RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8244
(163 letters)
>gnl|CDD|199813 cd10489, MH1_SMAD_6_7, N-terminal Mad Homology 1 (MH1) domain in
SMAD6 and SMAD7. The MH1 is a small DNA-binding domain
present in SMAD (small mothers against decapentaplegic)
family of proteins, which are signal transducers and
transcriptional modulators that mediate multiple
signaling pathways. MH1 binds to the DNA major groove
in an unusual manner via a beta hairpin structure. It
negatively regulates the functions of the MH2 domain,
the C-terminal domain of SMAD. This MH1 domain is found
in SMAD6 and SMAD7, both inhibitory SMADs (I-SMADs) and
negative regulators of signaling mediated by TGF-beta
superfamily. SMAD6 specifically inhibits bone
morphogenetic protein (BMP) type I receptor mediated
signaling while SMAD7 enhances muscle differentiation
and is often associated with cancer, tissue fibrosis and
inflammatory diseases.
Length = 119
Score = 96.7 bits (241), Expect = 1e-26
Identities = 46/98 (46%), Positives = 60/98 (61%), Gaps = 12/98 (12%)
Query: 30 RHTLIKRLKDSELETLVEAIESHGTNMSPCILLPSHLLPNA----HFLCCQLWRWPDVSE 85
H L+KRLK+ +LE L++A+ES G + C+LLP + H LCCQL+RWPD+
Sbjct: 27 FHALLKRLKEKQLELLLQAVESRGGDYLACVLLPRRDPRSMPQDPHVLCCQLFRWPDLRH 86
Query: 86 PYELKKLPNCDSYECSDPSPSSSDLYICCNPYHWSRRC 123
ELK+LP C S P +Y+CCNPYHWSR C
Sbjct: 87 SSELKRLPTC----ESAKDP----VYVCCNPYHWSRLC 116
>gnl|CDD|217397 pfam03165, MH1, MH1 domain. The MH1 (MAD homology 1) domain is
found at the amino terminus of MAD related proteins such
as Smads. This domain is separated from the MH2 domain
by a non-conserved linker region. The crystal structure
of the MH1 domain shows that a highly conserved 11
residue beta hairpin is used to bind the DNA consensus
sequence GNCN in the major groove, shown to be vital for
the transcriptional activation of target genes. Not all
examples of MH1 can bind to DNA however. Smad2 cannot
bind DNA and has a large insertion within the hairpin
that presumably abolishes DNA binding. A basic helix
(H2) in MH1 with the nuclear localisation signal KKLKK
has been shown to be essential for Smad3 nuclear import.
Smads also use the MH1 domain to interact with
transcription factors such as Jun, TFE3, Sp1, and Runx.
Length = 103
Score = 84.7 bits (210), Expect = 4e-22
Identities = 35/104 (33%), Positives = 51/104 (49%), Gaps = 17/104 (16%)
Query: 31 HTLIKRLKD--SELETLVEAIESHGTNMSPCILLPSHLLPNA---------HFLCCQLWR 79
+L+K+LK +LE L A+ES G + C+ +P L H + C+LWR
Sbjct: 6 ESLLKKLKKKKQQLEELELAVESRGGPPTKCVTIPRSLDGRLQVAGRKGLPHVIYCRLWR 65
Query: 80 WPDVSEPYELKKLPNCDSYECSDPSPSSSDLYICCNPYHWSRRC 123
WPD+ +ELK +P C+ S +C NPYH+SR
Sbjct: 66 WPDLQSQHELKAIPTCEYAFRSKKDE------VCINPYHYSRVE 103
>gnl|CDD|214708 smart00523, DWA, Domain A in dwarfin family proteins.
Length = 109
Score = 83.2 bits (206), Expect = 2e-21
Identities = 39/102 (38%), Positives = 57/102 (55%), Gaps = 15/102 (14%)
Query: 31 HTLIKRLKDSELETLVEAIESHGTNMSPCILLP---------SHLLPNAHFLCCQLWRWP 81
+L+K+LK +LE L++A+ES G + C+L+P +H H L C+L+RWP
Sbjct: 11 ESLLKKLKKKQLEELLQAVESKGGPPTRCVLIPRSLDGRLQVAHRKGLPHVLYCRLFRWP 70
Query: 82 DVSEPYELKKLPNCDSYECSDPSPSSSDLYICCNPYHWSRRC 123
D+ P+ELK LP C+ S +CCNPYH+SR
Sbjct: 71 DLQSPHELKALPTCEHAFESKSD------EVCCNPYHYSRVE 106
>gnl|CDD|199817 cd10493, MH1_SMAD_6, N-terminal Mad Homology 1 (MH1) domain in
SMAD6. The MH1 is a small DNA-binding domain present in
SMAD (small mothers against decapentaplegic) family of
proteins, which are signal transducers and
transcriptional modulators that mediate multiple
signaling pathways. MH1 binds to the DNA major groove
in an unusual manner via a beta hairpin structure. It
negatively regulates the functions of the MH2 domain,
the C-terminal domain of SMAD. This MH1 belongs to
SMAD6, an inhibitory SMAD (I-SMAD) or antagonistic SMAD,
which acts as a negative regulator of signaling mediated
by TGF-beta superfamily ligands, by competing with SMAD4
and preventing the transcription of SMAD4's gene
products. SMAD6 specifically inhibits bone morphogenetic
protein (BMP) type I receptor mediated signaling.
Length = 113
Score = 82.1 bits (203), Expect = 5e-21
Identities = 40/99 (40%), Positives = 58/99 (58%), Gaps = 12/99 (12%)
Query: 31 HTLIKRLKDSELETLVEAIESHGTNMSPCILLPSHLL------PNAHFLCCQLWRWPDVS 84
+ L+KRLK+ L+ L+EA+ES G S C+++P L L C+L+RWPD+
Sbjct: 18 YALLKRLKERSLDVLLEAVESRGGLPSGCVMVPRTELRLGGRRVPPQLLLCRLFRWPDLQ 77
Query: 85 EPYELKKLPNCDSYECSDPSPSSSDLYICCNPYHWSRRC 123
P +LK L +C S+ D P+ +CCNPYH+SR C
Sbjct: 78 HPAQLKALCHCQSFGAQD-GPT-----VCCNPYHYSRLC 110
>gnl|CDD|199818 cd10494, MH1_SMAD_7, N-terminal Mad Homology 1 (MH1) domain in
SMAD7. The MH1 is a small DNA-binding domain present in
SMAD (small mothers against decapentaplegic) family of
proteins. It binds to the major groove in an unusual
manner via a beta hairpin structure. It negatively
regulates the functions of the MH2 domain, the
C-terminal domain of SMAD. This MH1 belongs to SMAD7, an
inhibitory SMAD (I-SMAD) or antagonistic SMAD, which
acts as a negative regulator of signaling mediated by
TGF-beta superfamily ligands, by blocking TGF-beta type
1 and activin association with the receptor as well as
access to SMAD2. SMAD7 enhances muscle differentiation,
playing pivotal roles in embryonic development and adult
homoeostasis. Altered expression of SMAD7 is often
associated with cancer, tissue fibrosis and inflammatory
diseases.
Length = 123
Score = 71.1 bits (174), Expect = 1e-16
Identities = 39/103 (37%), Positives = 64/103 (62%), Gaps = 13/103 (12%)
Query: 29 LRHTLIKRLKDSELETLVEAIESHGTNMSPCILLP----SHLLPNAH---FLCCQLWRWP 81
L H+++K+LK+ +LE L++A+ES G +PC+LLP + L ++ L C+++RWP
Sbjct: 23 LTHSVLKKLKERQLEGLLQAVESRGGARTPCLLLPARLDARLGQQSYSLPLLLCKVFRWP 82
Query: 82 DVSEPYELKKLPNCDSYECSDPSPSSSDLYICCNPYHWSRRCK 124
D+ E+K+L C+SY +P +CCNP+H SR C+
Sbjct: 83 DLRHSSEVKRLSCCESYGKINPE------LVCCNPHHLSRLCE 119
>gnl|CDD|199811 cd00049, MH1, N-terminal Mad Homology 1 (MH1) domain. The MH1 is a
small DNA-binding domain present in SMAD (small mothers
against decapentaplegic) family of proteins, which are
signal transducers and transcriptional modulators that
mediate multiple signaling pathways. MH1 binds to the
DNA major groove in an unusual manner via a beta hairpin
structure. It negatively regulates the functions of the
MH2 domain, the C-terminal domain of SMAD.
Receptor-regulated SMAD proteins (R-SMADs, including
SMAD1, SMAD2, SMAD3, SMAD5, and SMAD9) are activated by
phosphorylation by transforming growth factor (TGF)-beta
type I receptors. The active R-SMAD associates with a
common mediator SMAD (Co-SMAD or SMAD4) and other
cofactors, which together translocate to the nucleus to
regulate gene expression. The inhibitory or antagonistic
SMADs (I-SMADs, including SMAD6 and SMAD7) negatively
regulate TGF-beta signaling by competing with R-SMADs
for type I receptor or Co-SMADs. MH1 domains of R-SMAD
and SMAD4 contain a nuclear localization signal as well
as DNA-binding activity. The activated R-SMAD/SMAD4
complex then binds with very low affinity to a DNA
sequence CAGAC called SMAD-binding element (SBE) via the
MH1 domain.
Length = 121
Score = 69.9 bits (171), Expect = 3e-16
Identities = 32/102 (31%), Positives = 50/102 (49%), Gaps = 16/102 (15%)
Query: 32 TLIKRLKD-SELETLVEAIESHGTNMSPCILLP---------SHLLPNAHFLCCQLWRWP 81
+L+K+LK+ +L++L +AI + G S C+ +P +H H + C+LWRWP
Sbjct: 25 SLVKKLKEKKQLDSLEKAITTQGGVPSKCVTIPRSLDGRLQVAHRKGLPHVIYCRLWRWP 84
Query: 82 DVSEPYELKKLPNCDSYECSDPSPSSSDLYICCNPYHWSRRC 123
D+ +ELK L C +C NPYH+ R
Sbjct: 85 DLHSHHELKALELCQFAFNMKKDE------VCVNPYHYQRVE 120
>gnl|CDD|199816 cd10492, MH1_SMAD_4, N-terminal Mad Homology 1 (MH1) domain in
SMAD4. The MH1 is a small DNA-binding domain present in
SMAD (small mothers against decapentaplegic) family of
proteins, which are signal transducers and
transcriptional modulators that mediate multiple
signaling pathways. MH1 binds to the DNA major groove
in an unusual manner via a beta hairpin structure. It
negatively regulates the functions of the MH2 domain,
the C-terminal domain of SMAD. This MH1 belongs to
SMAD4, a common mediator SMAD (co-SMAD), which belongs
to the Dwarfin family of proteins and is involved in
many cell functions such as differentiation, apoptosis,
gastrulation, embryonic development and cell cycle.
SMAD4 binds receptor regulated SMADs (R-SMADs) such as
SMAD1 or SMAD2, and forms an oligomeric complex that
binds to DNA and serves as a transcription factor. SMAD4
is often mutated in several cancers, such as multiploid
colorectal cancer and pancreatic carcinoma, as well as
in juvenile polyposis syndrome (JPS).
Length = 125
Score = 55.2 bits (133), Expect = 2e-10
Identities = 34/103 (33%), Positives = 52/103 (50%), Gaps = 22/103 (21%)
Query: 32 TLIKRLKDS--ELETLVEAIESHGTNMSPCILLPSHL-----------LPNAHFLCCQLW 78
+L+K+LKD EL++L+ AI S+G + S C+ + L P H + ++W
Sbjct: 29 SLVKKLKDKRDELDSLITAITSNGAHPSKCVTIQRTLDGRLQVAGRKGFP--HVIYARIW 86
Query: 79 RWPDVSEPYELKKLPNCDSYECSDPSPSSSDLYICCNPYHWSR 121
RWPD+ + ELK + C D S +C NPYH+ R
Sbjct: 87 RWPDLHK-NELKHVKFCQY--AFDLKCDS----VCVNPYHYER 122
>gnl|CDD|199815 cd10491, MH1_SMAD_2_3, N-terminal Mad Homology 1 (MH1) domain in
SMAD2 and SMAD3. The MH1 is a small DNA-binding domain
present in SMAD (small mothers against decapentaplegic)
family of proteins, which are signal transducers and
transcriptional modulators that mediate multiple
signaling pathways. MH1 binds to the DNA major groove
in an unusual manner via a beta hairpin structure. It
negatively regulates the functions of the MH2 domain,
the C-terminal domain of SMAD. This MH1 is found in
SMAD2 as well as SMAD3. SMAD2 mediates the signal of the
transforming growth factor (TGF)-beta, and thereby
regulates multiple cellular processes, such as cell
proliferation, apoptosis, and differentiation. It plays
a role in the transmission of extracellular signals from
ligands of the TGF-beta superfamily growth factors into
the cell nucleus. SMAD3 modulates signals of activin and
TGF-beta. It binds SMAD4, enabling its transmigration
into the nucleus where it forms complexes with other
proteins and acts as a transcription factor. Increased
SMAD3 activity has been implicated in the pathogenesis
of scleroderma.
Length = 124
Score = 51.0 bits (122), Expect = 6e-09
Identities = 32/102 (31%), Positives = 53/102 (51%), Gaps = 21/102 (20%)
Query: 32 TLIKRLKDS-ELETLVEAIESHGTNMSPCILLPSHL-----------LPNAHFLCCQLWR 79
+L+K+LK + L+ L +AI + +N + CI +P L LP H + C+LWR
Sbjct: 29 SLVKKLKKTGGLDELEKAITTQNSN-TKCITIPRSLDGRLQVSHRKGLP--HVIYCRLWR 85
Query: 80 WPDVSEPYELKKLPNCDSYECSDPSPSSSDLYICCNPYHWSR 121
WPD+ +EL+ + C+ + + +C NPYH+ R
Sbjct: 86 WPDLQSHHELRAIETCEY------AFNLKKDEVCVNPYHYQR 121
>gnl|CDD|199814 cd10490, MH1_SMAD_1_5_9, N-terminal Mad Homology 1 (MH1) domain in
SMAD1, SMAD5 and SMAD9 (also known as SMAD8). The MH1
is a small DNA-binding domain present in SMAD (small
mothers against decapentaplegic) family of proteins,
which are signal transducers and transcriptional
modulators that mediate multiple signaling pathways. MH1
binds to the DNA major groove in an unusual manner via a
beta hairpin structure. It negatively regulates the
functions of the MH2 domain, the C-terminal domain of
SMAD. This MH1 domain is found in SMAD1, SMAD5 and
SMAD9, all closely related receptor regulated SMADs
(R-SMADs). SMAD1 plays an essential role in bone
development and postnatal bone formation through
activation by bone morphogenetic protein (BMP) type 1
receptor kinase. SMAD5 is involved in bone morphogenetic
proteins (BMP) signal modulation and may also play a
role in the pathway involving inhibition of
hematopoietic progenitor cells by TGF-beta. SMAD9
mediates the differentiation of mesenchymal stem cells
(MSCs) into tendon-like cells by inhibiting the
osteogenic pathway.
Length = 124
Score = 50.6 bits (121), Expect = 8e-09
Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 18/101 (17%)
Query: 32 TLIKRLKDSE--LETLVEAIESHGTNMSPCILLP---------SHLLPNAHFLCCQLWRW 80
+L+K+LK + LE L +A+ S S C+ +P SH H + C++WRW
Sbjct: 28 SLVKKLKKKKGALEELEKAL-SCPGQPSKCVTIPRSLDGRLQVSHRKGLPHVIYCRVWRW 86
Query: 81 PDVSEPYELKKLPNCDSYECSDPSPSSSDLYICCNPYHWSR 121
PD+ +ELK L C+ S +C NPYH+ R
Sbjct: 87 PDLQSHHELKPLECCEF------PFGSKQKEVCINPYHYKR 121
>gnl|CDD|199812 cd10488, MH1_R-SMAD, N-terminal Mad Homology 1 (MH1) domain of
receptor regulated SMADs. The MH1 is a small
DNA-binding domain present in SMAD (small mothers
against decapentaplegic) family of proteins, which are
signal transducers and transcriptional modulators that
mediate multiple signaling pathways. It binds to the
major groove in an unusual manner via a beta hairpin
structure. It negatively regulates the functions of the
MH2 domain, the C-terminal domain of SMAD. This MH1
domain is found in all receptor regulated SMADs
(R-SMADs) including SMAD1, SMAD2, SMAD3, SMAD5 and
SMAD9. SMAD1 plays an essential role in bone development
and postnatal bone formation through activation by bone
morphogenetic protein (BMP) type 1 receptor kinase.
SMAD2 regulates multiple cellular processes, such as
cell proliferation, apoptosis and differentiation, while
SMAD3 modulates signals of activin and TGF-beta. SMAD4,
a common mediator SMAD (co-SMAD) binds R-SMADs, forming
an oligomeric complex that binds to DNA and serves as a
transcription factor. SMAD5 is involved in bone
morphogenetic proteins (BMP) signal modulation, possibly
playing a role in the pathway involving inhibition of
hematopoietic progenitor cells by TGF-beta. SMAD9 (also
known as SMAD8) can mediate the differentiation of
mesenchymal stem cells (MSCs) into tendon-like cells by
inhibiting the osteogenic pathway.
Length = 123
Score = 50.7 bits (121), Expect = 9e-09
Identities = 34/102 (33%), Positives = 52/102 (50%), Gaps = 21/102 (20%)
Query: 32 TLIKRLK-DSELETLVEAIESHGTNMSPCILLPSHL-----------LPNAHFLCCQLWR 79
+L+K+LK +LE L +AI + N + C+ +P L LP H + C+LWR
Sbjct: 28 SLVKKLKKKGQLEELEKAISTQNVN-TRCVTIPRSLDGRLQVSHRKGLP--HVIYCRLWR 84
Query: 80 WPDVSEPYELKKLPNCDSYECSDPSPSSSDLYICCNPYHWSR 121
WPD+ +ELK L E + + + +C NPYH+ R
Sbjct: 85 WPDLQSHHELKPL------ELCEFAFNMKKEEVCINPYHYKR 120
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 30.0 bits (67), Expect = 0.61
Identities = 9/34 (26%), Positives = 12/34 (35%)
Query: 17 KTLDEVPYYESLLRHTLIKRLKDSELETLVEAIE 50
V YYE +R + EL +L E
Sbjct: 1622 TDEGRVKYYERFIRKPVFVFCCYPELASLRNIYE 1655
>gnl|CDD|218114 pfam04501, Baculo_VP39, Baculovirus major capsid protein VP39.
This family constitutes the 39 kDa major capsid protein
of the Baculoviridae.
Length = 300
Score = 28.1 bits (63), Expect = 2.1
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 4/33 (12%)
Query: 94 NCDSY--ECSDPSPSSSDLYICCNPYHWSRRCK 124
C +Y CS + + +IC YH SRR K
Sbjct: 27 ACRTYGSPCSSDASNDDGWFIC--NYHLSRRFK 57
>gnl|CDD|223621 COG0547, TrpD, Anthranilate phosphoribosyltransferase [Amino acid
transport and metabolism].
Length = 338
Score = 27.5 bits (62), Expect = 3.3
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 4/40 (10%)
Query: 19 LDEVPYYESLLRHTLIKRLKDSELETLVEAIESHGTNMSP 58
LDEV + TL+ LKD E+ E G +P
Sbjct: 226 LDEV----TPTGTTLVAELKDGEIREYTLTPEDFGLERAP 261
>gnl|CDD|236097 PRK07788, PRK07788, acyl-CoA synthetase; Validated.
Length = 549
Score = 27.6 bits (62), Expect = 3.9
Identities = 8/47 (17%), Positives = 14/47 (29%)
Query: 20 DEVPYYESLLRHTLIKRLKDSELETLVEAIESHGTNMSPCILLPSHL 66
++ + + S ETL + I T P P +
Sbjct: 165 PDLGRLRAWGGNPDDDEPSGSTDETLDDLIAGSSTAPLPKPPKPGGI 211
>gnl|CDD|206313 pfam14144, DOG1, Seed dormancy control. This family of plant
proteins appears to be a highly specific controller
seed dormancy.
Length = 79
Score = 26.0 bits (58), Expect = 4.1
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 27 SLLRHTLIKRLKDSELETLVEAIESH 52
+ LR L D EL +LV+ + +H
Sbjct: 4 AELRAALNAHASDDELRSLVDKVLAH 29
>gnl|CDD|227625 COG5309, COG5309, Exo-beta-1,3-glucanase [Carbohydrate transport
and metabolism].
Length = 305
Score = 27.1 bits (60), Expect = 4.2
Identities = 8/28 (28%), Positives = 12/28 (42%)
Query: 101 SDPSPSSSDLYICCNPYHWSRRCKSVSE 128
S + +S L PY+ CKS +
Sbjct: 37 SSRASASGFLAFTLGPYNDDGTCKSADQ 64
>gnl|CDD|221296 pfam11894, DUF3414, Protein of unknown function (DUF3414). This
family of proteins are functionally uncharacterized. This
protein is found in eukaryotes. Proteins in this family
are typically between 764 to 2011 amino acids in length.
This protein has a conserved LLG sequence motif.
Length = 1612
Score = 26.9 bits (60), Expect = 6.9
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 2/47 (4%)
Query: 42 LETLVEAIESHGTNMSPCILL--PSHLLPNAHFLCCQLWRWPDVSEP 86
L +++ +E ++S + P L A+ L +L P S P
Sbjct: 982 LHSILNLLEKSLDSISGLNIDEAPPRLAELAYQLLYKLCSNPLTSGP 1028
>gnl|CDD|238589 cd01184, INT_SG2_C, INT_SG2, DNA breaking-rejoining enzymes,
integrase/recombinases subgroup 2, C-terminal catalytic
domain. The CD contains mainly predicted
integrase/recombinases and phage-related integrases.
Some have N-terminal domains, which show little sequence
similarity to each other. Members of this subgroup are
predominantly found in proteobacteria.
Length = 181
Score = 26.1 bits (58), Expect = 7.3
Identities = 10/44 (22%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 16 AKTLDEVPYYESL-----LRHTLIKRLKDSEL-ETLVEAIESHG 53
++ L ++ + RHT I L+++ + L+ AI H
Sbjct: 127 SRYLKKLGLKDKGKSFHSFRHTFITELRNAGVSRELIAAIMGHE 170
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
0.321 0.138 0.472
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,199,442
Number of extensions: 693457
Number of successful extensions: 633
Number of sequences better than 10.0: 1
Number of HSP's gapped: 616
Number of HSP's successfully gapped: 27
Length of query: 163
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 74
Effective length of database: 6,990,096
Effective search space: 517267104
Effective search space used: 517267104
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: 55 (25.0 bits)