RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4442
(655 letters)
>gnl|CDD|206020 pfam13849, Y_phosphatase_m, Myotubularin Y_phosphatase-like. This
short region is highly conserved and seems to be common
to many myotubularin proteins with protein tyrosine
pyrophosphate activity. As the family has a number of
highly conserved residues such as histidine, cysteine,
glutamine and aspartate, it is possible that this
represents a catalytic core of the active enzymatic part
of the proteins.
Length = 55
Score = 124 bits (314), Expect = 2e-34
Identities = 43/55 (78%), Positives = 49/55 (89%)
Query: 550 RSVLVHCSDGWDRTPQLVSLAEILLDPYYRTVKGFQVLVEREWLEFGHKFDDRCG 604
SVLVHCSDGWDRT QL SLA++LLDPYYRT++GFQVL+E+EWL FGH F DRCG
Sbjct: 1 SSVLVHCSDGWDRTSQLSSLAQLLLDPYYRTIEGFQVLIEKEWLSFGHPFSDRCG 55
>gnl|CDD|219103 pfam06602, Myotub-related, Myotubularin-related. This family
represents a region within eukaryotic
myotubularin-related proteins that is sometimes found
with pfam02893. Myotubularin is a dual-specific lipid
phosphatase that dephosphorylates phosphatidylinositol
3-phosphate and phosphatidylinositol (3,5)-bi-phosphate.
Mutations in gene encoding myotubularin-related proteins
have been associated with disease.
Length = 118
Score = 121 bits (306), Expect = 1e-32
Identities = 45/82 (54%), Positives = 52/82 (63%)
Query: 374 YELCETYPKYVIVPSGIDDGLLKSSADFRSNQRFPVVVWRHQKNGAVIARSSQPQVGVLG 433
YELC TYP ++VP I D LK A FRS R PV+ WRH +NGAVI R SQP VG G
Sbjct: 1 YELCPTYPAKLVVPKSISDDELKKVAKFRSRGRLPVLSWRHPENGAVIVRCSQPLVGFSG 60
Query: 434 WRKKEDEMLLEQITKAGSGGDE 455
R KEDE LL+ I KA + +
Sbjct: 61 KRCKEDEKLLQAIRKANAQSRK 82
>gnl|CDD|241496 cd13342, PH-GRAM_MTMR4, Myotubularian (MTM) related 4 protein
(MTMR4) Pleckstrin Homology-Glucosyltransferases,
Rab-like GTPase activators and Myotubularins (PH-GRAM)
domain. MTMR4 is 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 = 147
Score = 56.9 bits (137), Expect = 1e-09
Identities = 32/84 (38%), Positives = 47/84 (55%), Gaps = 7/84 (8%)
Query: 101 LYPLREPVYEHKSLVEPSIPKLNGEYYDYVGSTVDGKLCLSNYRLCHQDNNGSNASITFF 160
L+P +E V E +SL P L GE +Y+G D + +SNYRL H S
Sbjct: 16 LFPPKELVKEEESLQVP-FTVLQGEGVEYLGHANDAVIAISNYRL-HIKFKDS-----VI 68
Query: 161 NIPLGLIENVEIKEVHWLQIVCKD 184
N+PL ++E+VE +++ L I+CKD
Sbjct: 69 NVPLRMMESVESRDMFQLHIICKD 92
>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 = 55.4 bits (133), Expect = 4e-09
Identities = 32/89 (35%), Positives = 50/89 (56%), Gaps = 10/89 (11%)
Query: 101 LYPLREPVYEHKSLVEPSIPKLNGEYYDYVGSTVDGKLCLSNYRLCHQDNNGSNASITFF 160
++P ++ + E ++L P P+L+GE +YVG D + LSNYRL +
Sbjct: 17 IFPRKQLIREDENLQVP-FPELHGESTEYVGRAEDAIIALSNYRLHIKFKESV------V 69
Query: 161 NIPLGLIENVEIKEVHWLQIVCKDVTSCK 189
N+PL LIE+VE +++ L + CKD CK
Sbjct: 70 NVPLQLIESVECRDIFQLHLTCKD---CK 95
>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 = 50.1 bits (119), Expect = 2e-07
Identities = 31/89 (34%), Positives = 49/89 (55%), Gaps = 10/89 (11%)
Query: 101 LYPLREPVYEHKSLVEPSIPKLNGEYYDYVGSTVDGKLCLSNYRLCHQDNNGSNASITFF 160
L+P +E + E +SL P L GE +Y+G D + +SNYRL + + +
Sbjct: 10 LFPPKELIKEEESLQVPFT-VLQGEGVEYLGHANDAVIAISNYRLHIKFKD------SVI 62
Query: 161 NIPLGLIENVEIKEVHWLQIVCKDVTSCK 189
N+PL ++E+VE +++ L IVCKD K
Sbjct: 63 NVPLRMMESVECRDMFQLHIVCKD---SK 88
>gnl|CDD|214649 smart00404, PTPc_motif, Protein tyrosine phosphatase, catalytic
domain motif.
Length = 105
Score = 41.6 bits (98), Expect = 1e-04
Identities = 14/48 (29%), Positives = 20/48 (41%)
Query: 535 LVSAVNLAATIELESRSVLVHCSDGWDRTPQLVSLAEILLDPYYRTVK 582
L+ AV S V+VHCS G RT V++ +L +
Sbjct: 25 LLRAVKKNLNQSESSGPVVVHCSAGVGRTGTFVAIDILLQQLEAEAGE 72
>gnl|CDD|214469 smart00012, PTPc_DSPc, Protein tyrosine phosphatase, catalytic
domain, undefined specificity. Protein tyrosine
phosphatases. Homologues detected by this profile and
not by those of "PTPc" or "DSPc" are predicted to be
protein phosphatases with a similar fold to DSPs and
PTPs, yet with unpredicted specificities.
Length = 105
Score = 41.6 bits (98), Expect = 1e-04
Identities = 14/48 (29%), Positives = 20/48 (41%)
Query: 535 LVSAVNLAATIELESRSVLVHCSDGWDRTPQLVSLAEILLDPYYRTVK 582
L+ AV S V+VHCS G RT V++ +L +
Sbjct: 25 LLRAVKKNLNQSESSGPVVVHCSAGVGRTGTFVAIDILLQQLEAEAGE 72
>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 = 40.3 bits (95), Expect = 2e-04
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 9/56 (16%)
Query: 136 GKLCLSNYRLCHQDNNGSNASITFFNIPLGLIENVEI-------KEVHWLQIVCKD 184
G L L+NYRL + + + ++PLG+I VE + + L+I CKD
Sbjct: 19 GTLYLTNYRLYFKSKERDSPTE--LDVPLGVISRVEKVGGSSSGENSYGLEITCKD 72
>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 = 0.003
Identities = 18/44 (40%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 131 GSTVDGKLCLSNYRLC-HQDNNGSNASITFFNIPLGLIENVEIK 173
S V G+L L+N RLC D G + IPL IE VE +
Sbjct: 19 ISPVQGRLYLTNNRLCFRSDKFGDLTVLV---IPLADIERVEKE 59
>gnl|CDD|214725 smart00568, GRAM, domain in glucosyltransferases, myotubularins and
other putative membrane-associated proteins.
Length = 60
Score = 32.6 bits (75), Expect = 0.046
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 4/39 (10%)
Query: 134 VDGKLCLSNYRLC-HQDNNGSNASITFFNIPLGLIENVE 171
V G+L +SNYRLC + G + IPL I +E
Sbjct: 22 VQGRLYISNYRLCFRSNLPGKLTKVV---IPLADITRIE 57
>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 = 30.8 bits (70), Expect = 0.95
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 10/59 (16%)
Query: 134 VDGKLCLSNYRLCHQDNNGSNASITFFNIPLGLIENVEI--------KEVHWLQIVCKD 184
V G++ ++NYRL + + ++ +T ++PLG+I +E + + L I CKD
Sbjct: 49 VKGRVYITNYRL-YFRSLEADPVVTL-DVPLGVISRIEKMGGASSRGENSYGLDITCKD 105
>gnl|CDD|198383 cd10436, GIY-YIG_EndoII_Hpy188I_like, Catalytic GIY-YIG domain of
coliphage T4 non-specific endonuclease II, type II
restriction endonuclease R.Hpy188I, and similar
proteins. This family includes two different GIY-YIG
enzymes, coliphage T4 non-specific endonuclease II
(EndoII), and type II restriction endonuclease
R.Hpy188I. They display high sequence similarity to each
other, and both of them contain an extra N-terminal
hairpin that lacks counterparts in other GIY-YIG
enzymes. EndoII encoded by gene denA catalyzes the
initial step in degradation of host DNA, which permits
scavenging of host-derived nucleotides for phage DNA
synthesis. R.Hpy188I recognizes the unique sequence,
5'-TCNGA-3', and cleaves the DNA between nucleotides N
and G in its recognition sequence to generate a single
nucleotide 3'-overhang. EndoII binds to two DNA
substrates as an X-shaped tetrameric structure composed
as a dimer of dimers. In contrast, two subunits of
R.Hpy188I form a dimer to embrace one bound DNA.
Divalent metal-ion cofactors are required for their
catalytic events, but not for the substrates binding.
Length = 97
Score = 29.6 bits (67), Expect = 1.1
Identities = 11/52 (21%), Positives = 23/52 (44%)
Query: 129 YVGSTVDGKLCLSNYRLCHQDNNGSNASITFFNIPLGLIENVEIKEVHWLQI 180
Y+G T D + ++YR NG + + L ++ ++ E++ Q
Sbjct: 14 YIGETQDLRKRFNSYRGGISPRNGQTTNCRINKLILKALKKGKVVELYVKQP 65
>gnl|CDD|225297 COG2453, CDC14, Predicted protein-tyrosine phosphatase [Signal
transduction mechanisms].
Length = 180
Score = 30.9 bits (70), Expect = 1.3
Identities = 15/76 (19%), Positives = 24/76 (31%), Gaps = 10/76 (13%)
Query: 532 HLLLVSAVNLAATIELESRSVLVHCSDGWDRTP----------QLVSLAEILLDPYYRTV 581
L V+ + + V+VHC G R+ +SLA+ + R
Sbjct: 88 LEDLDKIVDFIEEALSKGKKVVVHCQGGIGRSGTVIAAYLMLYGGLSLADEAIAVKRRRR 147
Query: 582 KGFQVLVEREWLEFGH 597
G V + E
Sbjct: 148 PGAVVTEIQHLFELEQ 163
>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 = 28.7 bits (65), Expect = 3.0
Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 11/65 (16%)
Query: 128 DYVGSTVDGKLCLSNYRLCHQDNNGSNASITFFNIPLGLIENVE-------IKEVHW-LQ 179
+ G V G L ++NYRL + + ++PLG+I VE E + L+
Sbjct: 11 PFSGP-VKGTLYITNYRLYFK--SLERDPPFVLDVPLGVISRVEKVGGASSRGENSYGLE 67
Query: 180 IVCKD 184
IVCKD
Sbjct: 68 IVCKD 72
>gnl|CDD|219369 pfam07307, HEPPP_synt_1, Heptaprenyl diphosphate synthase (HEPPP
synthase) subunit 1. This family contains subunit 1 of
bacterial heptaprenyl diphosphate synthase (HEPPP
synthase) (EC:2.5.1.30) (approximately 230 residues
long). The enzyme consists of two subunits, both of
which are required for catalysis of heptaprenyl
diphosphate synthesis.
Length = 212
Score = 29.6 bits (67), Expect = 3.7
Identities = 7/28 (25%), Positives = 12/28 (42%)
Query: 20 ALVVMVNAALFVKLAQHTYANLFGTFLC 47
V + +ALF K A+H + +
Sbjct: 126 ESVKTIESALFAKFAEHFQLPHWKPLIS 153
>gnl|CDD|113159 pfam04378, DUF519, Protein of unknown function (DUF519). Bacterial
family of unknown function, possibly secreted. The
structure solved for the hypothetical protein Lpl1258 is
putatively involved in the catabolism of external DNA.
Length = 245
Score = 28.9 bits (65), Expect = 8.1
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 550 RSVLVHCSDGWDRT----PQLVSLAEILLDPYYRTVKGFQVLVE 589
R V VH +DG+ P +L+DP + +Q +V
Sbjct: 103 RRVRVHQADGFAALKAFLPPKERRGLVLIDPPFELKDEYQRVVA 146
>gnl|CDD|220272 pfam09508, Lact_bio_phlase, Lacto-N-biose phosphorylase. The gene
which codes for this protein in gut-bacteria is located
in a novel putative operon for galactose metabolism. The
protein appears to be a carbohydrate-processing
phosphorolytic enzyme (EC:2.4.1.211), unlike either
glycoside hydrolases or glycoside lyase. Intestinal
colonisation by bifidobacteria is important for human
health, especially in pediatrics, because colonisation
seems to prevent infection by some pathogenic bacteria
that cause diarrhoea or other illnesses. The operon
seems to be involved in intestinal colonisation by
bifidobacteria mediated by metabolism of mucin sugars.
In addition, it may also resolve the question of the
nature of the bifidus factor in human milk as the
lacto-N-biose structure found in milk oligosaccharides.
Length = 716
Score = 29.3 bits (66), Expect = 9.0
Identities = 21/110 (19%), Positives = 38/110 (34%), Gaps = 6/110 (5%)
Query: 486 FRERTLPGKDEIRSGWWKAVDGTSWRAPSNTSW-WKAVDGTSWLQNMHLLLVSAVNLAAT 544
F+E+ P D WW+ VD T+ W + + + V+ A
Sbjct: 93 FKEQFEPNDDHDPKRWWEVVDRTTGEVVPTDKWSYDPENQEVTITGAEPYHEYTVSFLAY 152
Query: 545 IELESRSVLVHCSDGWDRTPQLVSLAEILLDPYYRTVKGFQVLVEREWLE 594
+ S+ H ++ W EI DP + + + +WL+
Sbjct: 153 QIWDPVSMYNHLTNDWGDKEH-----EIPYDPRHPKTREHVLEALDQWLK 197
>gnl|CDD|217759 pfam03845, Spore_permease, Spore germination protein.
Length = 320
Score = 28.7 bits (65), Expect = 9.4
Identities = 15/66 (22%), Positives = 26/66 (39%), Gaps = 8/66 (12%)
Query: 531 MHLLLVSAVNLAATIELESRSVLVHCSDGWDRTPQLVSLAEILLDPYYRTVKGFQVLVER 590
++ L ++ L E+ +L TP + + +LL Y KG +VL R
Sbjct: 86 LYFLYLAGRVLRDFSEVLQTFLL-------PDTPTWIIILTLLLVSIYLISKGIEVLA-R 137
Query: 591 EWLEFG 596
E+
Sbjct: 138 EFCFII 143
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 0.418
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: 32,641,423
Number of extensions: 3089009
Number of successful extensions: 2004
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1999
Number of HSP's successfully gapped: 24
Length of query: 655
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 552
Effective length of database: 6,369,140
Effective search space: 3515765280
Effective search space used: 3515765280
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: 62 (27.6 bits)