RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy558
(692 letters)
>gnl|CDD|199822 cd10497, MH2_SMAD_1_5_9, C-terminal Mad Homology 2 (MH2) domain in
SMAD1, SMAD5 and SMAD9. The MH2 domain is located at
the C-terminus of the SMAD (small mothers against
decapentaplegic) family of proteins, which are signal
transducers and transcriptional modulators that mediate
multiple signaling pathways. The MH2 domain is
responsible for type I receptor interaction,
phosphorylation-triggered homo- and
hetero-oligomerization, and transactivation. It is
negatively regulated by the N-terminal MH1 domain, which
prevents it from forming a complex with SMAD4. SMAD1,
SMAD5 and SMAD9 (also known as SMAD8), are 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 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 = 201
Score = 404 bits (1039), Expect = e-138
Identities = 178/239 (74%), Positives = 187/239 (78%), Gaps = 39/239 (16%)
Query: 293 QEQPFWASIAYYELNSRVGEVFHCQSHSVIVDGFTNPSNNLNRFCLGQLSNVNRNSTIEN 352
QE +W SIAYYELN+RVGE FH S S+IVDGFT+PSNN +RFCLG LSNVNRNSTIEN
Sbjct: 2 QEPKYWCSIAYYELNNRVGEAFHASSTSIIVDGFTDPSNNSDRFCLGLLSNVNRNSTIEN 61
Query: 353 TRRHIGKGVHLYYVGGEVYAECLSDSAIFVQSRNCNHHHGFHQSTVCKIPAGCSLKIFNN 412
TRRHIGKGVHLYYVGGEVYAECLSDS+IFVQSRNCN+HHGFH +TVCKIP GCSLKIFNN
Sbjct: 62 TRRHIGKGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPTTVCKIPPGCSLKIFNN 121
Query: 413 QEFAELLSQSVNHGFEAVYELTKMCTISPIFCIRNKCNRTEIPFAVKVPRQFSLSVIILW 472
QEFA+LLSQSVNHGFEAVYELTKMCTI
Sbjct: 122 QEFAQLLSQSVNHGFEAVYELTKMCTI--------------------------------- 148
Query: 473 YFVLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQMGSPHQPISSVS 531
RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVL QMGSPH PISSVS
Sbjct: 149 ------RMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHNPISSVS 201
>gnl|CDD|199820 cd10495, MH2_R-SMAD, C-terminal Mad Homology 2 (MH2) domain in
receptor regulated SMADs. The MH2 domain is located at
the C-terminus of the SMAD (small mothers against
decapentaplegic) family of proteins, which are signal
transducers and transcriptional modulators that mediate
multiple signaling pathways. The MH2 domain is
responsible for type I receptor interaction,
phosphorylation-triggered homo- and
hetero-oligomerization, and transactivation. It is
negatively regulated by the N-terminal MH1 domain.
Receptor regulated SMADs (R-SMADs) include 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. SMAD5 is involved in 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 into
tendon-like cells by inhibiting the osteogenic pathway.
Length = 182
Score = 363 bits (934), Expect = e-123
Identities = 155/220 (70%), Positives = 166/220 (75%), Gaps = 39/220 (17%)
Query: 298 WASIAYYELNSRVGEVFHCQSHSVIVDGFTNPSNNLNRFCLGQLSNVNRNSTIENTRRHI 357
W SI+YYELNSRVGE F + S+IVDGFT+PSNN +RFCLG LSNVNRN+TIENTRRHI
Sbjct: 1 WCSISYYELNSRVGEQFKASNPSIIVDGFTDPSNNSDRFCLGLLSNVNRNATIENTRRHI 60
Query: 358 GKGVHLYYVGGEVYAECLSDSAIFVQSRNCNHHHGFHQSTVCKIPAGCSLKIFNNQEFAE 417
G+GVHL+YVGGEVYAECLSDSAIFVQSRNCN HGFH +TVCKIP GCSLKIFNNQ FA+
Sbjct: 61 GRGVHLFYVGGEVYAECLSDSAIFVQSRNCNLRHGFHPATVCKIPPGCSLKIFNNQSFAQ 120
Query: 418 LLSQSVNHGFEAVYELTKMCTISPIFCIRNKCNRTEIPFAVKVPRQFSLSVIILWYFVLI 477
LL QSVN GFEAVYELTKMCTI
Sbjct: 121 LLEQSVNRGFEAVYELTKMCTI-------------------------------------- 142
Query: 478 SRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVL 517
R+SFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVL
Sbjct: 143 -RISFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVL 181
>gnl|CDD|199826 cd10985, MH2_SMAD_2_3, C-terminal Mad Homology 2 (MH2) domain in
SMAD2 and SMAD3. The MH2 domain is located at the
C-terminus of the SMAD (small mothers against
decapentaplegic) family of proteins, which are signal
transducers and transcriptional modulators that mediate
multiple signaling pathways. The MH2 domain is
responsible for type I receptor interaction,
phosphorylation-triggered homo- and
hetero-oligomerization, and transactivation. It is
negatively regulated by the N-terminal MH1 domain. SMAD2
and SMAD3 are receptor regulated SMADs (R-SMADs). SMAD2
regulates multiple cellular processes, such as cell
proliferation, apoptosis and differentiation, while
SMAD3 modulates signals of activin and TGF-beta.
Length = 191
Score = 319 bits (819), Expect = e-106
Identities = 144/228 (63%), Positives = 162/228 (71%), Gaps = 40/228 (17%)
Query: 293 QEQPFWASIAYYELNSRVGEVFHCQSHSVIVDGFTNPSNNLNRFCLGQLSNVNRNSTIEN 352
E FW SI+YYE+N+RVGE FH S+ VDGFT+PSN+ RFCLG LSNVNRN +E
Sbjct: 4 CEPAFWCSISYYEMNTRVGETFHASQPSLTVDGFTDPSNS-ERFCLGLLSNVNRNPQVEL 62
Query: 353 TRRHIGKGVHLYYVGGEVYAECLSDSAIFVQSRNCNHHHGFHQSTVCKIPAGCSLKIFNN 412
TRRHIGKGV LYY+GGEV+AECLSDSAIFVQS NCN +G+H +TVCKIP GC+LKIFNN
Sbjct: 63 TRRHIGKGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNN 122
Query: 413 QEFAELLSQSVNHGFEAVYELTKMCTISPIFCIRNKCNRTEIPFAVKVPRQFSLSVIILW 472
QEFA LLSQSVN GFEAVY+LT+MCTI
Sbjct: 123 QEFAALLSQSVNQGFEAVYQLTRMCTI--------------------------------- 149
Query: 473 YFVLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLIQM 520
RMSFVKGWGAEY RQ VTSTPCWIE+HL+GPLQWLD+VL QM
Sbjct: 150 ------RMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDRVLTQM 191
>gnl|CDD|199819 cd00050, MH2, C-terminal Mad Homology 2 (MH2) domain. The MH2
domain is found in the SMAD (small mothers against
decapentaplegic) family of proteins and is responsible
for type I receptor interactions,
phosphorylation-triggered homo- and
hetero-oligomerization, and transactivation. It is
negatively regulated by the N-terminal MH1 domain which
prevents it from forming a complex with SMAD4. The MH2
domain is multifunctional and provides SMADs with their
specificity and selectivity, as well as transcriptional
activity. Several transcriptional co-activators and
repressors have also been reported to regulate SMAD
signaling by interacting with the MH2 domain. Mutations
in the MH2 domains of SMAD2 and especially SMAD4 have
been detected in colorectal and other human cancers.
Length = 170
Score = 294 bits (753), Expect = 2e-96
Identities = 139/210 (66%), Positives = 151/210 (71%), Gaps = 40/210 (19%)
Query: 298 WASIAYYELNSRVGEVFHCQSHSVIVDGFTNPSNNLNRFCLGQLSNVNRNSTIENTRRHI 357
W SIAYYELN+RVGE+FH S SV VDGFT+PSN +RFCLGQLSNVNRN TIE TRRHI
Sbjct: 1 WCSIAYYELNTRVGELFHVYSPSVAVDGFTDPSNG-DRFCLGQLSNVNRNETIERTRRHI 59
Query: 358 GKGVHLYYVGGEVYAECLSDSAIFVQSRNCNHHHGFHQSTVCKIPAGCSLKIFNNQEFAE 417
GKGVHLYYVGGEV+AECLSD AIFVQSRN ++ HG H TVCKIP GCS+K+F+NQEFA+
Sbjct: 60 GKGVHLYYVGGEVWAECLSDHAIFVQSRNLDYPHGRHPLTVCKIPPGCSIKVFDNQEFAQ 119
Query: 418 LLSQSVNHGFEAVYELTKMCTISPIFCIRNKCNRTEIPFAVKVPRQFSLSVIILWYFVLI 477
LL QSVN GFE VYELTKMCTI
Sbjct: 120 LLHQSVNTGFEGVYELTKMCTI-------------------------------------- 141
Query: 478 SRMSFVKGWGAEYHRQDVTSTPCWIEIHLH 507
RMSFVKGWG EYHRQD+TSTPCWIEIHLH
Sbjct: 142 -RMSFVKGWGPEYHRQDITSTPCWIEIHLH 170
>gnl|CDD|217398 pfam03166, MH2, MH2 domain. This is the MH2 (MAD homology 2)
domain found at the carboxy terminus of MAD related
proteins such as Smads. This domain is separated from
the MH1 domain by a non-conserved linker region. The MH2
domain mediates interaction with a wide variety of
proteins and provides specificity and selectivity to
Smad function and also is critical for mediating
interactions in Smad oligomers. Unlike MH1, MH2 does not
bind DNA. The well-studied MH2 domain of Smad4 is
composed of five alpha helices and three loops enclosing
a beta sandwich. Smads are involved in the propagation
of TGF-beta signals by direct association with the
TGF-beta receptor kinase which phosphorylates the last
two Ser of a conserved 'SSXS' motif located at the
C-terminus of MH2.
Length = 179
Score = 288 bits (739), Expect = 5e-94
Identities = 114/219 (52%), Positives = 133/219 (60%), Gaps = 41/219 (18%)
Query: 292 PQEQPFWASIAYYELNSRVGEVFHCQSHSVIVDGFTNPSNNLNRFCLGQLSNVNRNSTIE 351
E FW SIAYYELN+RVGE F +SV VDGFT+PSN +RFCLGQLSNVNRN IE
Sbjct: 1 YSEPEFWCSIAYYELNTRVGETFKVSGNSVTVDGFTDPSNG-DRFCLGQLSNVNRNEAIE 59
Query: 352 NTRRHIGKGVHLYYVG-GEVYAECLSDSAIFVQSRNCNHHHGFHQSTVCKIPAGCSLKIF 410
TRRHIGKGV L Y GEV+ SDS IFVQS ++ GFH TV KIP G SLK+F
Sbjct: 60 KTRRHIGKGVQLSYKADGEVWVYNRSDSPIFVQSPYLDYPAGFHPLTVHKIPPGASLKVF 119
Query: 411 NNQEFAELLSQSVNHGFEAVYELTKMCTISPIFCIRNKCNRTEIPFAVKVPRQFSLSVII 470
+ + F +LL Q+ N GFEAV +L +MCTI
Sbjct: 120 DFRLFYQLLRQASNSGFEAVDDLRRMCTI------------------------------- 148
Query: 471 LWYFVLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGP 509
R+SFVKGWG +Y RQD+TSTPCWIE+HL+ P
Sbjct: 149 --------RISFVKGWGEDYPRQDITSTPCWIEVHLNRP 179
>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 = 274 bits (703), Expect = 2e-89
Identities = 114/124 (91%), Positives = 120/124 (96%)
Query: 1 FTSPAVKKLLGWKQGDEEEKWAEKAVDSLVKKLKKSKGDIEELERALSCPGQPSKCVTIP 60
FTSPAVK+LLGWKQGDEEEKWAEKAVDSLVKKLKK KG +EELE+ALSCPGQPSKCVTIP
Sbjct: 1 FTSPAVKRLLGWKQGDEEEKWAEKAVDSLVKKLKKKKGALEELEKALSCPGQPSKCVTIP 60
Query: 61 RSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYK 120
RSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLE C+FPF +KQK+VCINPYHYK
Sbjct: 61 RSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLECCEFPFGSKQKEVCINPYHYK 120
Query: 121 RVES 124
RVES
Sbjct: 121 RVES 124
Score = 138 bits (348), Expect = 2e-38
Identities = 58/87 (66%), Positives = 66/87 (75%), Gaps = 9/87 (10%)
Query: 508 GPLQWLDKVLIQMGSPHQPIS---------SVSHRKGLPHVIYCRVWRWPDLQSHHELKP 558
G L+ L+K L G P + ++ VSHRKGLPHVIYCRVWRWPDLQSHHELKP
Sbjct: 38 GALEELEKALSCPGQPSKCVTIPRSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKP 97
Query: 559 LEHCQFPFSAKQKDVCINPYHYKRVES 585
LE C+FPF +KQK+VCINPYHYKRVES
Sbjct: 98 LECCEFPFGSKQKEVCINPYHYKRVES 124
>gnl|CDD|197770 smart00524, DWB, Domain B in dwarfin family proteins.
Length = 171
Score = 265 bits (680), Expect = 2e-85
Identities = 101/211 (47%), Positives = 125/211 (59%), Gaps = 40/211 (18%)
Query: 297 FWASIAYYELNSRVGEVFHCQSHSVIVDGFTNPSNNLNRFCLGQLSNVNRNSTIENTRRH 356
W IAYYELN+RVGE F S SV VDGFT+PS+ NRFCLGQLSNVNRN E R+H
Sbjct: 1 SWCKIAYYELNTRVGETFKVSSPSVTVDGFTDPSDG-NRFCLGQLSNVNRNEATELIRKH 59
Query: 357 IGKGVHLYYVGGEVYAECLSDSAIFVQSRNCNHHHGFHQSTVCKIPAGCSLKIFNNQEFA 416
IGKGV L Y G+V+ SDS IFVQS + G TV K+P G S+K+F+ ++FA
Sbjct: 60 IGKGVQLSYENGDVWLYNRSDSPIFVQSPYLDEPGGRTLDTVHKLPPGYSIKVFDMEKFA 119
Query: 417 ELLSQSVNHGFEAVYELTKMCTISPIFCIRNKCNRTEIPFAVKVPRQFSLSVIILWYFVL 476
+LL++ + GFE VY+L +MCTI
Sbjct: 120 QLLARELAKGFEGVYDLARMCTI------------------------------------- 142
Query: 477 ISRMSFVKGWGAEYHRQDVTSTPCWIEIHLH 507
R+SFVKGWG +Y RQ +TSTPCWIE+HL+
Sbjct: 143 --RISFVKGWGPDYSRQTITSTPCWIEVHLN 171
>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 = 225 bits (574), Expect = 1e-70
Identities = 94/124 (75%), Positives = 108/124 (87%), Gaps = 4/124 (3%)
Query: 4 PAVKKLLGWKQG---DEEEKWAEKAVDSLVKKLKKSKGDIEELERALSCPGQPSKCVTIP 60
P VK+LLGWK+G EEEKWAEKAV SLVKKLKK KG +EELE+A+S ++CVTIP
Sbjct: 1 PIVKRLLGWKKGEQNGEEEKWAEKAVKSLVKKLKK-KGQLEELEKAISTQNVNTRCVTIP 59
Query: 61 RSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYK 120
RSLDGRLQVSHRKGLPHVIYCR+WRWPDLQSHHELKPLE C+F F+ K+++VCINPYHYK
Sbjct: 60 RSLDGRLQVSHRKGLPHVIYCRLWRWPDLQSHHELKPLELCEFAFNMKKEEVCINPYHYK 119
Query: 121 RVES 124
RVE+
Sbjct: 120 RVET 123
Score = 123 bits (310), Expect = 4e-33
Identities = 46/56 (82%), Positives = 53/56 (94%)
Query: 530 VSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKRVES 585
VSHRKGLPHVIYCR+WRWPDLQSHHELKPLE C+F F+ K+++VCINPYHYKRVE+
Sbjct: 68 VSHRKGLPHVIYCRLWRWPDLQSHHELKPLELCEFAFNMKKEEVCINPYHYKRVET 123
>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 = 216 bits (552), Expect = 2e-67
Identities = 84/125 (67%), Positives = 107/125 (85%), Gaps = 3/125 (2%)
Query: 2 TSPAVKKLLGWKQG--DEEEKWAEKAVDSLVKKLKKSKGDIEELERALSCPGQPSKCVTI 59
T P VK+LLGWK+G +EEKW+EKAV SLVKKLKK+ G ++ELE+A++ +KC+TI
Sbjct: 1 TPPVVKRLLGWKKGENGQEEKWSEKAVKSLVKKLKKT-GGLDELEKAITTQNSNTKCITI 59
Query: 60 PRSLDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHY 119
PRSLDGRLQVSHRKGLPHVIYCR+WRWPDLQSHHEL+ +E C++ F+ K+ +VC+NPYHY
Sbjct: 60 PRSLDGRLQVSHRKGLPHVIYCRLWRWPDLQSHHELRAIETCEYAFNLKKDEVCVNPYHY 119
Query: 120 KRVES 124
+RVE+
Sbjct: 120 QRVET 124
Score = 117 bits (294), Expect = 5e-31
Identities = 40/56 (71%), Positives = 51/56 (91%)
Query: 530 VSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKRVES 585
VSHRKGLPHVIYCR+WRWPDLQSHHEL+ +E C++ F+ K+ +VC+NPYHY+RVE+
Sbjct: 69 VSHRKGLPHVIYCRLWRWPDLQSHHELRAIETCEYAFNLKKDEVCVNPYHYQRVET 124
>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 = 212 bits (540), Expect = 1e-65
Identities = 90/122 (73%), Positives = 105/122 (86%), Gaps = 2/122 (1%)
Query: 4 PAVKKLLGWKQGDEEEKWAEKAVDSLVKKLKKSKGDIEELERALSCPG-QPSKCVTIPRS 62
P VK+LLGWKQG EEEKWA+KAV SLVKKLK+ K ++ LE+A++ G PSKCVTIPRS
Sbjct: 1 PIVKRLLGWKQGGEEEKWAKKAVKSLVKKLKE-KKQLDSLEKAITTQGGVPSKCVTIPRS 59
Query: 63 LDGRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKRV 122
LDGRLQV+HRKGLPHVIYCR+WRWPDL SHHELK LE CQF F+ K+ +VC+NPYHY+RV
Sbjct: 60 LDGRLQVAHRKGLPHVIYCRLWRWPDLHSHHELKALELCQFAFNMKKDEVCVNPYHYQRV 119
Query: 123 ES 124
ES
Sbjct: 120 ES 121
Score = 116 bits (291), Expect = 1e-30
Identities = 43/56 (76%), Positives = 50/56 (89%)
Query: 530 VSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKRVES 585
V+HRKGLPHVIYCR+WRWPDL SHHELK LE CQF F+ K+ +VC+NPYHY+RVES
Sbjct: 66 VAHRKGLPHVIYCRLWRWPDLHSHHELKALELCQFAFNMKKDEVCVNPYHYQRVES 121
>gnl|CDD|214708 smart00523, DWA, Domain A in dwarfin family proteins.
Length = 109
Score = 179 bits (456), Expect = 1e-53
Identities = 70/111 (63%), Positives = 86/111 (77%), Gaps = 3/111 (2%)
Query: 17 EEEKWAEKAVDSLVKKLKKSKGDIEELERALSCPG-QPSKCVTIPRSLDGRLQVSHRKGL 75
EEKWA+KA +SL+KKLKK + +EEL +A+ G P++CV IPRSLDGRLQV+HRKGL
Sbjct: 1 VEEKWAKKATESLLKKLKKKQ--LEELLQAVESKGGPPTRCVLIPRSLDGRLQVAHRKGL 58
Query: 76 PHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKRVESPV 126
PHV+YCR++RWPDLQS HELK L C+ F +K +VC NPYHY RVE P
Sbjct: 59 PHVLYCRLFRWPDLQSPHELKALPTCEHAFESKSDEVCCNPYHYSRVERPE 109
Score = 110 bits (278), Expect = 5e-29
Identities = 38/58 (65%), Positives = 45/58 (77%)
Query: 530 VSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKRVESPV 587
V+HRKGLPHV+YCR++RWPDLQS HELK L C+ F +K +VC NPYHY RVE P
Sbjct: 52 VAHRKGLPHVLYCRLFRWPDLQSPHELKALPTCEHAFESKSDEVCCNPYHYSRVERPE 109
>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 = 174 bits (442), Expect = 8e-52
Identities = 71/103 (68%), Positives = 85/103 (82%), Gaps = 1/103 (0%)
Query: 22 AEKAVDSLVKKLKKSKGDIEELERALSCPG-QPSKCVTIPRSLDGRLQVSHRKGLPHVIY 80
A+KAV+SL+KKLKK K +EELE A+ G P+KCVTIPRSLDGRLQV+ RKGLPHVIY
Sbjct: 1 AKKAVESLLKKLKKKKQQLEELELAVESRGGPPTKCVTIPRSLDGRLQVAGRKGLPHVIY 60
Query: 81 CRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKRVE 123
CR+WRWPDLQS HELK + C++ F +K+ +VCINPYHY RVE
Sbjct: 61 CRLWRWPDLQSQHELKAIPTCEYAFRSKKDEVCINPYHYSRVE 103
Score = 110 bits (276), Expect = 1e-28
Identities = 38/55 (69%), Positives = 46/55 (83%)
Query: 530 VSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKRVE 584
V+ RKGLPHVIYCR+WRWPDLQS HELK + C++ F +K+ +VCINPYHY RVE
Sbjct: 49 VAGRKGLPHVIYCRLWRWPDLQSQHELKAIPTCEYAFRSKKDEVCINPYHYSRVE 103
>gnl|CDD|199823 cd10498, MH2_SMAD_4, C-terminal Mad Homology 2 (MH2) domain in
SMAD4. The MH2 domain is located at the C-terminus of
the SMAD (small mothers against decapentaplegic) family
of proteins, which are signal transducers and
transcriptional modulators that mediate multiple
signaling pathways. The MH2 domain is responsible for
type I receptor interaction, phosphorylation-triggered
homo- and hetero-oligomerization, and transactivation.
It is negatively regulated by the N-terminal MH1 domain.
SMAD4, which belongs to the Dwarfin family of proteins,
is involved in many cell functions such as
differentiation, apoptosis, gastrulation, embryonic
development and the 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,
cervical cancer and pancreatic carcinoma, as well as in
juvenile polyposis syndrome.
Length = 222
Score = 176 bits (448), Expect = 6e-51
Identities = 93/226 (41%), Positives = 123/226 (54%), Gaps = 12/226 (5%)
Query: 297 FWASIAYYELNSRVGEVFHCQS--HSVIVDGFTNPSNNLNRFCLGQLSNVNRNSTIENTR 354
+W SIAY+EL+++VGE F S +V VDG+ +PS NRFCLGQLSNV+R E R
Sbjct: 3 YWCSIAYFELDTQVGETFKVPSSCPTVTVDGYVDPSG-GNRFCLGQLSNVHRTEASERAR 61
Query: 355 RHIGKGVHLYYVG-GEVYAECLSDSAIFVQSRNCNHHHGFHQ-STVCKIPAGCSLKIFN- 411
HIGKGV L G G+V+ CLSD ++FVQS + G V KI +K+F+
Sbjct: 62 LHIGKGVQLDCKGEGDVWLRCLSDHSVFVQSYYLDREAGRAPGDAVHKIYPSAYIKVFDL 121
Query: 412 NQEFAELLSQSVNHGFEAVYELTKMCTISPIFCIRNKCNRTEIPFAVKVPRQFSLSVIIL 471
Q ++ Q+ A + + P + I A+ + + V L
Sbjct: 122 RQCHRQMQQQAATAQAAAAAQAAAVAGNIP-----GPGSVGGIAPAISLSAAAGIGVDDL 176
Query: 472 WYFVLISRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVL 517
+ I RMSFVKGWG +Y RQ + TPCWIEIHLH LQ LD+VL
Sbjct: 177 RR-LCILRMSFVKGWGPDYPRQSIKETPCWIEIHLHRALQLLDEVL 221
>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 = 153 bits (389), Expect = 4e-44
Identities = 65/120 (54%), Positives = 87/120 (72%), Gaps = 2/120 (1%)
Query: 6 VKKLLGWKQGDEEEKWAEKAVDSLVKKLKKSKGDIEELERALSCPG-QPSKCVTIPRSLD 64
V L+ +QG E E +A++A++SLVKKLK + +++ L A++ G PSKCVTI R+LD
Sbjct: 7 VHSLMCHRQGGESESFAKRAIESLVKKLKDKRDELDSLITAITSNGAHPSKCVTIQRTLD 66
Query: 65 GRLQVSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKRVES 124
GRLQV+ RKG PHVIY R+WRWPDL +ELK ++ CQ+ F K VC+NPYHY+RV S
Sbjct: 67 GRLQVAGRKGFPHVIYARIWRWPDLHK-NELKHVKFCQYAFDLKCDSVCVNPYHYERVVS 125
Score = 85.6 bits (212), Expect = 7e-20
Identities = 33/56 (58%), Positives = 41/56 (73%), Gaps = 1/56 (1%)
Query: 530 VSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKRVES 585
V+ RKG PHVIY R+WRWPDL + ELK ++ CQ+ F K VC+NPYHY+RV S
Sbjct: 71 VAGRKGFPHVIYARIWRWPDLHKN-ELKHVKFCQYAFDLKCDSVCVNPYHYERVVS 125
>gnl|CDD|199821 cd10496, MH2_I-SMAD, C-terminal Mad Homology 2 (MH2) domain in
Inhibitory SMADs. The MH2 domain is located at the
C-terminus of the SMAD (small mothers against
decapentaplegic) family of proteins, which are signal
transducers and transcriptional modulators that mediate
multiple signaling pathways. The MH2 domain is
responsible for type I receptor interaction,
phosphorylation-triggered homo- and
hetero-oligomerization, and transactivation. It is
negatively regulated by the N-terminal MH1 domain, which
prevents it from forming a complex with SMAD4. SMAD6 and
SMAD7 are inhibitory SMADs (I-SMADs) that function as
negative regulators of signaling mediated by the
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 = 165
Score = 108 bits (273), Expect = 1e-27
Identities = 62/210 (29%), Positives = 87/210 (41%), Gaps = 47/210 (22%)
Query: 298 WASIAYYELNSRVGEVFHCQSHSVIVDGFTNPSNNLNRFCLGQL-SNVNRNSTIENTRRH 356
W +IAY+EL RVG ++ + +V + + + FCLG L N + + R
Sbjct: 1 WCTIAYWELRERVGRLYPVKQPAVNI---FDDLPKGDGFCLGALNRQGNASEAVARVRSK 57
Query: 357 IGKGVHLYYVGGEVYAECLSDSAIFVQSRNCNHHHGFHQSTVCKIPAGCSLKIFNNQEFA 416
IG GV L V+ S+ IFV S + + V K+P G SLK+F+ + A
Sbjct: 58 IGLGVTLSREPDGVWIYNRSEYPIFVNSPTLDSPPSRNL-LVTKVPPGYSLKVFDYERAA 116
Query: 417 ELLSQSVNHGFEAVYELTKMCTISPIFCIRNKCNRTEIPFAVKVPRQFSLSVIILWYFVL 476
L Q + F P+ P +V
Sbjct: 117 LL--QRRDDHFSPQ---------GPV-----------DPNSV------------------ 136
Query: 477 ISRMSFVKGWGAEYHRQDVTSTPCWIEIHL 506
R+SFVKGWG Y RQ +TS PCW+EI L
Sbjct: 137 --RISFVKGWGPNYSRQFITSCPCWLEILL 164
>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 = 82.5 bits (204), Expect = 5e-19
Identities = 42/113 (37%), Positives = 63/113 (55%), Gaps = 9/113 (7%)
Query: 15 GDEEEKWAEKAVDSLVKKLKKSKGDIEELERAL-SCPGQPSKCVTIPRSLDGRLQVSHRK 73
++E K +L+K+LK+ ++ L A+ S G PS CV +PR+ L++ R+
Sbjct: 9 LEQELK---SVTYALLKRLKE--RSLDVLLEAVESRGGLPSGCVMVPRT---ELRLGGRR 60
Query: 74 GLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKRVESPV 126
P ++ CR++RWPDLQ +LK L HCQ + VC NPYHY R+ P
Sbjct: 61 VPPQLLLCRLFRWPDLQHPAQLKALCHCQSFGAQDGPTVCCNPYHYSRLCGPE 113
Score = 69.8 bits (171), Expect = 2e-14
Identities = 24/51 (47%), Positives = 31/51 (60%)
Query: 537 PHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKRVESPV 587
P ++ CR++RWPDLQ +LK L HCQ + VC NPYHY R+ P
Sbjct: 63 PQLLLCRLFRWPDLQHPAQLKALCHCQSFGAQDGPTVCCNPYHYSRLCGPE 113
>gnl|CDD|199824 cd10499, MH2_SMAD_6, C-terminal Mad Homology 2 (MH2) domain in
SMAD6. The MH2 domain is located at the C-terminus of
the SMAD (small mothers against decapentaplegic) family
of proteins, which are signal transducers and
transcriptional modulators that mediate multiple
signaling pathways. The MH2 domain is responsible for
type I receptor interaction, phosphorylation-triggered
homo- and hetero-oligomerization, and transactivation.
It is negatively regulated by the N-terminal MH1 domain,
which prevents it from forming a complex with SMAD4.
SMAD6, an inhibitory or antagonistic SMAD (I-SMAD), acts
as a negative regulator of signaling mediated by the
TGF-beta superfamily of 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. SMAD6
and SMAD7 act as critical mediators for effective
TGF-beta I-mediated suppression of
Interleukin-1/Toll-like receptor (IL-1R/TLR) signaling
through simultaneous binding to Pellino-1, an adaptor
protein of interleukin-1 receptor associated kinase 1
(IRAK1), via their MH2 domains.
Length = 174
Score = 78.7 bits (194), Expect = 6e-17
Identities = 62/209 (29%), Positives = 89/209 (42%), Gaps = 46/209 (22%)
Query: 298 WASIAYYELNSRVGEVFHCQSHSVIVDGFTNPSNNLNRFCLGQLSNVNRNSTIENTRRHI 357
W S+AY+E +RVG ++ SV + F + + FCLGQL+ R+ ++ TR I
Sbjct: 10 WCSVAYWEHRTRVGRLYAVYDQSVSI--FYDLPQG-SGFCLGQLNLEQRSESVRRTRSKI 66
Query: 358 GKGVHLYYVGGEVYAECLSDSAIFVQSRNCNHHHGFHQSTVCKIPAGCSLKIFNNQEFAE 417
G G+ L V+A S+ IFV S + V K+P G S+K+F+
Sbjct: 67 GYGILLSKEPDGVWAYNRSEHPIFVNSPTLDIPGS-RTLVVRKVPPGYSIKVFD------ 119
Query: 418 LLSQSVNHGFEAVYELTKMCTISPIFCIRNKCNRTEIPFAVKVPRQFSLSVIILWYFVLI 477
YE + + + E+ P SV
Sbjct: 120 -------------YERSCLLQHTA---------EPELADGPYDPN----SV--------- 144
Query: 478 SRMSFVKGWGAEYHRQDVTSTPCWIEIHL 506
R+SF KGWG Y RQ +TS PCW+EI L
Sbjct: 145 -RISFAKGWGPCYSRQFITSCPCWLEILL 172
>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 = 77.0 bits (190), Expect = 6e-17
Identities = 39/104 (37%), Positives = 55/104 (52%), Gaps = 12/104 (11%)
Query: 24 KAVDSLVKKLKKSKGDIEELERAL-SCPGQPSKCVTIPRSLDGRLQVSHRKGLPHVIYCR 82
A +L+K+LK+ +E L +A+ S G CV +PR PHV+ C+
Sbjct: 25 AAFHALLKRLKEK--QLELLLQAVESRGGDYLACVLLPRRD-----PRSMPQDPHVLCCQ 77
Query: 83 VWRWPDLQSHHELKPLEHCQFPFSAKQKD-VCINPYHYKRVESP 125
++RWPDL+ ELK L C+ SAK VC NPYH+ R+ P
Sbjct: 78 LFRWPDLRHSSELKRLPTCE---SAKDPVYVCCNPYHWSRLCRP 118
Score = 62.8 bits (153), Expect = 6e-12
Identities = 26/62 (41%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 526 PISSVSHRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKD-VCINPYHYKRVE 584
P PHV+ C+++RWPDL+ ELK L C+ SAK VC NPYH+ R+
Sbjct: 60 PRRDPRSMPQDPHVLCCQLFRWPDLRHSSELKRLPTCE---SAKDPVYVCCNPYHWSRLC 116
Query: 585 SP 586
P
Sbjct: 117 RP 118
>gnl|CDD|199825 cd10500, MH2_SMAD_7, C-terminal Mad Homology 2 (MH2) domain in
SMAD7. The MH2 domain is located at the C-terminus of
the SMAD (small mothers against decapentaplegic) family
of proteins, which are signal transducers and
transcriptional modulators that mediate multiple
signaling pathways. The MH2 domain is responsible for
type I receptor interaction, phosphorylation-triggered
homo- and hetero-oligomerization, and transactivation.
It is negatively regulated by the N-terminal MH1 domain,
which prevents it from forming a complex with SMAD4.
SMAD7, an inhibitory or antagonistic SMAD (I-SMAD), acts
as a negative regulator of signaling mediated by the
TGF-beta superfamily of 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. SMAD7 and SMAD6 act
as critical mediators for effective TGF-beta I-mediated
suppression of Interleukin-1/Toll-like receptor
(IL-1R/TLR) signaling through simultaneous binding to
Pellino-1, an adaptor protein of interleukin-1 receptor
associated kinase 1(IRAK1), via their MH2 domains.
Altered expression of SMAD7 is often associated with
cancer, tissue fibrosis and inflammatory diseases.
Length = 171
Score = 68.5 bits (167), Expect = 2e-13
Identities = 57/213 (26%), Positives = 91/213 (42%), Gaps = 46/213 (21%)
Query: 292 PQEQPFWASIAYYELNSRVGEVFHCQSHSVIVDGFTNPSNNLNRFCLGQLSNVNRNSTIE 351
+Q W +AY+E +RVG ++ Q S+ D F + N FCLGQL++ N++ ++
Sbjct: 2 RGDQSHWCVVAYWEEKTRVGRLYSVQEPSL--DIFYDLPQG-NGFCLGQLNSDNKSQLVQ 58
Query: 352 NTRRHIGKGVHLYYVGGEVYAECLSDSAIFVQSRNCNHHHGFHQSTVCKIPAGCSLKIFN 411
R IG G+ L V+ S IF++S ++ V K+ G S+K F+
Sbjct: 59 KVRSKIGYGIQLTREVDGVWVYNRSSYPIFIKSATLDNPDS-RTLLVHKVFPGFSIKAFD 117
Query: 412 NQEFAELLSQSVNHGFEAVYELTKMCTISPIFCIRNKCNRTEIPFAVKVPRQFSLSVIIL 471
++ A L + +H F + F V++
Sbjct: 118 YEK-AYSLQRPNDHEFM---------------------QQPWTGFTVQI----------- 144
Query: 472 WYFVLISRMSFVKGWGAEYHRQDVTSTPCWIEI 504
SFVKGWG Y RQ ++S PCW+E+
Sbjct: 145 ---------SFVKGWGQCYTRQFISSCPCWLEV 168
>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 = 59.9 bits (145), Expect = 6e-11
Identities = 37/102 (36%), Positives = 57/102 (55%), Gaps = 8/102 (7%)
Query: 28 SLVKKLKKSKGDIEELERALSCPGQP-SKCVTIPRSLDGRLQVSHRKGLPHVIYCRVWRW 86
S++KKLK+ + +E L +A+ G + C+ +P LD RL LP ++ C+V+RW
Sbjct: 26 SVLKKLKERQ--LEGLLQAVESRGGARTPCLLLPARLDARLG-QQSYSLP-LLLCKVFRW 81
Query: 87 PDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKR---VESP 125
PDL+ E+K L C+ + VC NP+H R +ESP
Sbjct: 82 PDLRHSSEVKRLSCCESYGKINPELVCCNPHHLSRLCELESP 123
Score = 44.5 bits (105), Expect = 2e-05
Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 532 HRKGLPHVIYCRVWRWPDLQSHHELKPLEHCQFPFSAKQKDVCINPYHYKR---VESP 586
LP ++ C+V+RWPDL+ E+K L C+ + VC NP+H R +ESP
Sbjct: 67 QSYSLP-LLLCKVFRWPDLRHSSEVKRLSCCESYGKINPELVCCNPHHLSRLCELESP 123
>gnl|CDD|220732 pfam10401, IRF-3, Interferon-regulatory factor 3. This is the
interferon-regulatory factor 3 chain of the
hetero-dimeric structure which also contains the shorter
chain CREB-binding protein. These two subunits make up
the DRAF1 (double-stranded RNA-activated factor 1).
Viral dsRNA produced during viral transcription or
replication leads to the activation of DRAF1. The
DNA-binding specificity of DRAF1 correlates with
transcriptional induction of ISG
(interferon-alpha,beta-stimulated gene). IRF-3 preexists
in the cytoplasm of uninfected cells and translocates to
the nucleus following viral infection. Translocation of
IRF-3 is accompanied by an increase in serine and
threonine phosphorylation, and association with the CREB
coactivator occurs only after infection.
Length = 180
Score = 31.9 bits (73), Expect = 0.70
Identities = 21/99 (21%), Positives = 35/99 (35%), Gaps = 19/99 (19%)
Query: 350 IENTRR---HIGKGVHLYYVGGEVYAECLSDSAIFVQSRNCNHHHGFHQSTVCKIPAGCS 406
E TRR H+ +G+ L G +YA+ L +F K+
Sbjct: 62 REYTRRLLKHLERGLLLEVNGQGIYAKRLCQCRVFWSGPEAPGSD-----RPNKLERNVP 116
Query: 407 LKIFNNQEFAELLSQSVNHGFEAVYELTKMCTISPIFCI 445
+K+F+ Q+F L++ SP + I
Sbjct: 117 VKLFDLQQFLRELARFPEGR-----------RRSPDYTI 144
>gnl|CDD|215361 PLN02673, PLN02673, quinolinate synthetase A.
Length = 724
Score = 32.7 bits (74), Expect = 0.87
Identities = 34/130 (26%), Positives = 50/130 (38%), Gaps = 21/130 (16%)
Query: 171 SPLSSVSSPASSNNPH-SPYQSNGLPG--KAQFNFEILSNFNYLVSTETPPPAYSPPQDE 227
SP SS SS S P+ SP P + I F ++PPP D
Sbjct: 4 SPTSSSSSSFLSLLPNPSPNFRTTHPNFGSQRRIGTINPLFKSFKCIQSPPP------DS 57
Query: 228 KHGSQSPHSENAMDTGISSDVTPVPYQVTYFELLTCLMPKMNPNFE--EYPTTHIIKMNL 285
+ SP S +A V P Q T EL+ C + ++ F+ P + ++
Sbjct: 58 APSNASPFSCSA--------VAFSPSQTT--ELVPCKLQRLIKEFKSLTEPVDRVKRLLH 107
Query: 286 YSSFSPPQEQ 295
Y+S PP +
Sbjct: 108 YASLLPPLPE 117
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 31.6 bits (71), Expect = 2.0
Identities = 26/101 (25%), Positives = 31/101 (30%), Gaps = 9/101 (8%)
Query: 125 PVLPPIVVPRHSEFAPGHSLLPYQQMAEPTMPHNISYSNNGFNQPHSPLSSVSSPASSNN 184
P+ PIV P P YQQ +P P Y QP +P P
Sbjct: 743 PLFTPIVEPVQQPQQPVAPQQQYQQPQQPVAPQP-QYQQP--QQPVAPQPQYQQPQQPVA 799
Query: 185 PHSPYQSNGLPGKAQFNFEILSNFNYLVSTETPPPAYSPPQ 225
P YQ P Q ++ P P Y PQ
Sbjct: 800 PQPQYQQPQQPVAPQPQYQQPQQ------PVAPQPQYQQPQ 834
Score = 30.1 bits (67), Expect = 4.9
Identities = 24/129 (18%), Positives = 39/129 (30%), Gaps = 21/129 (16%)
Query: 129 PIVVPRHSEFAPGHSLLPYQQMAEPTMPHNISYSNNGFNQPHSPLSSVSSPASSNNPHSP 188
P++ P + Q A+P + +N QP P +PA+ P
Sbjct: 371 PVIAPAPEGYPQ------QSQYAQPAVQYN-----EPLQQPVQPQQPYYAPAAEQPAQQP 419
Query: 189 YQSNGLPGKAQFNFEILSNFNYLVSTETPPPAYSPPQDEKHGSQSPHSENAMDTGISSDV 248
Y + AQ Y P A + Q E+ QS + + +
Sbjct: 420 YYAPAPEQPAQ--------QPYYAPAPEQPVAGNAWQAEE--QQSTFAPQSTYQTEQTYQ 469
Query: 249 TPVPYQVTY 257
P + Y
Sbjct: 470 QPAAQEPLY 478
Score = 30.1 bits (67), Expect = 6.0
Identities = 21/105 (20%), Positives = 31/105 (29%), Gaps = 13/105 (12%)
Query: 122 VESPVLPPIVVPRHSEFAPGHSLLPYQQMAEPTMPHNISYSNNGFNQPHSPLSSVSSPAS 181
V+ P P ++ + P + P Q +P P QP +P P
Sbjct: 752 VQQPQQPVAPQQQYQQ--PQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQ 809
Query: 182 SNNPHSPYQSNGLPGKAQFNFEILSNFNYLVSTETPPPAYSPPQD 226
P YQ P Q ++ + P PQD
Sbjct: 810 PVAPQPQYQQPQQPVAPQPQYQ-----------QPQQPVAPQPQD 843
>gnl|CDD|165021 PHA02638, PHA02638, CC chemokine receptor-like protein;
Provisional.
Length = 417
Score = 30.8 bits (69), Expect = 2.6
Identities = 24/107 (22%), Positives = 42/107 (39%), Gaps = 17/107 (15%)
Query: 174 SSVSSPASSNNPHSPYQSNGLPGKAQFNFEILSNFNYLVSTETPPPAYSPPQDEKHGSQS 233
+++SS S++ SP + + I+S F ++ TE P S+S
Sbjct: 6 TTLSSIILSSSTLSPTTFFTIETSMDESKSIISTFTEIIPTEIPT------------SES 53
Query: 234 PHSENAMDTGISSDVTPVPYQVTY-----FELLTCLMPKMNPNFEEY 275
P + + SS + + Y Y +EL+ M P+ EY
Sbjct: 54 PSPNSNSSSSSSSSSSSITYDYEYENNITYELINIKNKCMYPSISEY 100
>gnl|CDD|191602 pfam06752, E_Pc_C, Enhancer of Polycomb C-terminus. This family
represents the C-terminus of eukaryotic enhancer of
polycomb proteins, which have roles in heterochromatin
formation. This family contains several conserved
motifs.
Length = 230
Score = 30.0 bits (67), Expect = 3.3
Identities = 29/126 (23%), Positives = 46/126 (36%), Gaps = 7/126 (5%)
Query: 124 SPVLPPIVVPRHSEFAPGHSLLPYQQMAEPTMPHNISYSNNGFNQPHSPLSSVSSPASSN 183
S P + R +PGH+ + A + NN S LS+VS+ + N
Sbjct: 112 SAGSPSGSLVR----SPGHTSTNHLVPALGPASPQVLPGNNICLSVPSHLSTVSAVSPLN 167
Query: 184 NPHSPYQSNGLPGKAQFNFEILSNFNYLVSTETPPPAYSPPQDEKHGSQSPHSENAMDTG 243
H P +P A ++ + N V TP A E H + P +
Sbjct: 168 VRHIPRTLAPVPSSA---LKLAAVANSRVPKVTPSSAIDSIARENHEPEKPALNGLAENT 224
Query: 244 ISSDVT 249
++ +VT
Sbjct: 225 VAMEVT 230
>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM3 of
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), and similar
proteins found in Metazoa. PTB is an important negative
regulator of alternative splicing in mammalian cells and
also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 also contains four RRMs. ROD1 coding
protein Rod1 is a mammalian PTB homolog of a regulator
of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It may play a role
controlling differentiation in mammals. All members in
this family contain four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 74
Score = 28.0 bits (63), Expect = 3.8
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 514 DKVLIQMGSPHQPISSVSHRKGLP 537
D LIQM P Q ++++H G+
Sbjct: 38 DTALIQMADPQQAQTALTHLNGIR 61
>gnl|CDD|219122 pfam06650, DUF1162, Protein of unknown function (DUF1162). This
family represents a conserved region within several
hypothetical eukaryotic proteins. Family members might
be vacuolar protein sorting related-proteins.
Length = 271
Score = 30.0 bits (68), Expect = 3.8
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 409 IFNNQEFAELLSQSVNHGFEAVYELTKMCTISPIFCIRNKCNRT 452
NN+ + SV+ G E Y+LTK+ TI+P + + NK +
Sbjct: 86 PSNNKYNEINVGISVSEG-EGKYKLTKIVTIAPRYILINKLSED 128
>gnl|CDD|204975 pfam12598, TBX, T-box transcription factor. This domain family is
found in eukaryotes, and is typically between 77 and 89
amino acids in length. The family is found in
association with pfam00907. There are two completely
conserved residues (S and P) that may be functionally
important. T-box genes encode transcription factors
involved in morphogenesis and organogenesis of
vertebrates and invertebrates.
Length = 91
Score = 27.8 bits (62), Expect = 5.3
Identities = 7/18 (38%), Positives = 8/18 (44%)
Query: 166 FNQPHSPLSSVSSPASSN 183
F+QP SP S P
Sbjct: 29 FDQPSSPAVSAVGPLRLK 46
Score = 27.8 bits (62), Expect = 5.3
Identities = 7/18 (38%), Positives = 8/18 (44%)
Query: 646 FNQPHSPLSSVSSPASSN 663
F+QP SP S P
Sbjct: 29 FDQPSSPAVSAVGPLRLK 46
>gnl|CDD|225953 COG3419, PilY1, Tfp pilus assembly protein, tip-associated adhesin
PilY1 [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 1036
Score = 29.8 bits (67), Expect = 6.2
Identities = 13/117 (11%), Positives = 33/117 (28%), Gaps = 3/117 (2%)
Query: 144 LLPYQQMAEPTMPHNISYSNNGFNQPHSPLSSVSSP-ASSNNPHSPYQSNGLPGKAQFNF 202
P + ++ G P + P +S + ++ Y ++ NF
Sbjct: 323 SKPNGTSPVGLNQYYLTTFYGGRCVAPRPNKNTKQPSVASQSTNAEYGADPTASSGAANF 382
Query: 203 EILSNFNYLVSTETPPPAYSPPQDEKHGSQSPHSENAMDTGISSDVTPVPYQVTYFE 259
+ +V++ + + S + S Y ++F+
Sbjct: 383 FSAPSAESMVASIKRIFSAISGYASSSAGTALSSGWINSSSGES--GSTDYLSSFFD 437
>gnl|CDD|189762 pfam00901, Orbi_VP5, Orbivirus outer capsid protein VP5.
cryoelectron microscopy indicates that VP5 is a trimer
implying that there are 360 copies of VP5 per virion.
Length = 507
Score = 29.6 bits (67), Expect = 7.0
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 6 VKKLLGW--KQGDEEEK---WAEKAVDSLVKKLKKSKGDIEELERAL 47
V K + K +EEEK EKA+ S +K +K+ ++ L +AL
Sbjct: 124 VYKFMKGEAKVEEEEEKQMEILEKALKSYLKIVKEENKSLQRLAKAL 170
>gnl|CDD|177547 PHA03164, PHA03164, hypothetical protein; Provisional.
Length = 88
Score = 27.6 bits (61), Expect = 7.1
Identities = 16/38 (42%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 215 ETPPPAYSPP--QDEKHGSQSPHSENAMDTGISSDVTP 250
TPPP+YS D G SPH EN DT + P
Sbjct: 5 RTPPPSYSEVLMMDVMDGQVSPHQEN--DTSFVECLPP 40
>gnl|CDD|236591 PRK09614, nrdF, ribonucleotide-diphosphate reductase subunit beta;
Reviewed.
Length = 324
Score = 29.0 bits (66), Expect = 9.1
Identities = 15/69 (21%), Positives = 23/69 (33%), Gaps = 24/69 (34%)
Query: 262 TCLMPKMNPNFEEYPTTHIIKMNLYSSFSPPQEQPFWASIAYYELNSRVGEVFHCQSHSV 321
MP + P+ TT + L A+IA+ E H +S+S
Sbjct: 75 NNGMPNLMPDI----TTPEEEAVL-------------ANIAFMEAV-------HAKSYSY 110
Query: 322 IVDGFTNPS 330
I +P
Sbjct: 111 IFSTLCSPE 119
>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional.
Length = 1560
Score = 29.3 bits (65), Expect = 9.9
Identities = 22/102 (21%), Positives = 37/102 (36%), Gaps = 11/102 (10%)
Query: 158 NISYSNNGFNQPHSPLSSVSSPASSNNPHSPYQSNGLPGKAQFNFEILSNFNYLVSTETP 217
N + SN + + S+P +SN ++ ++ P +N SN Y +
Sbjct: 396 NAAQSNAAQSNAGFSNAGYSNPGNSNPGYNNAPNSNTP----YNNPPNSNTPY-----SN 446
Query: 218 PPAYSPPQDEKHGSQSPHSENAMDTGISSDVT--PVPYQVTY 257
PP +PP S +P+S + S Y Y
Sbjct: 447 PPNSNPPYSNLPYSNTPYSNAPLSNAPPSSAKDHHSAYHAAY 488
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 0.432
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 34,683,845
Number of extensions: 3266188
Number of successful extensions: 3012
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2970
Number of HSP's successfully gapped: 87
Length of query: 692
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 588
Effective length of database: 6,324,786
Effective search space: 3718974168
Effective search space used: 3718974168
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 (27.7 bits)