RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10492
(78 letters)
>gnl|CDD|223068 PHA03384, PHA03384, early DNA-binding protein E2A; Provisional.
Length = 445
Score = 30.1 bits (68), Expect = 0.067
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 47 SRPPFRIPEFKWSYIHQ 63
PP IPEFKWS +Q
Sbjct: 409 EPPPLVIPEFKWSPRYQ 425
Score = 29.7 bits (67), Expect = 0.093
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 6 PARPPFRIPEFKWSYIHQ 23
PP IPEFKWS +Q
Sbjct: 408 GEPPPLVIPEFKWSPRYQ 425
>gnl|CDD|191610 pfam06799, DUF1230, Protein of unknown function (DUF1230). This
family consists of several hypothetical plant and
photosynthetic bacterial proteins of around 160 residues
in length. The function of this family is unknown
although looking at the species distribution the protein
may play a part in photosynthesis.
Length = 145
Score = 27.2 bits (61), Expect = 0.56
Identities = 11/28 (39%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 18 WSYIHQRLLSDVLFSLET---DIQEYLK 42
WSY+ +RLLS+ + E+ D Q ++K
Sbjct: 87 WSYVRKRLLSETVEYEESGWYDGQVWVK 114
Score = 26.8 bits (60), Expect = 0.92
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 58 WSYIHQRLLSDVLFSLETD 76
WSY+ +RLLS+ + E+
Sbjct: 87 WSYVRKRLLSETVEYEESG 105
>gnl|CDD|241495 cd13341, PH-GRAM_MTMR3, Myotubularian (MTM) related 3 protein
(MTMR3) Pleckstrin Homology-Glucosyltransferases,
Rab-like GTPase activators and Myotubularins (PH-GRAM)
domain. MTMR3 is a member of the myotubularin dual
specificity protein phosphatase gene family. MTMR3 binds
to phosphoinositide lipids through its PH-GRAM domain,
and can hydrolyze phosphatidylinositol(3)-phosphate and
phosphatidylinositol(3,5)-biphosphate in vitro. The
protein can self-associate and also form heteromers with
MTMR4. Both MTMR3 and MTMR4 contain a N-terminal PH-GRAM
domain, a Rac-induced recruitment domain (RID) domain,
an active PTP domain, a SET-interaction domain, a
coiled-coil region, and a C-terminal lipid-binding FYVE
domain which binds phosphotidylinositol-3-phosphate.
Myotubularin-related proteins are a subfamily of protein
tyrosine phosphatases (PTPs) that dephosphorylate
D3-phosphorylated inositol lipids. Mutations in this
family cause the human neuromuscular disorders
myotubular myopathy and type 4B Charcot-Marie-Tooth
syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain
naturally occurring substitutions of residues required
for catalysis by PTP family enzymes. Although these
proteins are predicted to be enzymatically inactive,
they are thought to function as antagonists of
endogenous phosphatase activity or interaction modules.
Most MTMRs contain a N-terminal PH-GRAM domain, a
Rac-induced recruitment domain (RID) domain, a PTP
domain (which may be active or inactive), a
SET-interaction domain, and a C-terminal coiled-coil
region. In addition some members contain DENN domain
N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH
domains C-terminal to the coiled-coil region. The GRAM
domain, found in myotubularins, glucosyltransferases,
and other putative membrane-associated proteins, is part
of a larger motif with a pleckstrin homology (PH) domain
fold. The PH domain family possesses multiple functions
including the ability to bind phosphoinositides via its
beta1/beta2, beta3/beta4, and beta6/beta7 connecting
loops and to other proteins. However, no
phosphoinositide binding sites have been found for the
MTMRs to date.
Length = 148
Score = 26.2 bits (57), Expect = 1.8
Identities = 15/32 (46%), Positives = 22/32 (68%), Gaps = 2/32 (6%)
Query: 31 FSLETDIQEYLKKVNNS-RPPFRIPE-FKWSY 60
FS QE+LK++NN+ RPP RI + F ++Y
Sbjct: 101 FSTFEQCQEWLKRLNNAIRPPSRIEDLFSFAY 132
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 25.5 bits (56), Expect = 2.9
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 12/60 (20%)
Query: 20 YIHQRLLSDVLFSLETD--------IQEYLKKVNNSRPPFRIPEFKWSYIHQRLLSDVLF 71
+IH +LL VL + + I EY +K+ ++P K +YI+ R D+ +
Sbjct: 86 FIHPKLLKYVLNWISEEYCAKVLSIINEYNQKILKNKPSND----KINYIYMRKEEDMFY 141
>gnl|CDD|233728 TIGR02102, pullulan_Gpos, pullulanase, extracellular,
Gram-positive. Pullulan is an unusual, industrially
important polysaccharide in which short alpha-1,4 chains
(maltotriose) are connected in alpha-1,6 linkages.
Enzymes that cleave alpha-1,6 linkages in pullulan and
release maltotriose are called pullulanases although
pullulan itself may not be the natural substrate. In
contrast, a glycogen debranching enzyme such GlgX,
homologous to this family, can release glucose at
alpha,1-6 linkages from glycogen first subjected to
limit degradation by phosphorylase. Characterized
members of this family include a surface-located
pullulanase from Streptococcus pneumoniae
(PMID:11083842) and an extracellular bifunctional
amylase/pullulanase with C-terminal pullulanase activity
(PMID:8798645).
Length = 1111
Score = 25.6 bits (56), Expect = 3.2
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 1 MFSPGPARPPFRIPEFK--WSYIHQRLLSDVL 30
M+S P P RI EFK + IH+R + +L
Sbjct: 542 MYSEDPKDPELRIAEFKNLINEIHKRGMGVIL 573
>gnl|CDD|217698 pfam03728, Viral_DNA_Zn_bi, Viral DNA-binding protein, zinc binding
domain. This family represents the zinc binding domain
of the viral DNA- binding protein, a multi functional
protein involved in DNA replication and transcription
control. Two copies of this domain are found at the
C-terminus of many members of the family.
Length = 126
Score = 25.0 bits (55), Expect = 3.6
Identities = 8/15 (53%), Positives = 8/15 (53%)
Query: 9 PPFRIPEFKWSYIHQ 23
PP EF WS I Q
Sbjct: 102 PPIEKAEFAWSQILQ 116
Score = 25.0 bits (55), Expect = 3.6
Identities = 8/15 (53%), Positives = 8/15 (53%)
Query: 49 PPFRIPEFKWSYIHQ 63
PP EF WS I Q
Sbjct: 102 PPIEKAEFAWSQILQ 116
>gnl|CDD|190521 pfam03096, Ndr, Ndr family. This family consists of proteins from
different gene families: Ndr1/RTP/Drg1, Ndr2, and Ndr3.
Their similarity was previously noted. The precise
molecular and cellular function of members of this
family is still unknown. Yet, they are known to be
involved in cellular differentiation events. The Ndr1
group was the first to be discovered. Their expression
is repressed by the proto-oncogenes N-myc and c-myc, and
in line with this observation, Ndr1 protein expression
is down-regulated in neoplastic cells, and is
reactivated when differentiation is induced by chemicals
such as retinoic acid. Ndr2 and Ndr3 expression is not
under the control of N-myc or c-myc. Ndr1 expression is
also activated by several chemicals: tunicamycin and
homocysteine induce Ndr1 in human umbilical endothelial
cells; nickel induces Ndr1 in several cell types.
Members of this family are found in wide variety of
multicellular eukaryotes, including an Ndr1 type protein
in Helianthus annuus (sunflower), known as Sf21.
Interestingly, the highest scoring matches in the noise
are all alpha/beta hydrolases pfam00561, suggesting that
this family may have an enzymatic function (Bateman A
pers. obs.).
Length = 284
Score = 25.0 bits (55), Expect = 4.8
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 1/59 (1%)
Query: 18 WSYIHQRLLSDVLFSLETDI-QEYLKKVNNSRPPFRIPEFKWSYIHQRLLSDVLFSLET 75
Y+ S +DI QEY K + P + + +Y ++R L+ LET
Sbjct: 162 KDYLLAHYFGKEELSNNSDIVQEYRKFLKERLNPKNLQLYLEAYNNRRDLTIERGGLET 220
>gnl|CDD|241363 cd13209, PH-GRAM_MTMR3_MTMR4, Myotubularian (MTM) related 3 and 4
proteins (MTMR3 and MTMR4) Pleckstrin
Homology-Glucosyltransferases, Rab-like GTPase
activators and Myotubularins (PH-GRAM) domain. MTMR3 is
a member of the myotubularin dual specificity protein
phosphatase gene family. MTMR3 binds to phosphoinositide
lipids through its PH-GRAM domain, and can hydrolyze
phosphatidylinositol(3)-phosphate and
phosphatidylinositol(3,5)-biphosphate in vitro. The
protein can self-associate and also form heteromers with
MTMR4. MTMR4, a member of the myotubularin dual
specificity protein phosphatase gene family. MTMR4 binds
to phosphoinositide lipids through its PH-GRAM domain,
and can hydrolyze phosphatidylinositol(3)-phosphate and
phosphatidylinositol(3,5)-biphosphate in vitro. The
protein form heteromers with MTMR3. Both MTMR3 and MTMR4
contain a N-terminal PH-GRAM domain, a Rac-induced
recruitment domain (RID) domain, an active PTP domain, a
SET-interaction domain, a coiled-coil region, and a
C-terminal lipid-binding FYVE domain which binds
phosphotidylinositol-3-phosphate. Myotubularin-related
proteins are a subfamily of protein tyrosine
phosphatases (PTPs) that dephosphorylate
D3-phosphorylated inositol lipids. Mutations in this
family cause the human neuromuscular disorders
myotubular myopathy and type 4B Charcot-Marie-Tooth
syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain
naturally occurring substitutions of residues required
for catalysis by PTP family enzymes. Although these
proteins are predicted to be enzymatically inactive,
they are thought to function as antagonists of
endogenous phosphatase activity or interaction modules.
Most MTMRs contain a N-terminal PH-GRAM domain, a
Rac-induced recruitment domain (RID) domain, a PTP
domain (which may be active or inactive), a
SET-interaction domain, and a C-terminal coiled-coil
region. In addition some members contain DENN domain
N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH
domains C-terminal to the coiled-coil region. The GRAM
domain, found in myotubularins, glucosyltransferases,
and other putative membrane-associated proteins, is part
of a larger motif with a pleckstrin homology (PH) domain
fold. The PH domain family possesses multiple functions
including the ability to bind phosphoinositides via its
beta1/beta2, beta3/beta4, and beta6/beta7 connecting
loops and to other proteins. However, no
phosphoinositide binding sites have been found for the
MTMRs to date.
Length = 121
Score = 24.6 bits (53), Expect = 5.0
Identities = 8/27 (29%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 31 FSLETDIQEYLKKVNNS-RPPFRIPEF 56
FS QE+LK++N + P + +
Sbjct: 94 FSTFKQCQEWLKRLNRAIARPAKPEDL 120
>gnl|CDD|215326 PLN02606, PLN02606, palmitoyl-protein thioesterase.
Length = 306
Score = 24.6 bits (53), Expect = 6.3
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 39 EYLKKVNNSRPPFRIPEFK 57
+YL K+NN RP R P FK
Sbjct: 186 KYLPKLNNERPGERNPTFK 204
>gnl|CDD|145542 pfam02456, Adeno_IVa2, Adenovirus IVa2 protein. IVa2 protein can
interact with the adenoviral packaging signal and that
this interaction involves DNA sequences that have
previously been demonstrated to be required for
packaging. During the course of lytic infection, the
adenovirus major late promoter (MLP) is induced to high
levels after replication of viral DNA has started. IVa2
is a transcriptional activator of the major late
promoter.
Length = 370
Score = 24.6 bits (54), Expect = 7.0
Identities = 10/41 (24%), Positives = 17/41 (41%), Gaps = 8/41 (19%)
Query: 1 MFSPGPARPPFRIPEFKWSYIHQRLLSDVLFSLETDIQEYL 41
+++ P F+ W Y+ R + L L +IQ L
Sbjct: 312 VYNTDPVSESFQ-----WCYLDPR---EGLIPLYLNIQSKL 344
>gnl|CDD|221178 pfam11709, Mit_ribos_Mrp51, Mitochondrial ribosomal protein
subunit. This family is the mitochondrial ribosomal
small-subunit protein Mrp51. Its function is not
entirely clear, but deletion of the MRP51 gene
completely blocked mitochondrial gene expression.
Length = 302
Score = 24.3 bits (53), Expect = 8.7
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 36 DIQEYLKKVNNSRPPFR 52
+ EYLKKV+ RP FR
Sbjct: 141 EFSEYLKKVSPLRPEFR 157
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
0.325 0.141 0.448
Gapped
Lambda K H
0.267 0.0689 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,203,874
Number of extensions: 325866
Number of successful extensions: 506
Number of sequences better than 10.0: 1
Number of HSP's gapped: 505
Number of HSP's successfully gapped: 26
Length of query: 78
Length of database: 10,937,602
Length adjustment: 47
Effective length of query: 31
Effective length of database: 8,852,964
Effective search space: 274441884
Effective search space used: 274441884
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.3 bits)