RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11457
(315 letters)
>gnl|CDD|216028 pfam00621, RhoGEF, RhoGEF domain. Guanine nucleotide exchange
factor for Rho/Rac/Cdc42-like GTPases Also called
Dbl-homologous (DH) domain. It appears that pfam00169
domains invariably occur C-terminal to RhoGEF/DH
domains.
Length = 179
Score = 107 bits (270), Expect = 2e-28
Identities = 43/137 (31%), Positives = 74/137 (54%), Gaps = 6/137 (4%)
Query: 2 LDIHSTFNNSMKLKRKESPVVGDVGDLLLDMFDGAAGEAFQRAAATFCSRQQIALESLRE 61
L++H F ++ + +E P + +GD+ L F + +T+CS ALE L++
Sbjct: 49 LELHQEFLEELEERLEEWPDIQRIGDIFLKFAP------FFKVYSTYCSNYPRALELLKK 102
Query: 62 RRRKDSRLNAFLTEAELNPLCRRLQLKDIIPTGMLRLTKYPLLFANLAKYTVDNENELTK 121
R+K+ R FL E E +PLCR L L + + R+ +YPLL L K+T + +
Sbjct: 103 LRKKNPRFAKFLKECEASPLCRGLDLNSFLIKPVQRIPRYPLLLKELLKHTPPDHPDYED 162
Query: 122 VKRALDRSKEILNYVNQ 138
+K+AL+ KE+ + +N+
Sbjct: 163 LKKALEAIKEVASQINE 179
>gnl|CDD|214619 smart00325, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange
factor for Rho/Rac/Cdc42-like GTPases Also called
Dbl-homologous (DH) domain. It appears that PH domains
invariably occur C-terminal to RhoGEF/DH domains.
Improved coverage.
Length = 180
Score = 92.7 bits (231), Expect = 8e-23
Identities = 44/137 (32%), Positives = 73/137 (53%), Gaps = 6/137 (4%)
Query: 2 LDIHSTFNNSMKLKRKESPVVGDVGDLLLDMFDGAAGEAFQRAAATFCSRQQIALESLRE 61
+ H F + ++ + +E D + + D+F F + + +CS ALE L +
Sbjct: 50 YEFHRDFLDELEERIEEWD---DSVERIGDVFLKLEE--FFKIYSEYCSNHPDALE-LLK 103
Query: 62 RRRKDSRLNAFLTEAELNPLCRRLQLKDIIPTGMLRLTKYPLLFANLAKYTVDNENELTK 121
+ +K+ R FL E E +P CRRL L+ ++ + RLTKYPLL L K+T ++ +
Sbjct: 104 KLKKNPRFQKFLKEIESSPQCRRLTLESLLLKPVQRLTKYPLLLKELLKHTPEDHEDRED 163
Query: 122 VKRALDRSKEILNYVNQ 138
+K+AL KE+ N VN+
Sbjct: 164 LKKALKAIKELANQVNE 180
>gnl|CDD|238091 cd00160, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous
(DH) domain. It appears that PH domains invariably occur
C-terminal to RhoGEF/DH domains.
Length = 181
Score = 85.8 bits (213), Expect = 3e-20
Identities = 42/136 (30%), Positives = 70/136 (51%), Gaps = 7/136 (5%)
Query: 2 LDIHSTFNNSMKLKRKESPVVGDVGDLLLDMFDGAAGEAFQRAAATFCSRQQIALESLRE 61
+ H F S++ + +E G + D+F A F + + +CS ALE L++
Sbjct: 53 YEFHRIFLKSLEERVEEWD---KSGPRIGDVFLKLAP--FFKIYSEYCSNHPDALELLKK 107
Query: 62 RRRKDSRLNAFLTEAELNPLCRRLQLKDIIPTGMLRLTKYPLLFANLAKYTVDNENELTK 121
++ + FL +AE C RL+L+ ++ + RLTKYPLL L K+T D +
Sbjct: 108 LKKFNKFFQEFLEKAESE--CGRLKLESLLLKPVQRLTKYPLLLKELLKHTPDGHEDRED 165
Query: 122 VKRALDRSKEILNYVN 137
+K+AL+ KE+ + VN
Sbjct: 166 LKKALEAIKEVASQVN 181
>gnl|CDD|241541 cd13390, PH_LARG, Leukemia-associated Rho guanine nucleotide
exchange factor Pleckstrin homology (PH) domain. LARG
(also called RhoGEF12) belongs to regulator of G-protein
signaling (RGS) domain-containing RhoGEFs that are
RhoA-selective and directly activated by the Galpha12/13
family of heterotrimeric G proteins. RhoGEFs activate
Rho GTPases regulating cytoskeletal structure, gene
transcription, and cell migration. LARG contains a
N-terminal extension, followed by Dbl homology (DH)-PH
domains which bind and catalyze the exchange of GDP for
GTP on RhoA in addition to a RGS domain. The active site
of RhoA adopts two distinct GDP-excluding conformations
among the four unique complexes in the asymmetric unit.
The LARG PH domain also contains a potential
protein-docking site. LARG forms a homotetramer via its
DH domains. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 149
Score = 81.6 bits (201), Expect = 5e-19
Identities = 52/167 (31%), Positives = 83/167 (49%), Gaps = 40/167 (23%)
Query: 153 QKRLDRTPFEKVDNPLVNEYRNLDLTRHKLIYEGNLQLRIATTRQKLIELYVLLLEDIIV 212
Q+RLD + ++ + P+++E+RNLDLT+ K+I+EG L ++ + K I+LY LLLEDI+V
Sbjct: 2 QRRLDLSSLKQSEYPMIDEFRNLDLTKRKMIHEGPLTWKV--NKDKTIDLYTLLLEDILV 59
Query: 213 LLQKQDDSKSFDSPSNSCEAVSSSGPPPPSSSSRVPWDSDTEAEPDPPDWTKSVPEDILR 272
LLQKQDD S + + S
Sbjct: 60 LLQKQDDRLILRCHSKILASTAESK----------------------------------H 85
Query: 273 SLSPREKKR----QEVINDRSALYLVNTSQHSAQIYDLVASSASERK 315
SP K ++V D A ++++ S++ AQIY+L+A + SE+
Sbjct: 86 IFSPIIKLSTVLVRQVATDNKAFFVISMSENGAQIYELMAQTVSEKN 132
>gnl|CDD|241542 cd13391, PH_PRG, PDZ Rho guanine nucleotide exchange factor
Pleckstrin homology (PH) domain. PRG (also called
RhoGEF11) belongs to regulator of G-protein signaling
(RGS) domain-containing RhoGEFs that are RhoA-selective
and directly activated by the Galpha12/13 family of
heterotrimeric G proteins. RhoGEFs activate Rho GTPases
regulating cytoskeletal structure, gene transcription,
and cell migration. PRG contains an N-terminal PDZ
domain, a regulators of G-protein signaling-like (RGSL)
domain, a linker region, and a C-terminal Dbl-homology
(DH) and pleckstrin-homology (PH) domains which bind and
catalyze the exchange of GDP for GTP on RhoA. As is the
case in p115-RhoGEF, it is thought that the PRG
activated by relieving autoinhibition caused by the
linker region. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 142
Score = 78.6 bits (193), Expect = 7e-18
Identities = 55/160 (34%), Positives = 87/160 (54%), Gaps = 32/160 (20%)
Query: 155 RLDRTPFEKVDNPLVNEYRNLDLTRHKLIYEGNLQLRIATTRQKLIELYVLLLEDIIVLL 214
RLD T E+ NPL E+++LDLT ++I+EG L R+ ++ K ++L+VLLLED++VLL
Sbjct: 1 RLDATALERASNPLAAEFKSLDLTTRRMIHEGPLTWRV--SKDKTLDLHVLLLEDLLVLL 58
Query: 215 QKQDDSKSFDSPSNSCEAVSSSGPPPPSSSSRVPWDSDTEAEPDPPDWTKSVPEDILRSL 274
QKQD+ C + ++ G SD++ P SV ++RS
Sbjct: 59 QKQDEKLVL-----KCHSKTAVG------------SSDSKQTFSPVLKLNSV---LIRS- 97
Query: 275 SPREKKRQEVINDRSALYLVNTSQHSAQIYDLVASSASER 314
V D+ A +++ TS+ QIY+LVA ++SE+
Sbjct: 98 ---------VATDKRAFFIICTSKLGPQIYELVALTSSEK 128
>gnl|CDD|241483 cd13329, PH_RhoGEF, Rho guanine nucleotide exchange factor
Pleckstrin homology domain. RhoGEFs belongs to
regulator of G-protein signaling (RGS) domain-containing
RhoGEFs that are RhoA-selective and directly activated
by the Galpha12/13 family of heterotrimeric G proteins.
The members here all contain Dbl homology (DH)-PH
domains. In addition some members contain N-terminal C1
(Protein kinase C conserved region 1) domains, PDZ (also
called DHR/Dlg homologous regions) domains, ANK
(ankyrin) domains, and RGS (Regulator of G-protein
signalling) domains or C-terminal ATP-synthase B
subunit. The DH-PH domains bind and catalyze the
exchange of GDP for GTP on RhoA. RhoGEF2/Rho guanine
nucleotide exchange factor 2, p114RhoGEF/p114 Rho
guanine nucleotide exchange factor, p115RhoGEF,
p190RhoGEF, PRG/PDZ Rho guanine nucleotide exchange
factor, RhoGEF 11, RhoGEF 12, RhoGEF 18, AKAP13/A-kinase
anchoring protein 13, and LARG/Leukemia-associated Rho
guanine nucleotide exchange factor are in this cd. PH
domains have diverse functions, but in generally are
involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from other
PIP-binding domains by their specific high-affinity
binding to PIPs with two vicinal phosphate groups:
PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which
results in targeting some PH domain proteins to the
plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 101
Score = 68.8 bits (169), Expect = 8e-15
Identities = 36/134 (26%), Positives = 64/134 (47%), Gaps = 40/134 (29%)
Query: 184 YEGNLQLRIATTRQKLIELYVLLLEDIIVLLQKQDDSKSFDSPSNSCEAVSSSGPPPPSS 243
+EG L + R K +E++V+LL D++VLLQ+QDD + + S +V S
Sbjct: 1 HEGPLTWKQ--ARGKTVEVHVVLLTDVLVLLQEQDDKYTLKFLTGSKASVVS-------- 50
Query: 244 SSRVPWDSDTEAEPDPPDWTKSVPED--ILRSLSPREKKRQEVINDRSALYLVNTSQHSA 301
+ + + ++R ++ +K A +L++TS++
Sbjct: 51 ------------------LSPLIKLEKALVRHVATDKK----------AFFLISTSKNGP 82
Query: 302 QIYDLVASSASERK 315
Q+Y+LVA+S SERK
Sbjct: 83 QMYELVANSPSERK 96
>gnl|CDD|241543 cd13392, PH_AKAP13, A-kinase anchoring protein 13 Pleckstrin
homology (PH) domain. The Rho-specific GEF activity of
AKAP13 (also called Brx-1, AKAP-Lbc, and proto-Lbc)
mediates signaling downstream of G-protein coupled
receptors and Toll-like receptor 2. It plays a role in
cell growth, cell development and actin fiber formation.
Protein kinase A (PKA) binds and phosphorylates AKAP13,
regulating its Rho-GEF activity. Alternative splicing of
this gene in humans has at least 3 transcript variants
encoding different isoforms (i.e. proto-/onco-Lymphoid
blast crisis, Lbc and breast cancer nuclear
receptor-binding auxiliary protein, Brx) containing a
dbl oncogene homology (DH) domain and PH domain which
are required for full transforming activity. The DH
domain is associated with guanine nucleotide exchange
activation while the PH domain has multiple functions
including determine protein sub-cellular localisation
via phosphoinositide interactions, while others bind
protein partners. Other ligands include protein kinase C
which is bound by the PH domain of AKAP13, serving to
activate protein kinase D and mobilize a cardiac
hypertrophy signaling pathway. PH domains have diverse
functions, but in general are involved in targeting
proteins to the appropriate cellular location or in the
interaction with a binding partner. They share little
sequence conservation, but all have a common fold, which
is electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 157
Score = 48.4 bits (115), Expect = 5e-07
Identities = 30/96 (31%), Positives = 49/96 (51%), Gaps = 4/96 (4%)
Query: 130 KEILNYVNQAVKEAEDQHRLAEIQKRLDRTPFEKVDNPLVNEYRNLDLTRHKLIYEGNLQ 189
K+++ V+ V E + RL EI R D ++ + + + DL R KL+ +G L
Sbjct: 5 KDVIAAVDSKVSNYEKKKRLKEIYGRTDSKSIMRMKSGQM--FAREDLKRRKLVRDGPLS 62
Query: 190 LRIATTRQKLIELYVLLLEDIIVLLQKQDDSKSFDS 225
L+ R K ++ +LL DI+V LQ++D F S
Sbjct: 63 LKNTAGRLK--DVQAVLLSDILVFLQEKDQKYVFAS 96
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 44.9 bits (106), Expect = 4e-05
Identities = 47/189 (24%), Positives = 87/189 (46%), Gaps = 16/189 (8%)
Query: 4 IHSTFNNSMKLKRKESPVVGDVGDLLLDMFDGAAGEAFQRAAATFCSRQQIALESLRERR 63
++S ++ ++ SP+V + D+ LD E F + A Q + ER
Sbjct: 542 VNSKLLKALTNRQCLSPIVNGIADIFLDYV--PKFEPFIKYGA-----SQPYAKYEFERE 594
Query: 64 RKDSRLNA-FLTEAELNPLCRRLQLKDIIPTGMLRLTKYPLLFANLAKYTVDNENELTKV 122
+ + A F E E R+L+L + RL +YPLL + K+T + + +
Sbjct: 595 KSVNPNFARFDHEVERLDESRKLELDGYLTKPTTRLARYPLLLEEVLKFTDPDNPDTEDI 654
Query: 123 KRALDRSKEILNYVNQAVKEAEDQHRLAEIQKRLDRTPFEKVDNPLVNEYRNLDLTRHKL 182
+ +D +E L+ +N +AE++ L + ++L P E V+ L +EYR K+
Sbjct: 655 PKVIDMLREFLSRLNFESGKAENRGDLFHLNQQLLFKP-EYVNLGLNDEYR-------KI 706
Query: 183 IYEGNLQLR 191
I++G L+ +
Sbjct: 707 IFKGVLKRK 715
Score = 33.3 bits (76), Expect = 0.18
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 256 EPDPPDWTKSVPEDILRSLSPREKKRQEVI 285
+ + WT SVP+++ SL +E KRQE I
Sbjct: 460 DEEKNLWTLSVPKEVWESLPKQEIKRQEAI 489
>gnl|CDD|241544 cd13393, PH_RhoGEF2, Rho guanine nucleotide exchange factor 2
Pleckstrin homology (PH) domain. RhoGEF2 acts as
guanine nucleotide exchange factor (GEF) for RhoA
GTPases. It is thought to play a role in actin
cytoskeleton reorganization in different tissues since
its activation induces formation of actin stress fibers.
RhoGEF2 contains a C1 domain followed by Dbl-homology
(DH) and pleckstrin-homology (PH) domains which bind and
catalyze the exchange of GDP for GTP on RhoA. PH domains
have diverse functions, but in generally are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 119
Score = 35.6 bits (82), Expect = 0.007
Identities = 32/136 (23%), Positives = 55/136 (40%), Gaps = 43/136 (31%)
Query: 179 RHKLIYEGNLQLRIATTRQKLIELYVLLLEDIIVLLQKQDDSKSFDSPSNSCEAVSSSGP 238
R +LI+EG L + AT R K ++ LLL D+++ LQ++D F +
Sbjct: 1 RRQLIHEGVLLWKTATGRLK--DVLALLLTDVLLFLQEKDQKYVFPTVDK---------- 48
Query: 239 PPPSSSSRVPWDSDTEAEPDPPDWTKSVPEDILRSLSPREKKRQEVINDRSALYLVNTSQ 298
PP S L+ L R EV N+ ++L++ S
Sbjct: 49 KPPVIS--------------------------LQKLIVR-----EVANEEKGMFLISASS 77
Query: 299 HSAQIYDLVASSASER 314
++Y++ +S +R
Sbjct: 78 AGPEMYEVHTASKEDR 93
>gnl|CDD|151322 pfam10873, DUF2668, Protein of unknown function (DUF2668). Members
in this family of proteins are annotated as Cysteine and
tyrosine-rich protein 1, however currently no function
is known.
Length = 154
Score = 32.9 bits (75), Expect = 0.10
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 232 AVSSSGPPPPSSSSRVPWDSDTEAEPD-PPDWTKSVPEDILRSLSP 276
A+S PPP + +D + E D PP ++ + RS P
Sbjct: 106 AISYPMAPPPYT-----YDHEMEYPTDLPPPYSPAPQASAQRSPPP 146
>gnl|CDD|218332 pfam04929, Herpes_DNAp_acc, Herpes DNA replication accessory
factor. Replicative DNA polymerases are capable of
polymerising tens of thousands of nucleotides without
dissociating from their DNA templates. The high
processivity of these polymerases is dependent upon
accessory proteins that bind to the catalytic subunit of
the polymerase or to the substrate. The Epstein-Barr
virus (EBV) BMRF1 protein is an essential component of
the viral DNA polymerase and is absolutely required for
lytic virus replication. BMRF1 is also a transactivator.
This family is predicted to have a UL42 like structure.
Length = 381
Score = 32.7 bits (75), Expect = 0.24
Identities = 15/84 (17%), Positives = 25/84 (29%), Gaps = 11/84 (13%)
Query: 209 DIIVLLQKQDDSKSFDS---------PSNSCEAVSSSGPPPPSSSSRVPWDSDTEAEPDP 259
+ V+L D S + S S P PP +S P
Sbjct: 281 SLSVVLLNADSSVEANGVEPEPTGSVSDRPRHLSSDSSPSPPDTSDSDPSTETPPPASLS 340
Query: 260 PDWTKSVPEDILRSLSPREKKRQE 283
+ + +LSP+ K+ +
Sbjct: 341 HSPPAAFERPL--ALSPKRKREGD 362
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 32.1 bits (73), Expect = 0.45
Identities = 18/84 (21%), Positives = 25/84 (29%)
Query: 218 DDSKSFDSPSNSCEAVSSSGPPPPSSSSRVPWDSDTEAEPDPPDWTKSVPEDILRSLSPR 277
S S S+S E+ + P S SR P S DP K S
Sbjct: 321 SRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRPPPPADPSSPRKRPRPSRAPSSPAA 380
Query: 278 EKKRQEVINDRSALYLVNTSQHSA 301
R R+A+ + +
Sbjct: 381 SAGRPTRRRARAAVAGRARRRDAT 404
>gnl|CDD|218439 pfam05109, Herpes_BLLF1, Herpes virus major outer envelope
glycoprotein (BLLF1). This family consists of the BLLF1
viral late glycoprotein, also termed gp350/220. It is
the most abundantly expressed glycoprotein in the viral
envelope of the Herpesviruses and is the major antigen
responsible for stimulating the production of
neutralising antibodies in vivo.
Length = 830
Score = 31.7 bits (71), Expect = 0.65
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 7/62 (11%)
Query: 225 SPSNSCEAVSSSGP-PPPSSSSRV--PWDSDTEAEPDPPDWTKSVPEDILRSLSPREKKR 281
PS + VS+ P P P ++S+V P +S T P T+ +P + SP
Sbjct: 637 VPSTT--HVSTLSPGPGPGTTSQVSGPGNSSTSRYPGEVHVTEGMPNP--NATSPSAPSG 692
Query: 282 QE 283
Q+
Sbjct: 693 QK 694
>gnl|CDD|185729 cd08988, GH43_ABN, Glycosyl hydrolase family 43. This glycosyl
hydrolase family 43 (GH43) includes mostly enzymes with
alpha-L-arabinofuranosidase (AFN; EC 3.2.1.55) and
endo-alpha-L-arabinanase (ABN; EC 3.2.1.99) activities.
These are inverting enzymes (i.e. they invert the
stereochemistry of the anomeric carbon atom of the
substrate) that have an aspartate as the catalytic
general base, a glutamate as the catalytic general acid
and another aspartate that is responsible for pKa
modulation and orienting the catalytic acid. The GH43
ABN enzymes hydrolyze alpha-1,5-L-arabinofuranoside
linkages while the ABF enzymes cleave arabinose side
chains so that the combined actions of these two enzymes
reduce arabinan to L-arabinose and/or
arabinooligosaccharides. These arabinan-degrading
enzymes are important in the food industry for efficient
production of L-arabinose from agricultural waste;
L-arabinose is often used as a bioactive sweetener. A
common structural feature of GH43 enzymes is a 5-bladed
beta-propeller domain that contains the catalytic acid
and catalytic base. A long V-shaped groove, partially
enclosed at one end, forms a single extended
substrate-binding surface across the face of the
propeller.
Length = 279
Score = 30.5 bits (69), Expect = 0.90
Identities = 11/35 (31%), Positives = 12/35 (34%)
Query: 234 SSSGPPPPSSSSRVPWDSDTEAEPDPPDWTKSVPE 268
+ G SS V W A P W K VP
Sbjct: 17 TGPGITILSSKDLVNWTYSGSAFATEPTWKKRVPP 51
>gnl|CDD|185681 cd09286, NMNAT_Eukarya, Nicotinamide/nicotinate mononucleotide
adenylyltransferase, Eukaryotic.
Nicotinamide/nicotinate mononucleotide (NMN/
NaMN)adenylyltransferase (NMNAT). NMNAT represents the
primary bacterial and eukaryotic adenylyltransferases
for nicotinamide-nucleotide and for the deamido form,
nicotinate nucleotide. It is an indispensable enzyme in
the biosynthesis of NAD(+) and NADP(+).
Nicotinamide-nucleotide adenylyltransferase synthesizes
NAD via the salvage pathway, while nicotinate-nucleotide
adenylyltransferase synthesizes the immediate precursor
of NAD via the de novo pathway. Human NMNAT displays
unique dual substrate specificity toward both NMN and
NaMN, and can participate in both de novo and salvage
pathways of NAD synthesis. This subfamily consists
strictly of eukaryotic members and includes secondary
structural elements not found in all NMNATs.
Length = 225
Score = 30.3 bits (69), Expect = 1.0
Identities = 15/42 (35%), Positives = 22/42 (52%)
Query: 108 LAKYTVDNENELTKVKRALDRSKEILNYVNQAVKEAEDQHRL 149
L K + N+ TKV+RAL R + + V E +QH+L
Sbjct: 183 LVKDWIPNDISSTKVRRALRRGMSVKYLLPDPVIEYIEQHQL 224
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 30.8 bits (70), Expect = 1.3
Identities = 34/172 (19%), Positives = 63/172 (36%), Gaps = 19/172 (11%)
Query: 50 SRQQIALESLRERRRKDSRLNAFLTEAELNPLCRRL-QLKDIIPTGMLRLTKYPLLFANL 108
+ +LRER + TE L L ++ +L + I + + + L L
Sbjct: 813 TLLNEEAANLRERL-ESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEEL 871
Query: 109 AKYTVDNENELTKVKRALDRSKEILNYVNQAVKEAEDQHRLAEIQKRLDRTPFEKVDNPL 168
NE ++ AL + L +++ ++E E + + R ++
Sbjct: 872 ESELEALLNERASLEEALALLRSELEELSEELRELESKRSELRRELEELREKLAQL---- 927
Query: 169 VNEYRNLDLTRHKLIYEGNLQLRIATTRQKLIELYVLLLEDIIVLLQKQDDS 220
L L L++RI +++L E Y L LE+ L K +D
Sbjct: 928 -----ELRLEG--------LEVRIDNLQERLSEEYSLTLEEAEALENKIEDD 966
>gnl|CDD|216066 pfam00695, vMSA, Major surface antigen from hepadnavirus.
Length = 364
Score = 29.6 bits (66), Expect = 2.3
Identities = 10/29 (34%), Positives = 13/29 (44%)
Query: 235 SSGPPPPSSSSRVPWDSDTEAEPDPPDWT 263
S PPP +S+R+ T P DW
Sbjct: 58 SGIPPPAGTSNRLGLRQPTPITPPLRDWH 86
>gnl|CDD|179361 PRK02048, PRK02048, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate
synthase; Provisional.
Length = 611
Score = 29.4 bits (66), Expect = 2.8
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 112 TVDNENELTKVKRALDRSKEILNYVNQAVKEAEDQHRLAEIQKRLDRTPFEKVDNPLV 169
T+D E + + KR +D E + Q V+EAE+ L I L + PLV
Sbjct: 37 TMDTEACVAQAKRIIDAGGEYVRLTTQGVREAEN---LMNINIGLRSQGY---MVPLV 88
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 29.5 bits (66), Expect = 3.1
Identities = 19/55 (34%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 224 DSPSNSCEAVSSSGPPPPSSSSRVPWDSDTEAEPDPPDWTKSVPEDILRSLSPRE 278
+P S E S GP PP + P + A DP D T+ D LR P E
Sbjct: 432 ATPLPSAEPGSDDGPAPPPER-QPPAPATEPAPDDPDDATRKA-LDALRERRPPE 484
>gnl|CDD|221170 pfam11696, DUF3292, Protein of unknown function (DUF3292). This
eukaryotic family of proteins has no known function.
Length = 641
Score = 29.4 bits (66), Expect = 3.3
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 231 EAVSSSGPPPPSSSSRVPWDSDTEAEPDPPDWTKSVPEDILRSLSP 276
EA ++ PPPPSSS R S + + S E+I ++ +P
Sbjct: 399 EANAAPLPPPPSSSLRKAPSSPASIDHKQLNLGAS-EEEIDQAAAP 443
>gnl|CDD|225461 COG2909, MalT, ATP-dependent transcriptional regulator
[Transcription].
Length = 894
Score = 29.3 bits (66), Expect = 3.4
Identities = 16/53 (30%), Positives = 21/53 (39%), Gaps = 4/53 (7%)
Query: 35 GAAGEAFQRAAATFCSRQQIALESLRERRRKDSRLNAFLTEAELNPLCRRLQL 87
A F + +R+QI L L E L + LTE L R L+L
Sbjct: 689 DKANAHFPQLQWRLIAREQILLGILLEAELALDELASRLTED----LNRNLRL 737
>gnl|CDD|215948 pfam00494, SQS_PSY, Squalene/phytoene synthase.
Length = 262
Score = 28.4 bits (64), Expect = 4.2
Identities = 13/64 (20%), Positives = 19/64 (29%), Gaps = 3/64 (4%)
Query: 24 DVGDLLLDMFDGAAGEAFQRAAATFCSRQQIALESLR---ERRRKDSRLNAFLTEAELNP 80
+ G + RA A R + E + D + + T AEL
Sbjct: 56 ALDAAFAGRRLGPSTHPVLRALADTVRRYGLPREPFLELIDGMEMDLEKDRYETLAELEE 115
Query: 81 LCRR 84
C R
Sbjct: 116 YCYR 119
>gnl|CDD|219404 pfam07415, Herpes_LMP2, Gammaherpesvirus latent membrane protein
(LMP2) protein. This family consists of several
Gammaherpesvirus latent membrane protein (LMP2)
proteins. Epstein-Barr virus is a human Gammaherpesvirus
that infects and establishes latency in B lymphocytes in
vivo. The latent membrane protein 2 (LMP2) gene is
expressed in latently infected B cells and encodes two
protein isoforms, LMP2A and LMP2B, that are identical
except for an additional N-terminal 119 aa cytoplasmic
domain which is present in the LMP2A isoform. LMP2A is
thought to play a key role in either the establishment
or the maintenance of latency and/or the reactivation of
productive infection from the latent state. The
significance of LMP2B and its role in pathogenesis
remain unclear.
Length = 489
Score = 28.7 bits (64), Expect = 4.7
Identities = 10/27 (37%), Positives = 10/27 (37%), Gaps = 3/27 (11%)
Query: 235 SSGPPPPSSSSRVPWDSDTEAEPDPPD 261
S P PSS WD P P D
Sbjct: 26 DSNPYYPSSFGS-SWDRPG--PPVPED 49
>gnl|CDD|234714 PRK00286, xseA, exodeoxyribonuclease VII large subunit; Reviewed.
Length = 438
Score = 27.9 bits (63), Expect = 8.0
Identities = 23/99 (23%), Positives = 49/99 (49%), Gaps = 4/99 (4%)
Query: 122 VKRALDRSKEILNYVNQAVKEAEDQHRLAEIQKRLDRTPFE---KVDNPLVNEYRNLDLT 178
++R L++ ++ L+ + + +K + LA+ Q+RLDR ++ L + L+
Sbjct: 280 MRRRLEQKRQRLDQLARRLKFQSPERLLAQQQQRLDRLQQRLQRALERRLRLAKQRLERL 339
Query: 179 RHKLIYEGNLQLRIATTRQKLIELYVLLLEDIIVLLQKQ 217
+L + N Q RI +Q+L +L L + L+++
Sbjct: 340 SQRLQQQ-NPQRRIERAQQRLEQLEQRLRRAMRRQLKRK 377
>gnl|CDD|236365 PRK09041, motB, flagellar motor protein MotB; Validated.
Length = 317
Score = 27.6 bits (62), Expect = 8.6
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 16/59 (27%)
Query: 138 QAVKEAEDQHRLAEIQKRLDRTPFEKVD-NPLVNEYRN---LDLTRHKLIYEGNLQLRI 192
Q KE +Q RL ++++ LD + ++ NP + +++ +DLT+ EG LRI
Sbjct: 108 QGEKERREQERLEKLKQELD----QAIESNPKLRQFKPQLLIDLTQ-----EG---LRI 154
>gnl|CDD|143482 cd00622, PLPDE_III_ODC, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Ornithine Decarboxylase. This
subfamily is composed mainly of eukaryotic ornithine
decarboxylases (ODC, EC 4.1.1.17) and ODC-like enzymes
from prokaryotes represented by Vibrio vulnificus
LysineOrnithine decarboxylase. These are fold type III
PLP-dependent enzymes that differ from most bacterial
ODCs which are fold type I PLP-dependent enzymes. ODC
participates in the formation of putrescine by
catalyzing the decarboxylation of ornithine, the first
step in polyamine biosynthesis. Members of this
subfamily contain an N-terminal PLP-binding TIM-barrel
domain and a C-terminal beta-sandwich domain, similar to
bacterial alanine racemases. They exist as homodimers
with active sites that lie at the interface between the
TIM barrel domain of one subunit and the beta-sandwich
domain of the other subunit. Homodimer formation and the
presence of the PLP cofactor are required for catalytic
activity. Also members of this subfamily are proteins
with homology to ODC but do not possess any catalytic
activity, the Antizyme inhibitor (AZI) and ODC-paralogue
(ODC-p). AZI binds to the regulatory protein Antizyme
with a higher affinity than ODC and prevents ODC
degradation. ODC-p is a novel ODC-like protein, present
only in mammals, that is specifically exressed in the
brain and testes. ODC-p may function as a
tissue-specific antizyme inhibitory protein.
Length = 362
Score = 27.5 bits (62), Expect = 9.0
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 110 KYTVDNENELTKVKRALDRSK 130
+T D+E+EL K+ + +K
Sbjct: 94 LFTFDSEDELEKIAKHAPGAK 114
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 0.131 0.364
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,919,893
Number of extensions: 1549397
Number of successful extensions: 1500
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1479
Number of HSP's successfully gapped: 71
Length of query: 315
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 218
Effective length of database: 6,635,264
Effective search space: 1446487552
Effective search space used: 1446487552
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: 42 (22.0 bits)
S2: 59 (26.5 bits)