216
+ L C R S P IFW +++++ R V + LLIQ A D G
Sbjct: 1 VRLEC--RVSGVPHPQIFWKKENESLTHNTDR----VSMHQDNCGYICLLIQGATKEDAG 54
Query: 217 KYQCNPAN 224
Y + N
Sbjct: 55 WYTVSAKN 62
>gnl|CDD|143248 cd05771, IgC_Tapasin_R, Tapasin-R immunoglobulin-like domain.
IgC_Tapasin_R: Immunoglobulin-like domain on Tapasin-R.
Tapasin is a V-C1 (variable-constant) immunoglobulin
superfamily molecule present in the endoplasmic
reticulum (ER), where it links MHC class I molecules to
the transporter associated with antigen processing
(TAP). Tapasin-R is a tapasin-related protein that
contains similar structural motifs to Tapasin, with some
marked differences, especially in the V domain,
transmembrane and cytoplasmic regions. The majority of
Tapasin-R is located within the ER; however, there may
be some expression of Tapasin-R at the cell surface.
Tapasin-R lacks an obvious ER retention signal.
Length = 139
Score = 28.3 bits (63), Expect = 2.2
Identities = 14/24 (58%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 101 DTGIYECQVSTTPHQA-HYIYLTV 123
D G Y C VST PHQA I L+V
Sbjct: 12 DEGTYICSVSTPPHQAQQIIQLSV 35
>gnl|CDD|183245 PRK11630, PRK11630, hypothetical protein; Provisional.
Length = 206
Score = 28.3 bits (63), Expect = 3.2
Identities = 12/35 (34%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 7 RDIHLLTTGRYTYTNDQRFRVINNPTSDDWTLQLK 41
RD+ L+T Y++ ++ FR++ N T ++T LK
Sbjct: 70 RDLSELST--YSFVDNVAFRLMKNNTPGNYTFILK 102
Score = 28.3 bits (63), Expect = 3.2
Identities = 12/35 (34%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 61 RDIHLLTTGRYTYTNDQRFRVINNPTSDDWTLQLK 95
RD+ L+T Y++ ++ FR++ N T ++T LK
Sbjct: 70 RDLSELST--YSFVDNVAFRLMKNNTPGNYTFILK 102
>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 = 27.2 bits (60), Expect = 3.4
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 23 QRFRVINNPT-SDDWTLQLKYPQHKDTGIYECQV 55
R + N P D TL++ + D+G Y C+V
Sbjct: 60 DRVSLPNYPAIPSDATLEITELRSNDSGTYRCEV 93
Score = 27.2 bits (60), Expect = 3.4
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 77 QRFRVINNPT-SDDWTLQLKYPQHKDTGIYECQV 109
R + N P D TL++ + D+G Y C+V
Sbjct: 60 DRVSLPNYPAIPSDATLEITELRSNDSGTYRCEV 93
>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 = 27.1 bits (60), Expect = 3.6
Identities = 21/84 (25%), Positives = 33/84 (39%), Gaps = 12/84 (14%)
Query: 149 VFIEN-----GSTINLTCVVRFSPEPPAYIFWNHNEAIISYDSQR--GGVNVITEKGETT 201
++EN I LTC +P I W S + G + V +G
Sbjct: 6 TYLENQTAVELEQITLTC--EAEGDPIPEITWRRATRNFSEGDKSLDGRIVV---RGHAR 60
Query: 202 VSYLLIQKARPSDNGKYQCNPANS 225
VS L ++ + +D G+Y C +N
Sbjct: 61 VSSLTLKDVQLTDAGRYDCEASNR 84
>gnl|CDD|143300 cd05892, Ig_Myotilin_C, C-terminal immunoglobulin (Ig)-like domain
of myotilin. Ig_Myotilin_C: C-terminal immunoglobulin
(Ig)-like domain of myotilin. Mytolin belongs to the
palladin-myotilin-myopalladin family. Proteins belonging
to the latter family contain multiple Ig-like domains
and function as scaffolds, modulating actin
cytoskeleton. Myotilin is most abundant in skeletal and
cardiac muscle, and is involved in maintaining sarcomere
integrity. It binds to alpha-actinin, filamin and actin.
Mutations in myotilin lead to muscle disorders.
Length = 75
Score = 26.5 bits (58), Expect = 3.9
Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 6/68 (8%)
Query: 157 INLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVSYLLIQKARPSDNG 216
+ L C + S PP IFW N ++ Y++ R + + + LLI+ D G
Sbjct: 1 VKLECQI--SAIPPPKIFWKRNNEMVQYNTDR----ISLYQDNSGRVTLLIKNVNKKDAG 54
Query: 217 KYQCNPAN 224
Y + N
Sbjct: 55 WYTVSAVN 62
>gnl|CDD|143295 cd05887, Ig1_Nectin-3_like, First immunoglobulin (Ig) domain of
nectin-3 (also known as poliovirus receptor related
protein 3) and similar proteins. Ig1_Nectin-3_like:
domain similar to the first immunoglobulin (Ig) domain
of nectin-3 (also known as poliovirus receptor related
protein 3). Nectin-3 belongs to the nectin family
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, during spermatid development, the
nectin-3,-2 trans-interaction is required for the
formation of Sertoli cell-spermatid junctions in testis,
and during morphogenesis of the ciliary body, the
nectin-3,-1 trans-interaction is important for apex-apex
adhesion between the pigment and non-pigment layers of
the ciliary epithelia. Nectins also heterophilically
trans-interact with other CAMs such as nectin-like
molecules (Necls); nectin-3 for example, trans-interacts
with Necl-5, regulating cell movement and proliferation.
Other proteins with which nectin-3 interacts include the
actin filament-binding protein, afadin, integrin
alpha-beta3, Par-3, and PDGF receptor; its interaction
with PDGF receptor regulates the latter's signaling for
anti-apoptosis.
Length = 96
Score = 26.8 bits (59), Expect = 3.9
Identities = 15/50 (30%), Positives = 20/50 (40%)
Query: 77 QRFRVINNPTSDDWTLQLKYPQHKDTGIYECQVSTTPHQAHYIYLTVVVL 126
Q N + D T+ L+ D G+Y C+ T P TV VL
Sbjct: 47 QGRVSFKNYSLLDATIMLENVGFSDIGVYICKAVTFPLGNTQSSTTVTVL 96
>gnl|CDD|199849 cd03867, M14_CPZ, Peptidase M14 carboxypeptidase subfamily
N/E-like; Carboxypeptidase Z subgroup. Peptidase
M14-like domain of carboxypeptidase (CP) Z (CPZ), CPZ
belongs to the N/E subfamily of the M14 family of
metallocarboxypeptidases (MCPs). The M14 family are
zinc-binding CPs which hydrolyze single, C-terminal
amino acids from polypeptide chains, and have a
recognition site for the free C-terminal carboxyl group,
which is a key determinant of specificity. CPZ is a
secreted Zn-dependent enzyme whose biological function
is largely unknown. Unlike other members of the N/E
subfamily, CPZ has a bipartite structure, which consists
of an N-terminal cysteine-rich domain (CRD) whose
sequence is similar to Wnt-binding proteins, and a
C-terminal CP catalytic domain that removes C-terminal
Arg residues from substrates. CPZ is enriched in the
extracellular matrix and is widely distributed during
early embryogenesis. That the CRD of CPZ can bind to
Wnt4 suggests that CPZ plays a role in Wnt signaling.
Length = 315
Score = 28.3 bits (63), Expect = 4.1
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 156 TINLTCVVRFSPEPPAYIFWNHN-EAIISY 184
T+ L C +F PE Y+ W N EA++S+
Sbjct: 284 TVELGCD-KFPPEEELYLIWQENKEALLSF 312
>gnl|CDD|143259 cd05851, Ig3_Contactin-1, Third Ig domain of contactin-1.
Ig3_Contactin-1: Third 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 = 88
Score = 26.5 bits (58), Expect = 4.8
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 44 QHKDTGIYECQVSFVRHRDIH 64
Q +D G YEC+ ++ +D H
Sbjct: 61 QPEDEGTYECEAENIKGKDKH 81
>gnl|CDD|143174 cd04973, Ig1_FGFR, First immunoglobulin (Ig)-like domain of
fibroblast growth factor receptor (FGFR). Ig1_FGFR: The
first immunoglobulin (Ig)-like domain of fibroblast
growth factor receptor (FGFR). 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 all FGFs.
Length = 79
Score = 26.4 bits (58), Expect = 5.0
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 204 YLLIQKARPSDNGKYQC---NPANSQAKSVMVNV 234
+ I+ A P D+G Y C +P+ S VNV
Sbjct: 46 EVQIKDAVPRDSGLYACVTSSPSGSDTTYFSVNV 79
>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 = 26.5 bits (58), Expect = 5.1
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 9/82 (10%)
Query: 150 FIENGST------INLTCVVRFSPEPPAYIFWNHNEAIISYDSQRGGVNVITEKGETTVS 203
++EN + I LTC P P I W + IS + + +++ + VS
Sbjct: 7 YVENQTAMELEEQITLTCEASGDPIPS--ITWRTSTRNISSEEKTLDGHIVV-RSHARVS 63
Query: 204 YLLIQKARPSDNGKYQCNPANS 225
L ++ + +D G+Y C +N+
Sbjct: 64 SLTLKYIQYTDAGEYLCTASNT 85
>gnl|CDD|239647 cd03675, Nudix_Hydrolase_2, Contains a crystal structure of the
Nudix hydrolase from Nitrosomonas europaea, which has an
unknown function. In general, members of the Nudix
hydrolase superfamily catalyze the hydrolysis of
NUcleoside DIphosphates linked to other moieties, X.
Enzymes belonging to this superfamily require a divalent
cation, such as Mg2+ or Mn2+, for their activity. They
also contain a highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which forms a
structural motif that functions as a metal binding and
catalytic site. Substrates of nudix hydrolases include
intact and oxidatively damaged nucleoside triphosphates,
dinucleoside polyphosphates, nucleotide-sugars and
dinucleotide enzymes. These substrates are metabolites
or cell signaling molecules that require regulation
during different stages of the cell cycle or during
periods of stress. In general, the role of the nudix
hydrolase is to sanitize the nucleotide pools and to
maintain cell viability, thereby serving as surveillance
& "house-cleaning" enzymes. Substrate specificity is
used to define families within the superfamily.
Differences in substrate specificity are determined by
the N-terminal extension or by residues in variable loop
regions. Mechanistically, substrate hydrolysis occurs by
a nucleophilic substitution reaction, with variation in
the numbers and roles of divalent cations required.
Length = 134
Score = 27.2 bits (61), Expect = 5.3
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 10/43 (23%)
Query: 121 LTVVVLVINDGKYLLVPEPETDIIGGPEVF------IENGSTI 157
+TV +V DG++LLV E G VF +E G ++
Sbjct: 1 VTVAAVVERDGRFLLVEE----ETDGGLVFNQPAGHLEPGESL 39
>gnl|CDD|200528 cd11267, Sema_6B, The Sema domain, a protein interacting module, of
semaphorin 6B (Sema6B). Sema6B functions as repellents
for axon growth; this repulsive activity is mediated by
its receptor Plexin A4. Sema6B is expressed in CA3, and
repels mossy fibers in a Plexin A4 dependent manner. In
human, it was shown that peroxisome
proliferator-activated receptors (PPARs) and
9-cis-retinoic acid receptor (RXR) regulate human
semaphorin 6B (Sema6B) gene expression. Sema6B is a
member of the class 6 semaphorin family of proteins,
which are membrane associated semaphorins. Semaphorins
are regulatory molecules in the development of the
nervous system and in axonal guidance. They also play
important roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 466
Score = 27.9 bits (62), Expect = 5.6
Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 109 VSTTPHQAHYIYLTVVVLVINDG---KYLLVPEPETDIIGGPEVFIENGSTIN 158
PH H TVV L G K+L++P + I VF+E T N
Sbjct: 378 TEAGPHGNH----TVVFLGSTRGTVLKFLIIPNASSSEISNQSVFLEELETYN 426
>gnl|CDD|173740 cd07842, STKc_CDK8_like, Catalytic domain of Cyclin-Dependent
protein Kinase 8-like Serine/Threonine Kinases.
Serine/Threonine Kinases (STKs), Cyclin-Dependent
protein Kinase 8 (CDK8)-like subfamily, catalytic (c)
domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The CDK8-like subfamily
is part of a larger superfamily that includes the
catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. CDKs belong to a large family of STKs that are
regulated by their cognate cyclins. Together, they are
involved in the control of cell-cycle progression,
transcription, and neuronal function. This subfamily is
composed of CDK8, CDC2L6, and similar proteins. CDK8
functions as a negative or positive regulator of
transcription, depending on the scenario. Together with
its regulator, cyclin C, it reversibly associates with
the multi-subunit core Mediator complex, a cofactor that
is involved in regulating RNA polymerase II (RNAP
II)-dependent transcription. CDC2L6 also associates with
Mediator in complexes lacking CDK8. In VP16-dependent
transcriptional activation, CDK8 and CDC2L6 exerts
opposing effects by positive and negative regulation,
respectively, in similar conditions.
Length = 316
Score = 27.6 bits (62), Expect = 5.8
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 25 FRVINNPTSDDWTLQLKYPQHKD 47
F V+ PT DW K P++
Sbjct: 238 FEVLGTPTEKDWPDIKKMPEYDT 260
Score = 27.6 bits (62), Expect = 5.8
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 79 FRVINNPTSDDWTLQLKYPQHKD 101
F V+ PT DW K P++
Sbjct: 238 FEVLGTPTEKDWPDIKKMPEYDT 260
>gnl|CDD|180648 PRK06663, PRK06663, flagellar hook-associated protein FlgL;
Validated.
Length = 419
Score = 27.3 bits (61), Expect = 8.1
Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 7/40 (17%)
Query: 144 IGGPEVFIENGSTINLTCVVRFSPEPPAYIFWNHNEAIIS 183
IG IENG I + P +FW N++IIS
Sbjct: 175 IGEQNREIENGIYIPVN-------YPGNKVFWGTNQSIIS 207
>gnl|CDD|178450 PLN02859, PLN02859, glutamine-tRNA ligase.
Length = 788
Score = 27.4 bits (61), Expect = 8.6
Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 16/65 (24%)
Query: 133 YLLVPEPETDIIGGPEVFIENGSTINLT----------------CVVRFSPEPPAYIFWN 176
Y + P+PE + EVF +GS + + RF PEP Y+
Sbjct: 221 YSIFPQPEENFKVHTEVFFSDGSVLRPSNTKEILEKHLKATGGKVYTRFPPEPNGYLHIG 280
Query: 177 HNEAI 181
H +A+
Sbjct: 281 HAKAM 285
>gnl|CDD|216720 pfam01818, Translat_reg, Bacteriophage translational regulator.
The translational regulator protein regA is encoded by
the T4 bacteriophage and binds to a region of messenger
RNA (mRNA) that includes the initiator codon. RegA is
unusual in that it represses the translation of about 35
early T4 mRNAs but does not affect nearly 200 other
mRNAs.
Length = 120
Score = 26.2 bits (58), Expect = 9.5
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 20 TNDQRFRVINNPTSDDWTLQLKY 42
FRVI++ +WTL KY
Sbjct: 94 APTNNFRVISHKQKAEWTLVSKY 116
Score = 26.2 bits (58), Expect = 9.5
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 74 TNDQRFRVINNPTSDDWTLQLKY 96
FRVI++ +WTL KY
Sbjct: 94 APTNNFRVISHKQKAEWTLVSKY 116
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
0.319 0.136 0.418
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: 11,974,346
Number of extensions: 1113408
Number of successful extensions: 1018
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1009
Number of HSP's successfully gapped: 95
Length of query: 236
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 142
Effective length of database: 6,768,326
Effective search space: 961102292
Effective search space used: 961102292
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 (21.7 bits)
S2: 57 (25.9 bits)