RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10292
(168 letters)
>gnl|CDD|197984 smart00916, L51_S25_CI-B8, Mitochondrial ribosomal protein L51 /
S25 / CI-B8 domain. Proteins containing this domain are
located in the mitochondrion and include ribosomal
protein L51, and S25. This domain is also found in
mitochondrial NADH-ubiquinone oxidoreductase B8 subunit
(CI-B8) . It is not known whether all members of this
family form part of the NADH-ubiquinone oxidoreductase
and whether they are also all ribosomal proteins.
Length = 70
Score = 73.7 bits (182), Expect = 3e-18
Identities = 20/70 (28%), Positives = 36/70 (51%)
Query: 40 ENHRGAKEFVFWHFTQIQFKNPNVQLQVFKNMTPTPFITTYLENGSEMLIDVDNKSKDEI 99
+ GA++F+ + ++FKNP+V + V + P +T ENG E I + N S +EI
Sbjct: 1 GSSAGARKFLESNLPTLKFKNPDVPILVRERSGVVPKLTAEYENGREKEISLRNLSAEEI 60
Query: 100 HDHVLKVLGK 109
+ ++
Sbjct: 61 LKKLQLLVNS 70
>gnl|CDD|191176 pfam05047, L51_S25_CI-B8, Mitochondrial ribosomal protein L51 /
S25 / CI-B8 domain. The proteins in this family are
located in the mitochondrion. The family includes
ribosomal protein L51, and S25. This family also
includes mitochondrial NADH-ubiquinone oxidoreductase
B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether
all members of this family form part of the
NADH-ubiquinone oxidoreductase and whether they are
also all ribosomal proteins.
Length = 52
Score = 58.7 bits (143), Expect = 2e-12
Identities = 15/51 (29%), Positives = 26/51 (50%)
Query: 45 AKEFVFWHFTQIQFKNPNVQLQVFKNMTPTPFITTYLENGSEMLIDVDNKS 95
A++F+ + +++KNP V + V + P + NG E ID+ N S
Sbjct: 1 ARDFLEKNLPTLKYKNPQVPILVRERSGKHPRLLARYLNGREKTIDLRNLS 51
>gnl|CDD|130366 TIGR01299, synapt_SV2, synaptic vesicle protein SV2. This model
describes a tightly conserved subfamily of the larger
family of sugar (and other) transporters described by
PFAM model pfam00083. Members of this subfamily include
closely related forms SV2A and SV2B of synaptic vesicle
protein from vertebrates and a more distantly related
homolog (below trusted cutoff) from Drosophila
melanogaster. Members are predicted to have two sets of
six transmembrane helices.
Length = 742
Score = 28.4 bits (63), Expect = 1.9
Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 11/74 (14%)
Query: 21 RIVFKDKIKIFAINYNFNAENHRGAK----EFVFWHFTQIQFKNPNVQLQVFKNMTPT-- 74
+ DK+ F+ N+ + HRG + +F+ F + F++ + F ++T +
Sbjct: 485 KNFPGDKVAHFSFNFTLENQIHRGGEYDNDKFIGLKFKSVSFEDSLFEECTFDDVTSSNT 544
Query: 75 -----PFITTYLEN 83
FI T EN
Sbjct: 545 FFKNCTFIDTLFEN 558
>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding
protein 11 (RBM11). This subfamily corresponds to the
RRM or RBM11, a novel tissue-specific splicing regulator
that is selectively expressed in brain, cerebellum and
testis, and to a lower extent in kidney. RBM11 is
localized in the nucleoplasm and enriched in
SRSF2-containing splicing speckles. It may play a role
in the modulation of alternative splicing during neuron
and germ cell differentiation. RBM11 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
The RRM of RBM11 is responsible for RNA binding, whereas
the C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 26.5 bits (58), Expect = 2.4
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 114 LKAEAIAREKKDNPANFGFKCEKH 137
L I ++K+ P +FGF C KH
Sbjct: 28 LTKVTICKDKEGKPKSFGFVCFKH 51
>gnl|CDD|223617 COG0543, UbiB, 2-polyprenylphenol hydroxylase and related
flavodoxin oxidoreductases [Coenzyme metabolism / Energy
production and conversion].
Length = 252
Score = 27.8 bits (62), Expect = 2.8
Identities = 12/73 (16%), Positives = 23/73 (31%), Gaps = 18/73 (24%)
Query: 1 MGFLIGEAPIRRTLKYL----------------NAGRIVFKDKIKIFAIN--YNFNAENH 42
+ G AP+ K L A ++ D+++ A + +
Sbjct: 113 IAGGTGIAPLYAIAKELKEKGDANKVTLLYGARTAKDLLLLDELEELAEKEVHPVTDDGW 172
Query: 43 RGAKEFVFWHFTQ 55
+G K FV +
Sbjct: 173 KGRKGFVTTDVLK 185
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 27.3 bits (61), Expect = 4.1
Identities = 26/138 (18%), Positives = 47/138 (34%), Gaps = 27/138 (19%)
Query: 10 IRRTLKYLNAGRIVFKDKIKIFAINYNFNAENHRGAKEFVFWHFTQIQFKNPNV------ 63
IR LK L + + +FA + R A + T+I NP
Sbjct: 656 IRDWLKTLR-----KLNGVVVFATQSILDILKSRIADAIIEQCPTKIFLPNPKAIEADYY 710
Query: 64 ------QLQVFKNMTPTPFITTY----LENGSEMLIDVDNKSKDEIHDHVLKVL-GKSEQ 112
+ ++ T+ + S +L ++ + L +L G++E
Sbjct: 711 RGFGLTEREIELIARALS-KTSRYFLSKQGSSSVLAELSLGGLGDE----LAILSGRTET 765
Query: 113 VLKAEAIAREKKDNPANF 130
V +AI E D+P +
Sbjct: 766 VSLLDAILAEVGDDPDAW 783
>gnl|CDD|173638 cd05065, PTKc_EphR_B, Catalytic domain of the Protein Tyrosine
Kinases, Class EphB Ephrin Receptors. Protein Tyrosine
Kinase (PTK) family; Ephrin Receptor (EphR) subfamily;
class EphB receptors; catalytic (c) domain. The PTKc
family is part of a larger superfamily that includes
the catalytic domains of other kinases such as protein
serine/threonine kinases, RIO kinases, and
phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. EphRs
comprise the largest subfamily of receptor tyr kinases
(RTKs). Class EphB receptors bind to transmembrane
ephrin-B ligands. There are six vertebrate EhpB
receptors (EphB1-6), which display promiscuous
interactions with three ephrin-B ligands. One exception
is EphB2, which also interacts with ephrin A5. EphRs
contain an ephrin-binding domain and two fibronectin
repeats extracellularly, a transmembrane segment, and a
cytoplasmic tyr kinase domain. Binding of the ephrin
ligand to EphR requires cell-cell contact since both
are anchored to the plasma membrane. The resulting
downstream signals occur bidirectionally in both
EphR-expressing cells (forward signaling) and
ephrin-expressing cells (reverse signaling).
Ephrin/EphR interaction mainly results in cell-cell
repulsion or adhesion. EphBRs play important roles in
synapse formation and plasticity, spine morphogenesis,
axon guidance, and angiogenesis. In the intestinal
epithelium, EphBRs are Wnt signaling target genes that
control cell compartmentalization. They function as
suppressors of color cancer progression.
Length = 269
Score = 27.1 bits (60), Expect = 4.3
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 57 QFKNPNV-QLQ-VFKNMTPTPFITTYLENGS 85
QF +PN+ L+ V P IT ++ENG+
Sbjct: 61 QFDHPNIIHLEGVVTKSRPVMIITEFMENGA 91
>gnl|CDD|114472 pfam05748, Rubella_E1, Rubella membrane glycoprotein E1. Rubella
virus (RV), the sole member of the genus Rubivirus
within the family Togaviridae, is a small enveloped,
positive strand RNA virus. The nucleocapsid consists of
40S genomic RNA and a single species of capsid protein
which is enveloped within a host-derived lipid bilayer
containing two viral glycoproteins, E1 (58 kDa) and E2
(42-46 kDa). In virus infected cells, RV matures by
budding either at the plasma membrane, or at the
internal membranes depending on the cell type and enters
adjacent uninfected cells by a membrane fusion process
in the endosome, directed by E1-E2 heterodimers. The
heterodimer formation is crucial for E1 transport out of
the endoplasmic reticulum to the Golgi and plasma
membrane. In RV E1, a cysteine at position 82 is crucial
for the E1-E2 heterodimer formation and cell surface
expression of the two proteins. The E1 has been shown to
be a type 1 membrane protein, rich in cysteine residues
with extensive intramolecular disulfide bonds.
Length = 496
Score = 27.0 bits (59), Expect = 5.2
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 138 CICQIPGQITCPGL 151
CIC+IP ++C GL
Sbjct: 64 CICEIPTDVSCEGL 77
>gnl|CDD|214625 smart00332, PP2Cc, Serine/threonine phosphatases, family 2C,
catalytic domain. The protein architecture and deduced
catalytic mechanism of PP2C phosphatases are similar to
the PP1, PP2A, PP2B family of protein Ser/Thr
phosphatases, with which PP2C shares no sequence
similarity.
Length = 252
Score = 26.6 bits (59), Expect = 6.1
Identities = 20/71 (28%), Positives = 28/71 (39%), Gaps = 10/71 (14%)
Query: 66 QVFKNMTPTPFITTYLENGS-EMLI---D--VDNKSKDEIHDHVLKVLGKSEQV----LK 115
+ ++ P +T + LI D D S E+ D V K L K + L
Sbjct: 176 FLKPYVSAEPDVTVVELTEKDDFLILASDGLWDVLSNQEVVDIVRKHLSKDPKEAAKRLI 235
Query: 116 AEAIAREKKDN 126
A+AR KDN
Sbjct: 236 DLALARGSKDN 246
>gnl|CDD|232926 TIGR00337, PyrG, CTP synthase. CTP synthase is involved in
pyrimidine ribonucleotide/ribonucleoside metabolism. The
enzyme catalyzes the reaction L-glutamine + H2O + UTP +
ATP = CTP + phosphate + ADP + L-glutamate. The enzyme
exists as a dimer of identical chains that aggregates as
a tetramer. This gene has been found circa 500 bp 5'
upstream of enolase in both beta (Nitrosomonas europaea)
and gamma (E.coli) subdivisions of proteobacterium (FEMS
Microbiol Lett 1998 Aug 1;165(1):153-7) [Purines,
pyrimidines, nucleosides, and nucleotides, Pyrimidine
ribonucleotide biosynthesis].
Length = 525
Score = 26.9 bits (60), Expect = 6.4
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 90 DVDNKSKDEIHDHVLKVLGKSEQVLKAEAIAREKKDNPANFGFKCEKH 137
+V+N+ ++++ + L V G S E I E D+P F C+ H
Sbjct: 462 EVNNEYREQLENKGLIVSGTSPDGRLVEII--ELPDHP--FFVACQFH 505
>gnl|CDD|173639 cd05066, PTKc_EphR_A, Catalytic domain of the Protein Tyrosine
Kinases, Class EphA Ephrin Receptors. Protein Tyrosine
Kinase (PTK) family; Ephrin Receptor (EphR) subfamily;
most class EphA receptors including EphA3, EphA4,
EphA5, and EphA7, but excluding EphA1, EphA2 and
EphA10; catalytic (c) domain. The PTKc family is part
of a larger superfamily that includes the catalytic
domains of other kinases such as protein
serine/threonine kinases, RIO kinases, and
phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. EphRs
comprise the largest subfamily of receptor tyr kinases
(RTKs). In general, class EphA receptors bind
GPI-anchored ephrin-A ligands. There are ten vertebrate
EphA receptors (EphA1-10), which display promiscuous
interactions with six ephrin-A ligands. One exception
is EphA4, which also binds ephrins-B2/B3. EphRs contain
an ephrin-binding domain and two fibronectin repeats
extracellularly, a transmembrane segment, and a
cytoplasmic tyr kinase domain. Binding of the ephrin
ligand to EphR requires cell-cell contact since both
are anchored to the plasma membrane. The resulting
downstream signals occur bidirectionally in both
EphR-expressing cells (forward signaling) and
ephrin-expressing cells (reverse signaling).
Ephrin/EphR interaction mainly results in cell-cell
repulsion or adhesion, making it important in neural
development and plasticity, cell morphogenesis,
cell-fate determination, embryonic development, tissue
patterning, and angiogenesis. EphARs and ephrin-A
ligands are expressed in multiple areas of the
developing brain, especially in the retina and tectum.
They are part of a system controlling retinotectal
mapping.
Length = 267
Score = 26.4 bits (58), Expect = 7.2
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 57 QFKNPNV-QLQ-VFKNMTPTPFITTYLENGS 85
QF +PN+ L+ V P +T Y+ENGS
Sbjct: 61 QFDHPNIIHLEGVVTKSKPVMIVTEYMENGS 91
>gnl|CDD|133165 cd05033, PTKc_EphR, Catalytic domain of Ephrin Receptor Protein
Tyrosine Kinases. Protein Tyrosine Kinase (PTK)
family; Ephrin Receptor (EphR) subfamily; catalytic (c)
domain. The PTKc family is part of a larger superfamily
that includes the catalytic domains of other kinases
such as protein serine/threonine kinases, RIO kinases,
and phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. EphRs
comprise the largest subfamily of receptor tyr kinases
(RTKs). They can be classified into two classes (EphA
and EphB), according to their extracellular sequences,
which largely correspond to binding preferences for
either GPI-anchored ephrin-A ligands or transmembrane
ephrin-B ligands. Vertebrates have ten EphA and six
EhpB receptors, which display promiscuous ligand
interactions within each class. EphRs contain an ephrin
binding domain and two fibronectin repeats
extracellularly, a transmembrane segment, and a
cytoplasmic tyr kinase domain. Binding of the ephrin
ligand to EphR requires cell-cell contact since both
are anchored to the plasma membrane. This allows
ephrin/EphR dimers to form, leading to the activation
of the intracellular tyr kinase domain. The resulting
downstream signals occur bidirectionally in both
EphR-expressing cells (forward signaling) and
ephrin-expressing cells (reverse signaling). The main
effect of ephrin/EphR interaction is cell-cell
repulsion or adhesion. Ephrin/EphR signaling is
important in neural development and plasticity, cell
morphogenesis and proliferation, cell-fate
determination, embryonic development, tissue
patterning, and angiogenesis.
Length = 266
Score = 26.1 bits (58), Expect = 9.1
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 57 QFKNPNV-QLQ-VFKNMTPTPFITTYLENGS 85
QF +PN+ +L+ V P IT Y+ENGS
Sbjct: 61 QFDHPNIIRLEGVVTKSRPVMIITEYMENGS 91
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
0.322 0.139 0.425
Gapped
Lambda K H
0.267 0.0824 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,569,226
Number of extensions: 766730
Number of successful extensions: 618
Number of sequences better than 10.0: 1
Number of HSP's gapped: 618
Number of HSP's successfully gapped: 28
Length of query: 168
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 78
Effective length of database: 6,945,742
Effective search space: 541767876
Effective search space used: 541767876
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 (21.9 bits)
S2: 55 (24.8 bits)