RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8646
(191 letters)
>gnl|CDD|241511 cd13357, PH-GRAM_MTMR2_insect-like, Myotubularian related 2 protein
(MTMR2) Pleckstrin Homology-Glucosyltransferases,
Rab-like GTPase activators and Myotubularins (PH-GRAM)
domain. MTMR2 is a member of the myotubularin protein
phosphatase gene family. MTMR2 binds to phosphoinositide
lipids through its PH-GRAM domain, and can hydrolyze
phosphatidylinositol(3)-phosphate and
phosphatidylinositol(3,5)-biphosphate in vitro.
Mutations in MTMR2 are a cause of Charcot-Marie-Tooth
disease type 4B, an autosomal recessive demyelinating
neuropathy. The protein can self-associate and form
heteromers with MTMR5 and MTMR12. MTMR2 contains 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 PDZ domain. 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. Members in this cd include Drosophila,
sea urchins, mosquitos, bees, ticks, and anemones.
Length = 148
Score = 109 bits (275), Expect = 5e-31
Identities = 57/152 (37%), Positives = 91/152 (59%), Gaps = 22/152 (14%)
Query: 53 QTSRPDDLPLLPGEIIQGFAREVTYLCPYSGPARGILSVTNYKLYFRSIDRETPYVVEVP 112
+ P++ LL GE Q A++VTYLCP+SGP RG L++TNYKLYFRS+D+E P++V+VP
Sbjct: 2 GLANPEEFTLLEGEKPQDIAKDVTYLCPFSGPVRGTLTITNYKLYFRSLDKEPPFIVDVP 61
Query: 113 LGVV----------SIKLNTRSNDIWF-------WLHKLKKSLEDEMLFDEVQQYAFPVS 155
LGV+ S N+ +I+ + HK +++ ++F+++Q YAFP+S
Sbjct: 62 LGVIYRVEKVGGATSRGENSYGIEIFCKDMRNLRFAHK-QENHSRRLVFEKLQAYAFPLS 120
Query: 156 HKLCRIVSSIIEYTDNYFRKMGWNIMNQYAEL 187
+ L + + EY + F + GW + + AE
Sbjct: 121 NSL-PLFA--FEYKE-RFSENGWAVYDPVAEY 148
>gnl|CDD|241510 cd13356, PH-GRAM_MTMR2_mammal-like, Myotubularian related 2 protein
(MTMR2) Pleckstrin Homology-Glucosyltransferases,
Rab-like GTPase activators and Myotubularins (PH-GRAM)
domain. MTMR2 is a member of the myotubularin protein
phosphatase gene family. MTMR2 binds to phosphoinositide
lipids through its PH-GRAM domain, and can hydrolyze
phosphatidylinositol(3)-phosphate and
phosphatidylinositol(3,5)-biphosphate in vitro.
Mutations in MTMR2 are a cause of Charcot-Marie-Tooth
disease type 4B, an autosomal recessive demyelinating
neuropathy. The protein can self-associate and form
heteromers with MTMR5 and MTMR12. MTMR2 contains 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 PDZ domain. 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.Members in this cd include mammals,
chickens, anoles, human body lice, and aphids.
Length = 144
Score = 90.8 bits (225), Expect = 1e-23
Identities = 50/147 (34%), Positives = 78/147 (53%), Gaps = 20/147 (13%)
Query: 58 DDLPLLPGEIIQGFAREVTYLCPYSGPARGILSVTNYKLYFRSIDRETPYVVEVPLGVVS 117
++ PLLPGE I+ A++VTY+CP++G RG L+VTNY+LYF+S++R+ P+V++ LGV++
Sbjct: 2 EEPPLLPGENIKDMAKDVTYICPFTGAVRGTLTVTNYRLYFKSMERDPPFVLDASLGVIN 61
Query: 118 ---------------IKLNTRSNDIWFWLHKLKKSLED-EMLFDEVQQYAFPVSHKLCRI 161
L DI K +F+ + +YAFPVS+ L
Sbjct: 62 RVEKIGGASSRGENSYGLEIVCKDIRNLRFAHKPEGRTRRSIFENLMKYAFPVSNNLPLF 121
Query: 162 VSSIIEYTDNYFRKMGWNIMNQYAELR 188
EY + F + GW + + E R
Sbjct: 122 A---FEYKEV-FPENGWKLYDPLLEYR 144
>gnl|CDD|241512 cd13358, PH-GRAM_MTMR1, Myotubularian related 1 protein (MTMR1)
Pleckstrin Homology-Glucosyltransferases, Rab-like
GTPase activators and Myotubularins (PH-GRAM) domain.
MTMR1 is a member of the myotubularin protein
phosphatase gene family. MTMR1 binds to phosphoinositide
lipids through its PH-GRAM domain, and can hydrolyze
phosphatidylinositol(3)-phosphate and
phosphatidylinositol(3,5)-biphosphate in vitro. MTMR1
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 PDZ domain. 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 = 153
Score = 87.6 bits (217), Expect = 2e-22
Identities = 44/147 (29%), Positives = 81/147 (55%), Gaps = 21/147 (14%)
Query: 58 DDLPLLPGEIIQGFAREVTYLCPYSGPARGILSVTNYKLYFRSIDRETPYVVEVPLGVVS 117
++ PL PGE I+ ++V Y+CP+SG G L++T++KLYF+S++R+ P++++V LGV+S
Sbjct: 12 EEAPLFPGETIKAIVKDVMYICPFSGAVSGTLTITDFKLYFKSVERDPPFILDVNLGVIS 71
Query: 118 ----------------IKLNTRSNDIWFWLHKLKKSLEDEMLFDEVQQYAFPVSHKLCRI 161
I++ + + +K ++ + E+ F+ + ++AFP+SH L
Sbjct: 72 RVEKIGVQSHGDNSCGIEIVCKDMRNPRFAYKQEEQSKLEI-FENLSKHAFPLSHGLPLF 130
Query: 162 VSSIIEYTDNYFRKMGWNIMNQYAELR 188
S E F GW + + AE +
Sbjct: 131 AFSYKE----KFPVDGWKVYDPVAEYK 153
>gnl|CDD|241377 cd13223, PH-GRAM_MTM-like, Myotubularian 1 and related proteins
Pleckstrin Homology-Glucosyltransferases, Rab-like
GTPase. MTM1, MTMR1, and MTMR2 are members of the
myotubularin protein phosphatase gene family. They
contain a N-terminal PH-GRAM domain, a Rac-induced
recruitment domain (RID) domain, an active PTP domain, a
SET-interaction domain, and a C-terminal coiled-coil
region. In addition MTMR1 (Myotubularian related 1
protein) and MTMR2 (Myotubularian related 2 protein)
contain a C-terminal PDZ domain. Mutations in MTMR2 are
a cause of Charcot-Marie-Tooth disease type 4B, an
autosomal recessive demyelinating neuropathy. The
protein can self-associate and form heteromers with
MTMR5 and MTMR12. Myotubularin-related proteins are a
subfamily of protein tyrosine phosphatases (PTPs) that
dephosphorylate D3-phosphorylated inositol lipids. 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 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 = 94
Score = 81.8 bits (203), Expect = 9e-21
Identities = 27/46 (58%), Positives = 42/46 (91%)
Query: 72 AREVTYLCPYSGPARGILSVTNYKLYFRSIDRETPYVVEVPLGVVS 117
A++VTY+CP+SGP +G L +TNY+LYF+S++R+ P+V++VPLGV+S
Sbjct: 3 AKDVTYICPFSGPVKGTLYITNYRLYFKSLERDPPFVLDVPLGVIS 48
>gnl|CDD|241509 cd13355, PH-GRAM_MTM1, Myotubularian 1 protein (MTM1) Pleckstrin
Homology-Glucosyltransferases, Rab-like GTPase
activators and Myotubularins (PH-GRAM) domain. MTM1 is
a member of the myotubularin protein phosphatase gene
family. It is required for muscle cell differentiation
and mutations in this gene have been identified as being
responsible for X-linked myotubular myopathy, a severe
congenital muscle disorder characterized by defective
muscle cell development. Since its initial discovery,
there have been an additional 14 myotubularin-related
proteins identified. MTM1 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 form heteromers with
MTMR12. MTM1 contains a N-terminal PH-GRAM domain, a
Rac-induced recruitment domain (RID) domain, an active
PTP domain, a SET-interaction domain, and a C-terminal
coiled-coil region. 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. 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. All 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 and PH domains C-terminal to the coiled-coil
region.
Length = 152
Score = 77.5 bits (191), Expect = 2e-18
Identities = 45/134 (33%), Positives = 73/134 (54%), Gaps = 25/134 (18%)
Query: 45 PSNNNEPIQTSRPDDLPLLPGE--IIQGFAREVTYLCPYSGPARGILSVTNYKLYFRSID 102
+ + ++ +D+P LPGE I +EV Y+CP++GP +G + +TNY+LYFRS++
Sbjct: 10 KRTSRDGLKMELLEDVPRLPGEERITD---KEVIYICPFNGPVKGRVYITNYRLYFRSLE 66
Query: 103 RETPYVVEVPLGVVSI--KL--------NTRSNDIW--------FWLHKLKKSLEDEMLF 144
+ ++VPLGV+S K+ N+ DI F L + S D +F
Sbjct: 67 ADPVVTLDVPLGVISRIEKMGGASSRGENSYGLDITCKDMRNLRFALKQEGHSRRD--IF 124
Query: 145 DEVQQYAFPVSHKL 158
+ + +YAFP+SH L
Sbjct: 125 EILTKYAFPLSHGL 138
>gnl|CDD|241306 cd10570, PH-GRAM, Pleckstrin Homology-Glucosyltransferases,
Rab-like GTPase activators and Myotubularins (PH-GRAM)
domain. 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.
Length = 94
Score = 61.5 bits (150), Expect = 6e-13
Identities = 24/48 (50%), Positives = 37/48 (77%), Gaps = 1/48 (2%)
Query: 71 FAREVTYLCPY-SGPARGILSVTNYKLYFRSIDRETPYVVEVPLGVVS 117
++VTY+CP+ GP G L +TNY+LYF+S +R++P ++VPLGV+S
Sbjct: 2 EKKDVTYICPFHVGPVEGTLYLTNYRLYFKSKERDSPTELDVPLGVIS 49
>gnl|CDD|214725 smart00568, GRAM, domain in glucosyltransferases, myotubularins and
other putative membrane-associated proteins.
Length = 60
Score = 41.8 bits (99), Expect = 6e-06
Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 7/59 (11%)
Query: 61 PLLPGEIIQGFAREVTYLCPYS--GPARGILSVTNYKLYFRSIDRETPYVVEVPLGVVS 117
L E + Y C S GP +G L ++NY+L FRS V +PL ++
Sbjct: 1 KLPEEEKLIA-----DYSCYLSRTGPVQGRLYISNYRLCFRSNLPGKLTKVVIPLADIT 54
>gnl|CDD|217271 pfam02893, GRAM, GRAM domain. The GRAM domain is found in in
glucosyltransferases, myotubularins and other putative
membrane-associated proteins.
Length = 60
Score = 36.1 bits (84), Expect = 8e-04
Identities = 17/59 (28%), Positives = 24/59 (40%), Gaps = 8/59 (13%)
Query: 62 LLPGEIIQGFAREVTYLCPYS---GPARGILSVTNYKLYFRSIDRETPYVVEVPLGVVS 117
L P E + Y C P +G L +TN +L FRS V+ +PL +
Sbjct: 1 LPPEEKLIA-----DYSCYLQRPISPVQGRLYLTNNRLCFRSDKFGDLTVLVIPLADIE 54
>gnl|CDD|197474 smart00021, DAX, Domain present in Dishevelled and axin. Domain of
unknown function.
Length = 83
Score = 28.5 bits (64), Expect = 0.64
Identities = 14/46 (30%), Positives = 25/46 (54%)
Query: 86 RGILSVTNYKLYFRSIDRETPYVVEVPLGVVSIKLNTRSNDIWFWL 131
+ +L+ NYK YF+S+D + VV+ + S +L + + WL
Sbjct: 34 KEVLTKKNYKYYFKSMDDDFGGVVKEEIRDDSARLPCFNGRVVSWL 79
>gnl|CDD|226036 COG3505, VirD4, Type IV secretory pathway, VirD4 components
[Intracellular trafficking and secretion].
Length = 596
Score = 29.3 bits (66), Expect = 1.3
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 85 ARGILSVTNYKLYFRSIDRETPYVVEVPLGVVSIKLNTRS 124
A IL +++F D ET V LG ++K+ +RS
Sbjct: 457 ANTILDNCAVRIFFAPNDDETARYVSKLLGDETVKVKSRS 496
>gnl|CDD|176490 cd08760, Cyt_b561_FRRS1_like, Eukaryotic cytochrome b(561),
including the FRRS1 gene product. Cytochrome b(561), as
found in eukaryotes, similar to and including the human
FRRS1 gene product (ferric-chelate reductase 1), also
called SDR-2 (stromal cell-derived receptor 2). This
family comprises a variety of domain architectures, many
of which contain dopamine beta-monooxygenase (DOMON)
domains. The protein might act as a ferric-chelate
reductase, catalyzing the reduction of Fe(3+) to Fe(2+),
such as associated with the transport of iron from the
endosome to the cytoplasm. It is assumed that this
protein uses ascorbate as the electron donor. Belongs to
the cytochrome b(561) family, which are secretory
vesicle-specific electron transport proteins.
Cytochromes b(561) are integral membrane proteins that
bind two heme groups non-covalently, and may have six
alpha-helical trans-membrane segments.
Length = 191
Score = 28.5 bits (64), Expect = 1.5
Identities = 6/22 (27%), Positives = 13/22 (59%)
Query: 111 VPLGVVSIKLNTRSNDIWFWLH 132
+P+G + + + +WF+LH
Sbjct: 51 MPIGALLARYFLLGDPVWFYLH 72
>gnl|CDD|200458 cd11319, AmyAc_euk_AmyA, Alpha amylase catalytic domain found in
eukaryotic Alpha-amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes eukaryotic alpha-amylases including proteins
from fungi, sponges, and protozoans. The Alpha-amylase
family comprises the largest family of glycoside
hydrolases (GH), with the majority of enzymes acting on
starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 375
Score = 27.9 bits (63), Expect = 3.9
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 6/34 (17%)
Query: 65 GEIIQGFAREVTYLCPYSGPARGILSVTNYKLYF 98
GE+ G + Y+CPY + V NY LY+
Sbjct: 229 GEVFDG---DPNYVCPYQNY---LDGVLNYPLYY 256
>gnl|CDD|222842 PHA01972, PHA01972, structural protein.
Length = 828
Score = 27.6 bits (61), Expect = 5.7
Identities = 7/35 (20%), Positives = 17/35 (48%), Gaps = 5/35 (14%)
Query: 119 KLNTRSNDIWFWLHKLKKSLEDEMLFDEVQQYAFP 153
T ++W+ K+ D ++ D++Q+ + P
Sbjct: 763 TQQTPFANLWYT-----KAATDRLIMDQLQELSSP 792
>gnl|CDD|211335 cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine synthase, PUS1/
PUS2 like. This group consists of eukaryotic
pseudouridine synthases similar to Saccharomyces
cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis
elegans Pus1p and human PUS1. Pseudouridine synthases
catalyze the isomerization of specific uridines in an
RNA molecule to pseudouridines (5-ribosyluracil, psi).
No cofactors are required. S. cerevisiae Pus1p catalyzes
the formation of psi34 and psi36 in the
intron-containing tRNAIle, psi35 in the
intron-containing tRNATyr, psi27 and/or psi28 in several
yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear
RNA (U2 snRNA). The presence of the intron is required
for the formation of psi 34, 35 and 36. In addition S.
cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans
Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p
makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle,
psi 34/36 in tRNAIle and, psi 32 and potentially 67 in
tRNAVal. Psi44 in U2 snRNA and psi32 in tRNAs are
highly phylogenetically conserved. Psi
26,27,28,34,35,36,65 and 67 in tRNAs are less highly
conserved. Mouse Pus1p regulates nuclear receptor
activity through pseudouridylation of Steroid Receptor
RNA Activator. Missense mutation in human PUS1 causes
mitochondrial myopathy and sideroblastic anemia (MLASA).
Length = 245
Score = 26.8 bits (60), Expect = 6.1
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 4/40 (10%)
Query: 97 YFRSIDRETPYVVEVPLGVVSIKLNTRSNDIWFWLHKLKK 136
+ +S P+V+E L +SIK++ +S F LH+++K
Sbjct: 165 FIKSFYVSEPFVIEEGLEWISIKIHGQS----FMLHQIRK 200
>gnl|CDD|149846 pfam08908, DUF1852, Domain of unknown function (DUF1852). This
family of proteins are functionally uncharacterized.
Length = 322
Score = 26.9 bits (60), Expect = 6.6
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 47 NNNEPIQTSRPDDLPLLPGEIIQGFAREVTYLCPYSGPARGILSVTNYKLYFRS 100
N ++P Q S PDD L G++ + F Y ++ P LSV++ K Y R+
Sbjct: 132 NKDKP-QFSTPDDFGDLHGKLFKHFVNSDAYKENFNKPPVICLSVSSNKTYHRT 184
>gnl|CDD|223723 COG0650, HyfC, Formate hydrogenlyase subunit 4 [Energy production
and conversion].
Length = 309
Score = 26.9 bits (60), Expect = 7.6
Identities = 12/42 (28%), Positives = 15/42 (35%), Gaps = 6/42 (14%)
Query: 57 PDDLPLLPGEIIQGFAREVTYLCPYSGPARGILSVTNYKLYF 98
P D+ EII+G L YSG +L F
Sbjct: 198 PFDIAEAETEIIEG------PLTEYSGKLLALLKWAEAIKQF 233
>gnl|CDD|221719 pfam12696, TraG-D_C, TraM recognition site of TraD and TraG. This
family includes both TraG and TraD as well as VirD4
proteins. TraG is essential for DNA transfer in
bacterial conjugation. These proteins are thought to
mediate interactions between the DNA-processing (Dtr)
and the mating pair formation (Mpf) systems. This domain
interacts with the relaxosome component TraM via the
latter's tetramerisation domain. TraD is a hexameric
ring ATPase that forms the cytoplasmic face of the
conjugative pore.
Length = 126
Score = 25.7 bits (57), Expect = 9.9
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 85 ARGILSVTNYKLYFRSIDRETP-YVVEVPLGVVSIKLNTRS 124
A IL + K++ D ET Y+ ++ LG ++++ TRS
Sbjct: 51 AETILGNCDVKIFLGGNDPETAEYISKL-LGKTTVEVKTRS 90
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
0.315 0.132 0.396
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,288,372
Number of extensions: 825133
Number of successful extensions: 746
Number of sequences better than 10.0: 1
Number of HSP's gapped: 744
Number of HSP's successfully gapped: 25
Length of query: 191
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 100
Effective length of database: 6,901,388
Effective search space: 690138800
Effective search space used: 690138800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.2 bits)