RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12724
(167 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 = 34.0 bits (78), Expect = 0.006
Identities = 23/92 (25%), Positives = 33/92 (35%), Gaps = 16/92 (17%)
Query: 74 DEHVLKGNSAVLKCHIPSFVADYVAVESWISDQGEELFVDMTESTDGKYLVLPSG---EL 130
V +G S L C V +W G+ L G++ V SG L
Sbjct: 3 SVTVKEGESVTLSCEASGSPPPEV---TWYKQGGKLLA------ESGRFSVSRSGSTSTL 53
Query: 131 HIRDVGPEDGYKSYQCR---TKHRLTGETRLS 159
I +V PED +Y C + + T L+
Sbjct: 54 TISNVTPED-SGTYTCAATNSSGSASSGTTLT 84
>gnl|CDD|214652 smart00409, IG, Immunoglobulin.
Length = 85
Score = 34.0 bits (78), Expect = 0.006
Identities = 23/92 (25%), Positives = 33/92 (35%), Gaps = 16/92 (17%)
Query: 74 DEHVLKGNSAVLKCHIPSFVADYVAVESWISDQGEELFVDMTESTDGKYLVLPSG---EL 130
V +G S L C V +W G+ L G++ V SG L
Sbjct: 3 SVTVKEGESVTLSCEASGSPPPEV---TWYKQGGKLLA------ESGRFSVSRSGSTSTL 53
Query: 131 HIRDVGPEDGYKSYQCR---TKHRLTGETRLS 159
I +V PED +Y C + + T L+
Sbjct: 54 TISNVTPED-SGTYTCAATNSSGSASSGTTLT 84
>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 = 33.2 bits (75), Expect = 0.011
Identities = 12/75 (16%), Positives = 22/75 (29%), Gaps = 4/75 (5%)
Query: 83 AVLKCHIPSFVADYVAVESWISDQGEELFVDMTESTDGKYLVLPSGELHIRDVGPEDGYK 142
L C + +W+ + +T + S L I +V ED
Sbjct: 1 VTLTCLASGPPPPTI---TWLKNGKPLPSSVLTRVRSSRGTSSGSSTLTISNVTLEDS-G 56
Query: 143 SYQCRTKHRLTGETR 157
+Y C + +
Sbjct: 57 TYTCVASNSAGTVSA 71
>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 = 31.8 bits (72), Expect = 0.030
Identities = 17/35 (48%), Positives = 22/35 (62%), Gaps = 3/35 (8%)
Query: 112 VDMTESTDGKYLVLPSGELHIRDVGPEDGYKSYQC 146
V +TES GK+ + P G L IRDVG D + Y+C
Sbjct: 22 VQVTES--GKFHISPEGYLAIRDVGVADQGR-YEC 53
>gnl|CDD|197706 smart00408, IGc2, Immunoglobulin C-2 Type.
Length = 63
Score = 29.7 bits (67), Expect = 0.14
Identities = 16/74 (21%), Positives = 23/74 (31%), Gaps = 14/74 (18%)
Query: 80 GNSAVLKCHIPSFVADYVAVESWISDQGEELFVDMTESTDGKYLVLPSGELHIRDVGPED 139
G S L C P+ + +W D + V L I+ V ED
Sbjct: 2 GQSVTLTC--PAEGNPVPNI-TW--------LKDGKPLPESNRFVASGSTLTIKSVSLED 50
Query: 140 -GYKSYQCRTKHRL 152
G Y C ++
Sbjct: 51 SGL--YTCVAENSA 62
>gnl|CDD|143199 cd05722, Ig1_Neogenin, First immunoglobulin (Ig)-like domain in
neogenin and similar proteins. Ig1_Neogenin: first
immunoglobulin (Ig)-like domain in neogenin and related
proteins. Neogenin is a cell surface protein which is
expressed in the developing nervous system of vertebrate
embryos in the growing nerve cells. It is also expressed
in other embryonic tissues, and may play a general role
in developmental processes such as cell migration,
cell-cell recognition, and tissue growth regulation.
Included in this group is the tumor suppressor protein
DCC, which is deleted in colorectal carcinoma . DCC and
neogenin each have four Ig-like domains followed by six
fibronectin type III domains, a transmembrane domain,
and an intracellular domain.
Length = 95
Score = 29.4 bits (66), Expect = 0.37
Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 16/86 (18%)
Query: 67 SYTVNIMDEHVLKGNSAVLKCHIPSFVADYVAVESWISDQGEELFVDMTESTDGKYLVLP 126
+ D ++G VL C S + W D V + +D + LP
Sbjct: 1 WFLSEPSDIVAVRGGPVVLNC---SAEGEPPPKIEWKKDG-----VLLNLVSDERRQQLP 52
Query: 127 SGEL------HIRDVGPEDGYKSYQC 146
+G L H + P++G+ YQC
Sbjct: 53 NGSLLITSVVHSKHNKPDEGF--YQC 76
>gnl|CDD|143187 cd04986, IgC_CH2, CH2 domain (second constant Ig domain of the
heavy chain) in immunoglobulin. IgC_CH2: The second
immunoglobulin constant domain (IgC), of immunoglobulin
(Ig) heavy chains. This domain is found on the Fc
fragment. The basic structure of Ig molecules is a
tetramer of two light chains and two heavy chains linked
by disulfide bonds. There are two types of light chains:
kappa and lambda; each composed of a constant domain and
a variable domain. There are five types of heavy chains:
alpha, delta, epsilon, gamma and mu, all consisting of a
variable domain (VH) and three (in alpha, delta and
gamma) or four (in epsilon and mu) constant domains (CH1
to CH4). Ig molecules are modular proteins, in which the
variable and constant domains have clear, conserved
sequence patterns.
Length = 99
Score = 26.9 bits (59), Expect = 2.3
Identities = 24/88 (27%), Positives = 33/88 (37%), Gaps = 4/88 (4%)
Query: 75 EHVLKGNSAVLKCHIPSFVADYVAVESWISDQGEELFVDMTES-TDGKYLVLPSGELHIR 133
E +L G+SA L C + AV +W G+E ES G Y V S L
Sbjct: 14 EDLLLGSSASLTCTLSGLRDPEGAVFTWTPSGGKEAVQTSAESDQCGCYSV--SSVLPGC 71
Query: 134 DVGPEDGYKSYQCRTKHRLTGETRLSAT 161
G + + C H + L+ T
Sbjct: 72 AEEWNKG-EPFACTVTHPEGDQEILTPT 98
>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 = 25.4 bits (56), Expect = 7.0
Identities = 23/70 (32%), Positives = 30/70 (42%), Gaps = 9/70 (12%)
Query: 77 VLKGNSAVLKCHIPSFVADYVAVESWISDQGEELFVDMTESTDGKYLVLPSGELHIRDVG 136
V++GNS L+C S +A V W+ G E + + LV G L IR V
Sbjct: 8 VVEGNSVFLECSPKSNLASVV----WLFQGGPLQR---KEEPEERLLVTEDGLL-IRSVS 59
Query: 137 PEDGYKSYQC 146
P D Y C
Sbjct: 60 PADA-GVYTC 68
>gnl|CDD|175983 cd04016, C2_Tollip, C2 domain present in Toll-interacting protein
(Tollip). Tollip is a part of the Interleukin-1
receptor (IL-1R) signaling pathway. Tollip is proposed
to link serine/threonine kinase IRAK to IL-1Rs as well
as inhibiting phosphorylation of IRAK. There is a single
C2 domain present in Tollip. C2 domains fold into an
8-standed beta-sandwich that can adopt 2 structural
arrangements: Type I and Type II, distinguished by a
circular permutation involving their N- and C-terminal
beta strands. Many C2 domains are Ca2+-dependent
membrane-targeting modules that bind a wide variety of
substances including bind phospholipids, inositol
polyphosphates, and intracellular proteins. Most C2
domain proteins are either signal transduction enzymes
that contain a single C2 domain, such as protein kinase
C, or membrane trafficking proteins which contain at
least two C2 domains, such as synaptotagmin 1. However,
there are a few exceptions to this including RIM
isoforms and some splice variants of piccolo/aczonin and
intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions.
Length = 121
Score = 25.4 bits (56), Expect = 9.3
Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 67 SYTVNIMDEHVLKGNSAVLKCHI--PSFVADYVAVESWIS---DQGEEL 110
S + I DE + + HI P V + ++ W S QGE+
Sbjct: 63 SIYIEIFDERAFTMDERIAWTHITIPESVFNGETLDDWYSLSGKQGEDK 111
>gnl|CDD|165270 PHA02965, PHA02965, hypothetical protein; Provisional.
Length = 466
Score = 26.1 bits (57), Expect = 9.7
Identities = 15/67 (22%), Positives = 28/67 (41%)
Query: 9 ISQYYEAQVYDVFVIKGNAAVFKCNLPSFVSDHLDVVSWADTDGGQYQIDNQDFVVSQSY 68
I Y A +Y V+ + L + + +D + D ++ IDN + ++S+
Sbjct: 398 IEHNYMANLYKVYGQNEYMITYILALINRIKKGMDAIKSNLGDIDEFNIDNINLIISERI 457
Query: 69 TVNIMDE 75
NI E
Sbjct: 458 KKNISGE 464
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 0.136 0.413
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: 8,393,595
Number of extensions: 744191
Number of successful extensions: 508
Number of sequences better than 10.0: 1
Number of HSP's gapped: 508
Number of HSP's successfully gapped: 12
Length of query: 167
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 77
Effective length of database: 6,945,742
Effective search space: 534822134
Effective search space used: 534822134
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)