RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11998
(245 letters)
>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 = 218 bits (558), Expect = 1e-72
Identities = 96/206 (46%), Positives = 112/206 (54%), Gaps = 43/206 (20%)
Query: 36 WCKLAYWELSHRVGRLYPVVTPYIHVFWAQPCGDGLCLETLATGNNSAPSGNGPHHVPDA 95
WC +AYWEL RVGRLYPV P +++F P GDG CL L N +A
Sbjct: 1 WCTIAYWELRERVGRLYPVKQPAVNIFDDLPKGDGFCLGALNRQGN----------ASEA 50
Query: 96 VRRTRTKIGLVVESRRLNPSFGAVCPYTKASGCGYVPGRDRQGLTLSLEADGVWAYNRSE 155
V R R+KIGL G+TLS E DGVW YNRSE
Sbjct: 51 VARVRSKIGL--------------------------------GVTLSREPDGVWIYNRSE 78
Query: 156 APVFVNSPGLDDPGPPTLLVYRIPPGHCLNIFDPALPPRLRE-SFPAPPTGPVDPNSIRI 214
P+FVNSP LD P LLV ++PPG+ L +FD L+ P GPVDPNS+RI
Sbjct: 79 YPIFVNSPTLDSPPSRNLLVTKVPPGYSLKVFDYERAALLQRRDDHFSPQGPVDPNSVRI 138
Query: 215 SFAKGWGPKYSRQEITACPAWLEVLL 240
SF KGWGP YSRQ IT+CP WLE+LL
Sbjct: 139 SFVKGWGPNYSRQFITSCPCWLEILL 164
>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 = 187 bits (477), Expect = 2e-60
Identities = 92/215 (42%), Positives = 113/215 (52%), Gaps = 44/215 (20%)
Query: 27 PAGERRPGEWCKLAYWELSHRVGRLYPVVTPYIHVFWAQPCGDGLCLETLATGNNSAPSG 86
+ WC +AYWE RVGRLY V + +F+ P G G CL L S
Sbjct: 1 SPDATKRSHWCSVAYWEHRTRVGRLYAVYDQSVSIFYDLPQGSGFCLGQLNLEQRS---- 56
Query: 87 NGPHHVPDAVRRTRTKIGLVVESRRLNPSFGAVCPYTKASGCGYVPGRDRQGLTLSLEAD 146
++VRRTR+KIG G+ LS E D
Sbjct: 57 -------ESVRRTRSKIGY--------------------------------GILLSKEPD 77
Query: 147 GVWAYNRSEAPVFVNSPGLDDPGPPTLLVYRIPPGHCLNIFDPALPPRLRE-SFPAPPTG 205
GVWAYNRSE P+FVNSP LD PG TL+V ++PPG+ + +FD L+ + P G
Sbjct: 78 GVWAYNRSEHPIFVNSPTLDIPGSRTLVVRKVPPGYSIKVFDYERSCLLQHTAEPELADG 137
Query: 206 PVDPNSIRISFAKGWGPKYSRQEITACPAWLEVLL 240
P DPNS+RISFAKGWGP YSRQ IT+CP WLE+LL
Sbjct: 138 PYDPNSVRISFAKGWGPCYSRQFITSCPCWLEILL 172
>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 = 145 bits (369), Expect = 7e-44
Identities = 77/216 (35%), Positives = 100/216 (46%), Gaps = 51/216 (23%)
Query: 33 PGEWCKLAYWELSHRVGRLYPVVTPYIHV-FWAQPC-GDGLCLETLATGNNSAPSGNGPH 90
P WC +AY+EL+ RVG + V + V + P GD CL L+ N +
Sbjct: 4 PEFWCSIAYYELNTRVGETFKVSGNSVTVDGFTDPSNGDRFCLGQLSNVNRNE------- 56
Query: 91 HVPDAVRRTRTKIGLVVESRRLNPSFGAVCPYTKASGCGYVPGRDRQGLTLSLEADG-VW 149
A+ +TR IG G+ LS +ADG VW
Sbjct: 57 ----AIEKTRRHIGK--------------------------------GVQLSYKADGEVW 80
Query: 150 AYNRSEAPVFVNSPGLDDP-GPPTLLVYRIPPGHCLNIFDPALPPRLRESFPAPPTGPVD 208
YNRS++P+FV SP LD P G L V++IPPG L +FD L +L VD
Sbjct: 81 VYNRSDSPIFVQSPYLDYPAGFHPLTVHKIPPGASLKVFDFRLFYQLLRQASNSGFEAVD 140
Query: 209 P----NSIRISFAKGWGPKYSRQEITACPAWLEVLL 240
+IRISF KGWG Y RQ+IT+ P W+EV L
Sbjct: 141 DLRRMCTIRISFVKGWGEDYPRQDITSTPCWIEVHL 176
>gnl|CDD|197770 smart00524, DWB, Domain B in dwarfin family proteins.
Length = 171
Score = 140 bits (355), Expect = 5e-42
Identities = 74/212 (34%), Positives = 98/212 (46%), Gaps = 50/212 (23%)
Query: 36 WCKLAYWELSHRVGRLYPVVTPYIHV--FWAQPCGDGLCLETLATGNNSAPSGNGPHHVP 93
WCK+AY+EL+ RVG + V +P + V F G+ CL L+ N +
Sbjct: 2 WCKIAYYELNTRVGETFKVSSPSVTVDGFTDPSDGNRFCLGQLSNVNRNE---------- 51
Query: 94 DAVRRTRTKIGLVVESRRLNPSFGAVCPYTKASGCGYVPGRDRQGLTLSLEADGVWAYNR 153
A R IG G+ LS E VW YNR
Sbjct: 52 -ATELIRKHIGK--------------------------------GVQLSYENGDVWLYNR 78
Query: 154 SEAPVFVNSPGLDDPGPPTL-LVYRIPPGHCLNIFDPALPPR-LRESFPAPPTGPVDPN- 210
S++P+FV SP LD+PG TL V+++PPG+ + +FD + L G D
Sbjct: 79 SDSPIFVQSPYLDEPGGRTLDTVHKLPPGYSIKVFDMEKFAQLLARELAKGFEGVYDLAR 138
Query: 211 --SIRISFAKGWGPKYSRQEITACPAWLEVLL 240
+IRISF KGWGP YSRQ IT+ P W+EV L
Sbjct: 139 MCTIRISFVKGWGPDYSRQTITSTPCWIEVHL 170
>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 = 129 bits (326), Expect = 9e-38
Identities = 66/213 (30%), Positives = 91/213 (42%), Gaps = 52/213 (24%)
Query: 36 WCKLAYWELSHRVGRLYPVVTPYIHV--FWAQPCGDGLCLETLATGNNSAPSGNGPHHVP 93
WC +AY+EL+ RVG L+ V +P + V F GD CL L+ N +
Sbjct: 1 WCSIAYYELNTRVGELFHVYSPSVAVDGFTDPSNGDRFCLGQLSNVNRN----------- 49
Query: 94 DAVRRTRTKIGLVVESRRLNPSFGAVCPYTKASGCGYVPGRDRQGLTLSLEADGVWAYNR 153
+ + RTR IG +G+ L VWA
Sbjct: 50 ETIERTRRHIG--------------------------------KGVHLYYVGGEVWAECL 77
Query: 154 SEAPVFVNSPGLDDP-GPPTLLVYRIPPGHCLNIFDPALPPRLRE-----SFPAPPTGPV 207
S+ +FV S LD P G L V +IPPG + +FD +L F
Sbjct: 78 SDHAIFVQSRNLDYPHGRHPLTVCKIPPGCSIKVFDNQEFAQLLHQSVNTGFEGVYELTK 137
Query: 208 DPNSIRISFAKGWGPKYSRQEITACPAWLEVLL 240
+IR+SF KGWGP+Y RQ+IT+ P W+E+ L
Sbjct: 138 MC-TIRMSFVKGWGPEYHRQDITSTPCWIEIHL 169
>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 = 127 bits (319), Expect = 1e-36
Identities = 76/216 (35%), Positives = 102/216 (47%), Gaps = 55/216 (25%)
Query: 33 PGE---WCKLAYWELSHRVGRLYPVVTPYIHVFWAQPCGDGLCLETLATGNNSAPSGNGP 89
G+ WC +AYWE RVGRLY V P + +F+ P G+G CL L + N S
Sbjct: 2 RGDQSHWCVVAYWEEKTRVGRLYSVQEPSLDIFYDLPQGNGFCLGQLNSDNKS------- 54
Query: 90 HHVPDAVRRTRTKIGLVVESRRLNPSFGAVCPYTKASGCGYVPGRDRQGLTLSLEADGVW 149
V++ R+KIG G+ L+ E DGVW
Sbjct: 55 ----QLVQKVRSKIGY--------------------------------GIQLTREVDGVW 78
Query: 150 AYNRSEAPVFVNSPGLDDPGPPTLLVYRIPPGHCLNIFD-----PALPPRLRESFPAPPT 204
YNRS P+F+ S LD+P TLLV+++ PG + FD P E P T
Sbjct: 79 VYNRSSYPIFIKSATLDNPDSRTLLVHKVFPGFSIKAFDYEKAYSLQRPNDHEFMQQPWT 138
Query: 205 GPVDPNSIRISFAKGWGPKYSRQEITACPAWLEVLL 240
G +++ISF KGWG Y+RQ I++CP WLEV+
Sbjct: 139 G----FTVQISFVKGWGQCYTRQFISSCPCWLEVIF 170
>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 = 90.1 bits (224), Expect = 2e-22
Identities = 60/215 (27%), Positives = 85/215 (39%), Gaps = 55/215 (25%)
Query: 36 WCKLAYWELSHRVGRLYPVVTPYIHV-FWAQPC--GDGLCLETLATGNNSAPSGNGPHHV 92
WC ++Y+EL+ RVG + P I V + P D CL L+ N +A
Sbjct: 1 WCSISYYELNSRVGEQFKASNPSIIVDGFTDPSNNSDRFCLGLLSNVNRNA--------- 51
Query: 93 PDAVRRTRTKIGLVVESRRLNPSFGAVCPYTKASGCGYVPGRDRQGLTLSLEADGVWAYN 152
+ TR IG +G+ L V+A
Sbjct: 52 --TIENTRRHIG--------------------------------RGVHLFYVGGEVYAEC 77
Query: 153 RSEAPVFVNSP--GLDDPGPPTLLVYRIPPGHCLNIFD-----PALPPRLRESFPAPPTG 205
S++ +FV S L P V +IPPG L IF+ L + F A
Sbjct: 78 LSDSAIFVQSRNCNLRHGFHPAT-VCKIPPGCSLKIFNNQSFAQLLEQSVNRGFEAV-YE 135
Query: 206 PVDPNSIRISFAKGWGPKYSRQEITACPAWLEVLL 240
+IRISF KGWG +Y RQ++T+ P W+E+ L
Sbjct: 136 LTKMCTIRISFVKGWGAEYHRQDVTSTPCWIEIHL 170
>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 = 62.3 bits (151), Expect = 6e-12
Identities = 58/224 (25%), Positives = 87/224 (38%), Gaps = 68/224 (30%)
Query: 33 PGEWCKLAYWELSHRVGRLYPVVTPYIHV--FWAQPCGDGLCLETLATGNNSAPSGNGPH 90
P WC ++Y+E++ RVG + P + V F + CL L+ N +
Sbjct: 6 PAFWCSISYYEMNTRVGETFHASQPSLTVDGFTDPSNSERFCLGLLSNVNRNPQ------ 59
Query: 91 HVPDAVRRTRTKIGLVVESRRLNPSFGAVCPYTKASGCGYVPGRDRQGLTLSLEADGVWA 150
V TR IG +G+ L V+A
Sbjct: 60 -----VELTRRHIG--------------------------------KGVRLYYIGGEVFA 82
Query: 151 YNRSEAPVFVNSPGLDDP---GPPTLLVYRIPPGHCLNIFDPALPPRLRESFPAPPTGPV 207
S++ +FV SP + P T V +IPPG L IF+ + F A + V
Sbjct: 83 ECLSDSAIFVQSPNCNQRYGWHPAT--VCKIPPGCNLKIFN-------NQEFAALLSQSV 133
Query: 208 DPN-----------SIRISFAKGWGPKYSRQEITACPAWLEVLL 240
+ +IR+SF KGWG +Y RQ +T+ P W+E+ L
Sbjct: 134 NQGFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHL 177
>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 = 60.9 bits (148), Expect = 3e-11
Identities = 61/256 (23%), Positives = 82/256 (32%), Gaps = 94/256 (36%)
Query: 33 PGEWCKLAYWELSHRVGRLYPVVTPYIHVF---WAQPCGDG-LCLETLATGNNSAPSGNG 88
P WC +AY+EL +VG + V + V + P G CL L+
Sbjct: 1 PEYWCSIAYFELDTQVGETFKVPSSCPTVTVDGYVDPSGGNRFCLGQLSN---------- 50
Query: 89 PHHVPDAVRRTRTKIGLVVESRRLNPSFGAVCPYTKASGCGYVPGRDRQGLTLSLEADG- 147
H +A R R IG +G+ L + +G
Sbjct: 51 -VHRTEASERARLHIG--------------------------------KGVQLDCKGEGD 77
Query: 148 VWAYNRSEAPVFVNSPGLDDPG--PPTLLVYRIPPGHCLNIFD----------------- 188
VW S+ VFV S LD P V++I P + +FD
Sbjct: 78 VWLRCLSDHSVFVQSYYLDREAGRAPGDAVHKIYPSAYIKVFDLRQCHRQMQQQAATAQA 137
Query: 189 ---------------------PALPPRLRESFPAPPTGPVDPN---SIRISFAKGWGPKY 224
A L A G D +R+SF KGWGP Y
Sbjct: 138 AAAAQAAAVAGNIPGPGSVGGIAPAISLSA---AAGIGVDDLRRLCILRMSFVKGWGPDY 194
Query: 225 SRQEITACPAWLEVLL 240
RQ I P W+E+ L
Sbjct: 195 PRQSIKETPCWIEIHL 210
>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 = 58.4 bits (141), Expect = 2e-10
Identities = 60/225 (26%), Positives = 89/225 (39%), Gaps = 69/225 (30%)
Query: 33 PGEWCKLAYWELSHRVGRLYPVVTPYIHV-FWAQPC--GDGLCLETLATGNNSAPSGNGP 89
P WC +AY+EL++RVG + + I V + P D CL L+ N ++
Sbjct: 4 PKYWCSIAYYELNNRVGEAFHASSTSIIVDGFTDPSNNSDRFCLGLLSNVNRNS------ 57
Query: 90 HHVPDAVRRTRTKIGLVVESRRLNPSFGAVCPYTKASGCGYVPGRDRQGLTLSLEADGVW 149
+ TR IG K YV G V+
Sbjct: 58 -----TIENTRRHIG-------------------KGVHLYYVGGE-------------VY 80
Query: 150 AYNRSEAPVFVNSPGLD---DPGPPTLLVYRIPPGHCLNIFDPALPPRLRESFPAPPTGP 206
A S++ +FV S + P T V +IPPG L IF+ + F +
Sbjct: 81 AECLSDSSIFVQSRNCNYHHGFHPTT--VCKIPPGCSLKIFN-------NQEFAQLLSQS 131
Query: 207 VDPN-----------SIRISFAKGWGPKYSRQEITACPAWLEVLL 240
V+ +IR+SF KGWG +Y RQ++T+ P W+E+ L
Sbjct: 132 VNHGFEAVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHL 176
>gnl|CDD|144222 pfam00551, Formyl_trans_N, Formyl transferase. This family
includes the following members. Glycinamide
ribonucleotide transformylase catalyzes the third step
in de novo purine biosynthesis, the transfer of a formyl
group to 5'-phosphoribosylglycinamide.
Formyltetrahydrofolate deformylase produces formate from
formyl- tetrahydrofolate. Methionyl-tRNA
formyltransferase transfers a formyl group onto the
amino terminus of the acyl moiety of the methionyl
aminoacyl-tRNA. Inclusion of the following members is
supported by PSI-blast. HOXX_BRAJA contains a related
domain of unknown function. PRTH_PORGI contains a
related domain of unknown function. Y09P_MYCTU (Q50721)
contains a related domain of unknown function.
Length = 181
Score = 27.7 bits (62), Expect = 3.9
Identities = 13/27 (48%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 170 PPTLLVYRIPPGHCLNIFDPALPPRLR 196
PP L + PG LNI P+L PR R
Sbjct: 93 PPEFL--QAFPGKILNI-HPSLLPRFR 116
>gnl|CDD|218440 pfam05110, AF-4, AF-4 proto-oncoprotein. This family consists of
AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental
retardation syndrome) nuclear proteins. These proteins
have been linked to human diseases such as acute
lymphoblastic leukaemia and mental retardation. The
family also contains a Drosophila AF4 protein homologue
Lilliputian which contains an AT-hook domain.
Lilliputian represents a novel pair-rule gene that acts
in cytoskeleton regulation, segmentation and
morphogenesis in Drosophila.
Length = 1154
Score = 28.3 bits (63), Expect = 5.1
Identities = 9/31 (29%), Positives = 12/31 (38%), Gaps = 1/31 (3%)
Query: 163 PGLDDPG-PPTLLVYRIPPGHCLNIFDPALP 192
+ P PP LV H + F P+L
Sbjct: 181 VNVQSPERPPDSLVLLPSSQHSVQNFPPSLM 211
>gnl|CDD|100091 cd03089, PMM_PGM, The phosphomannomutase/phosphoglucomutase
(PMM/PGM) bifunctional enzyme catalyzes the reversible
conversion of 1-phospho to 6-phospho-sugars (e.g.
between mannose-1-phosphate and mannose-6-phosphate or
glucose-1-phosphate and glucose-6-phosphate) via a
bisphosphorylated sugar intermediate. The reaction
involves two phosphoryl transfers, with an intervening
180 degree reorientation of the reaction intermediate
during catalysis. Reorientation of the intermediate
occurs without dissociation from the active site of the
enzyme and is thus, a simple example of processivity, as
defined by multiple rounds of catalysis without release
of substrate. Glucose-6-phosphate and
glucose-1-phosphate are known to be utilized for energy
metabolism and cell surface construction, respectively.
PMM/PGM belongs to the alpha-D-phosphohexomutase
superfamily which includes several related enzymes that
catalyze a reversible intramolecular phosphoryl transfer
on their sugar substrates. Other members of this
superfamily include phosphoglucosamine mutase (PNGM),
phosphoacetylglucosamine mutase (PAGM), the bacterial
phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the
phosphoglucomutases (PGM1 and PGM2). Each of these
enzymes has four domains with a centrally located active
site formed by four loops, one from each domain. All
four domains are included in this alignment model.
Length = 443
Score = 27.9 bits (63), Expect = 5.2
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 194 RLRESFPAPPTGPVDPNSIRISFAKGWG 221
RL+E F P +D + +R+ F GWG
Sbjct: 382 RLKEHFEFPGAEIIDIDGVRVDFEDGWG 409
>gnl|CDD|218940 pfam06209, COBRA1, Cofactor of BRCA1 (COBRA1). This family
consists of several cofactor of BRCA1 (COBRA1) like
proteins. It is thought that COBRA1 along with BRCA1 is
involved in chromatin unfolding. COBRA1 is recruited to
the chromosome site by the first BRCT repeat of BRCA1,
and is itself sufficient to induce chromatin unfolding.
BRCA1 mutations that enhance chromatin unfolding also
increase its affinity for, and recruitment of, COBRA1.
It is thought that that reorganisation of higher levels
of chromatin structure is an important regulated step in
BRCA1-mediated nuclear functions.
Length = 475
Score = 27.8 bits (62), Expect = 6.1
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 8/43 (18%)
Query: 17 HLSNVHLFFSPAGE-RRPGEWCKLAYWELSHRVGR---LYPVV 55
LS +H FFSP+ + RR GE + +L+ +G+ LY +V
Sbjct: 75 DLSVLHNFFSPSPKTRRQGEVVQ----KLTQMIGKNVKLYDMV 113
>gnl|CDD|132082 TIGR03037, anthran_nbaC, 3-hydroxyanthranilate 3,4-dioxygenase.
Members of this protein family, from both bacteria and
eukaryotes, are the enzyme 3-hydroxyanthranilate
3,4-dioxygenase. This enzyme acts on the tryptophan
metabolite 3-hydroxyanthranilate and produces
2-amino-3-carboxymuconate semialdehyde, which can
rearrange spontaneously to quinolinic acid and feed into
nicotinamide biosynthesis, or undergo further enzymatic
degradation.
Length = 159
Score = 27.0 bits (60), Expect = 6.8
Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 9/61 (14%)
Query: 89 PHHVPDAVRRTRTKIGLVVESRRL---NPSFGAVCPYTKASGCGYVPGRDRQGLTLSLEA 145
P HVP + +R IGLV+E +R F CP CG+ R L ++
Sbjct: 83 PPHVPHSPQRPAGSIGLVIERKRPQGELDGFQWFCP-----QCGHKLHRAEVQLE-NIVT 136
Query: 146 D 146
D
Sbjct: 137 D 137
>gnl|CDD|233969 TIGR02669, SpoIID_LytB, SpoIID/LytB domain. This model describes a
domain found typically in two or three proteins per
genome in Cyanobacteria and Firmicutes, and sporadically
in other genomes. One member is SpoIID of Bacillus
subtilis. Another in B. subtilis is the C-terminal half
of LytB, encoded immediately upstream of an amidase, the
autolysin LytC, to which its N-terminus is homologous.
Gene neighborhoods are not well conserved for members of
this family, as many, such as SpoIID, are monocistronic.
One early modelling-based study suggests a DNA-binding
role for SpoIID, but the function of this domain is
unknown [Unknown function, General].
Length = 267
Score = 27.4 bits (61), Expect = 7.4
Identities = 10/19 (52%), Positives = 10/19 (52%)
Query: 2 GFKIREILKFYYWVAHLSN 20
G REILK YY LS
Sbjct: 249 GKDYREILKHYYPGTELSR 267
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
0.322 0.141 0.480
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: 13,157,560
Number of extensions: 1241472
Number of successful extensions: 950
Number of sequences better than 10.0: 1
Number of HSP's gapped: 932
Number of HSP's successfully gapped: 40
Length of query: 245
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 151
Effective length of database: 6,768,326
Effective search space: 1022017226
Effective search space used: 1022017226
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 (21.9 bits)
S2: 58 (26.1 bits)