RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9140
(114 letters)
>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 = 32.9 bits (75), Expect = 0.005
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 6/46 (13%)
Query: 40 LIAWLREGVSEARSIIHSGGRYSITTAGALHIRDTGMEDSYIRYYC 85
I W ++GV S G++ I+ G L IRD G+ D RY C
Sbjct: 14 TITWNKDGVQVTES-----GKFHISPEGYLAIRDVGVADQG-RYEC 53
>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 = 31.7 bits (71), Expect = 0.020
Identities = 15/74 (20%), Positives = 25/74 (33%), Gaps = 5/74 (6%)
Query: 25 AVLQCNIPAYNHNLLLIAWLREG--VSEARSIIHSGGRYSITTAGALHIRDTGMEDSYIR 82
L C A I WL+ G + + R + + + L I + +EDS
Sbjct: 1 VTLTC--LASGPPPPTITWLKNGKPLPSSVLTRVRSSRGTSSGSSTLTISNVTLEDSG-T 57
Query: 83 YYCQTTHKLTGERK 96
Y C ++
Sbjct: 58 YTCVASNSAGTVSA 71
>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 = 31.2 bits (71), Expect = 0.029
Identities = 22/71 (30%), Positives = 29/71 (40%), Gaps = 6/71 (8%)
Query: 18 FVLRGNIAVLQCNIPAYNHNLLLIAWLREGVSEARSIIHSGGRYSITTAGALHIRDTGME 77
V+ GN L+C P NL + WL +G R R +T G L IR
Sbjct: 7 TVVEGNSVFLEC-SP--KSNLASVVWLFQGGPLQRK-EEPEERLLVTEDGLL-IRSVSPA 61
Query: 78 DSYIRYYCQTT 88
D+ Y CQ+
Sbjct: 62 DAG-VYTCQSV 71
>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 = 28.9 bits (65), Expect = 0.24
Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 8/90 (8%)
Query: 16 NTFVLRGNIAVLQCNIPAYNHNLLLIAWLREGVSEARSIIHSGGRYSITTAGALHIRDTG 75
+T V G +AVL+C+ P H ++W ++G + R I G L I +
Sbjct: 5 DTQVAVGEMAVLECS-PPRGHPEPTVSWRKDGQ----PLNLDNERVRIVDDGNLLIAEAR 59
Query: 76 MEDSYIRYYCQTTHKLTGERKISPPSQVMV 105
D Y C T+ + GER S +++ V
Sbjct: 60 KSDEG-TYKCVATN-MVGER-ESAAARLSV 86
>gnl|CDD|182169 PRK09959, PRK09959, hybrid sensory histidine kinase in
two-component regulatory system with EvgA; Provisional.
Length = 1197
Score = 28.2 bits (62), Expect = 1.1
Identities = 10/29 (34%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 29 CNIPAYNHNLLLIAWLREGVSEARSIIHS 57
CN+PA +H + + W + ++E R +IH+
Sbjct: 671 CNLPASDHAVYICGW--QDITETRDLIHA 697
>gnl|CDD|143215 cd05738, Ig2_RPTP_IIa_LAR_like, Second immunoglobulin (Ig)-like
domain of the receptor protein tyrosine phosphatase
(RPTP)-F, also known as LAR. Ig2_RPTP_IIa_LAR_like:
domain similar to the second immunoglobulin (Ig)-like
domain found in the receptor protein tyrosine
phosphatase (RPTP)-F, also known as LAR. LAR belongs to
the RPTP type IIa subfamily. Members of this subfamily
are cell adhesion molecule-like proteins involved in
central nervous system (CNS) development. They have
large extracellular portions, comprised of multiple
Ig-like domains and two to nine fibronectin type III
(FNIII) domains, and a cytoplasmic portion having two
tandem phosphatase domains.
Length = 74
Score = 26.5 bits (58), Expect = 1.3
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 6/65 (9%)
Query: 41 IAWLREGVSEARSIIHSGGRYSITTAGALHIRDTGMEDSYIRYYCQTTHKLTGERKISPP 100
I W ++ + S GR +GAL I ++ D +Y C T+ G R S P
Sbjct: 15 ITWFKDFLPVD---TTSNGRIKQLRSGALQIENSEESDQG-KYECVATNSA-GTR-YSAP 68
Query: 101 SQVMV 105
+ + V
Sbjct: 69 ANLYV 73
>gnl|CDD|143218 cd05741, Ig_CEACAM_D1_like, First immunoglobulin (Ig)-like domain
of carcinoembryonic antigen (CEA) related cell adhesion
molecule (CEACAM) and similar proteins.
Ig_CEACAM_D1_like : immunoglobulin (IG)-like domain 1
in carcinoembryonic antigen (CEA) related cell adhesion
molecule (CEACAM) protein subfamily-like. The CEA
family is a group of anchored or secreted
glycoproteins, expressed by epithelial cells,
leukocytes, endothelial cells and placenta. The CEA
family is divided into the CEACAM and
pregnancy-specific glycoprotein (PSG) subfamilies. This
group represents the CEACAM subfamily. CEACAM1 has many
important cellular functions, it is a cell adhesion
molecule, and a signaling molecule that regulates the
growth of tumor cells, it is an angiogenic factor, and
is a receptor for bacterial and viral pathogens,
including mouse hepatitis virus (MHV). In mice, four
isoforms of CEACAM1 generated by alternative splicing
have either two [D1, D4] or four [D1-D4] Ig-like
domains on the cell surface. This family corresponds to
the D1 Ig-like domain. Also belonging to this group is
the N-terminal immunoglobulin (Ig)-like domain of the
signaling lymphocyte activation molecule (SLAM) family,
CD84-like family. The SLAM family is a group of
immune-cell specific receptors that can regulate both
adaptive and innate immune responses. SLAM family
proteins are organized as an extracellular domain with
having 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 = 92
Score = 26.5 bits (59), Expect = 1.8
Identities = 15/56 (26%), Positives = 21/56 (37%), Gaps = 13/56 (23%)
Query: 37 NLLLIAWLREGVSEARSIIHSG-------------GRYSITTAGALHIRDTGMEDS 79
NL I W + + I S GR +I G+L I++ EDS
Sbjct: 14 NLQEITWYKGKDKSVEAEIASYIATNSTVFGPAYSGRETIYPNGSLLIQNLTKEDS 69
>gnl|CDD|236774 PRK10839, PRK10839, 16S rRNA pseudouridylate synthase A;
Provisional.
Length = 232
Score = 27.0 bits (60), Expect = 2.2
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 55 IHSGGRYSITTAGALHIRDTGMEDSYI---RYYCQTTHKLTGERKISP 99
+H+ GR I T G + + D G I R++C+ T+ +T E ++
Sbjct: 95 LHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVAD 142
>gnl|CDD|238929 cd01967, Nitrogenase_MoFe_alpha_like, Nitrogenase_MoFe_alpha_like:
Nitrogenase MoFe protein, alpha subunit_like. The
nitrogenase enzyme catalyzes the ATP-dependent reduction
of dinitrogen to ammonia. Three genetically distinct
types of nitrogenase systems are known to exist: a
molybdenum-dependent nitrogenase (Mo-nitrogenase), a
vanadium dependent nitrogenase (V-nitrogenase), and an
iron-only nitrogenase (Fe-nitrogenase). These
nitrogenase systems consist of component 1 (MoFe
protein, VFe protein or, FeFe protein respectively) and,
component 2 (Fe protein). This group contains the alpha
subunit of component 1 of all three different forms. The
most widespread and best characterized of these systems
is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer,
the alternative nitrogenases are alpha2beta2delta2
hexamers having alpha and beta subunits similar to the
alpha and beta subunits of MoFe. The role of the delta
subunit is unknown. For MoFe, each alphabeta pair of
subunits contains one P-cluster (located at the
alphabeta interface) and, one molecule of iron
molybdenum cofactor (FeMoco) contained within the alpha
subunit. The Fe protein is a homodimer which contains, a
single [4Fe-4S] cluster from which electrons are
transferred to the P-cluster of the MoFe and in turn,
to FeMoCo the site of substrate reduction. The
V-nitrogenase requires an iron-vanadium cofactor
(FeVco), the iron only-nitrogenase an iron only cofactor
(FeFeco). These cofactors are analogous to the FeMoco.
The V-nitrogenase has P clusters identical to those of
MoFe. In addition to N2, nitrogenase also catalyzes the
reduction of a variety of other substrates such as
acetylene The V-nitrogenase differs from the Mo-
nitrogenase in that it produces free hydrazine, as a
minor product during dinitrogen reduction and, ethane
as a minor product during acetylene reduction.
Length = 406
Score = 26.0 bits (58), Expect = 4.6
Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 41 IAWLREGVSEARSIIHSGGRYSITTAGALHIRDTGMEDSYIRYYCQTTHKLTGERKIS 98
+ RE + + II++GG S AL R+ GME + + H ER
Sbjct: 277 LEKYRERLKGKKVIIYTGGARSWHVIAAL--RELGME--VVAAGYEFGHDDDYERIRK 330
>gnl|CDD|215308 PLN02568, PLN02568, polyamine oxidase.
Length = 539
Score = 26.3 bits (58), Expect = 4.6
Identities = 11/41 (26%), Positives = 18/41 (43%)
Query: 43 WLREGVSEARSIIHSGGRYSITTAGALHIRDTGMEDSYIRY 83
W R+ + EA +H + + T+A L D E Y +
Sbjct: 190 WSRKLLEEAIFTMHENTQRTYTSADDLSTLDLAAESEYRMF 230
>gnl|CDD|216633 pfam01660, Vmethyltransf, Viral methyltransferase. This RNA
methyltransferase domain is found in a wide range of
ssRNA viruses, including Hordei-, Tobra-, Tobamo-,
Bromo-, Clostero- and Caliciviruses. This
methyltransferase is involved in mRNA capping. Capping
of mRNA enhances its stability. This usually occurs in
the nucleus. Therefore, many viruses that replicate in
the cytoplasm encode their own. This is a specific
guanine-7-methyltransferase domain involved in viral
mRNA cap0 synthesis. Specificity for guanine 7 position
is shown by NMR in and in vivo role in cap synthesis.
Based on secondary structure prediction, the basic fold
is believed to be similar to the common AdoMet-dependent
methyltransferase fold. A curious feature of this
methyltransferase domain is that it together with
flanking sequences seems to have guanylyltransferase
activity coupled to the methyltransferase activity. The
domain is found throughout the so-called Alphavirus
superfamily, (including alphaviruses and several other
groups). It forms the defining, unique feature of this
superfamily.
Length = 305
Score = 25.3 bits (56), Expect = 9.1
Identities = 18/83 (21%), Positives = 30/83 (36%), Gaps = 17/83 (20%)
Query: 33 AYNHNLLLIAWLREGVSEARSIIHSGGR-YSIT---TAGALHIRDTGMEDSYIRYYCQTT 88
+Y H L L++WL I GG Y++ + GA H+ +
Sbjct: 192 SYTHPLNLLSWLT-----TSKITLPGGFTYTVERLESRGAHHL--------FKITRGDGL 238
Query: 89 HKLTGERKISPPSQVMVSEIALP 111
R P V++ +I +P
Sbjct: 239 TLKPDSRTFGPFEAVLLPKIFVP 261
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 0.134 0.395
Gapped
Lambda K H
0.267 0.0782 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,702,712
Number of extensions: 475032
Number of successful extensions: 321
Number of sequences better than 10.0: 1
Number of HSP's gapped: 321
Number of HSP's successfully gapped: 15
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
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: 53 (24.1 bits)