RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy225
(450 letters)
>gnl|CDD|239750 cd03781, MATH_TRAF4, Tumor Necrosis Factor Receptor
(TNFR)-Associated Factor (TRAF) family, TRAF4 subfamily,
TRAF domain, C-terminal MATH subdomain; composed of
proteins with similarity to human TRAF4, including the
Drosophila protein DTRAF1. TRAF molecules serve as
adapter proteins that link TNFRs and downstream kinase
cascades resulting in the activation of transcription
factors and the regulation of cell survival,
proliferation and stress responses. TRAF4 is highly
expressed during embryogenesis, especially in the
central and peripheral nervous system. Studies using
TRAF4-deficient mice show that TRAF4 is required for
neurogenesis, as well as the development of the trachea
and the axial skeleton. In addition, TRAF4 augments
nuclear factor-kappaB activation triggered by GITR
(glucocorticoid-induced TNFR), a receptor expressed in
T-cells, B-cells and macrophages. It also participates
in counteracting the signaling mediated by Toll-like
receptors through its association with TRAF6 and TRIF.
DTRAF1 plays a pivotal role in the development of eye
imaginal discs and photosensory neuron arrays in
Drosophila. TRAF4 contains a RING finger domain, seven
zinc finger domains, and a TRAF domain. The TRAF domain
can be divided into a more divergent N-terminal alpha
helical region (TRAF-N), and a highly conserved
C-terminal MATH subdomain (TRAF-C) with an
eight-stranded beta-sandwich structure. TRAF-N mediates
trimerization while TRAF-C interacts with receptors.
Length = 154
Score = 242 bits (619), Expect = 3e-79
Identities = 91/154 (59%), Positives = 121/154 (78%), Gaps = 12/154 (7%)
Query: 302 GTLIWKITDYSLKCQES-----IELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYI 356
GTL+WKITDYS K QE+ +EL SP FYT ++GYKLQVS FLNGNG+GEG+H+SVYI
Sbjct: 1 GTLLWKITDYSRKLQEAKGRDNLELFSPPFYTHRYGYKLQVSAFLNGNGSGEGSHLSVYI 60
Query: 357 KLLPGEYDALLKWPFSHSVSFTLFDQSE----KPVNVVESFVPDPTWENFQRPSK---QP 409
++LPGEYD LL+WPFSH ++FTL DQS+ KP ++ E+F PDPTW+NFQ+PS
Sbjct: 61 RVLPGEYDNLLEWPFSHRITFTLLDQSDPSLSKPQHITETFTPDPTWKNFQKPSASRLDE 120
Query: 410 DSLGFGFPRFVSLDTIRKRQFLKDDAIFIRVKVD 443
+LGFG+P+F+S + ++KR ++KDDAIF+R V+
Sbjct: 121 STLGFGYPKFISHEDLKKRNYIKDDAIFLRASVE 154
>gnl|CDD|238168 cd00270, MATH_TRAF_C, Tumor Necrosis Factor Receptor
(TNFR)-Associated Factor (TRAF) family, TRAF domain,
C-terminal MATH subdomain; TRAF molecules serve as
adapter proteins that link cell surface TNFRs and
receptors of the interleukin-1/Toll-like family to
downstream kinase signaling cascades which results in
the activation of transcription factors and the
regulation of cell survival, proliferation and stress
responses in the immune and inflammatory systems. There
are at least six mammalian and three Drosophila proteins
containing TRAF domains. The mammalian TRAFs display
varying expression profiles, indicating independent and
cell type-specific regulation. They display distinct, as
well as overlapping functions and interactions with
receptors. Most TRAFs, except TRAF1, share N-terminal
homology and contain a RING domain, multiple zinc finger
domains, and a TRAF domain. TRAFs form homo- and
heterotrimers through its TRAF domain. The TRAF domain
can be divided into a more divergent N-terminal alpha
helical region (TRAF-N), and a highly conserved
C-terminal MATH subdomain (TRAF-C) with an
eight-stranded beta-sandwich structure. TRAF-N mediates
trimerization while TRAF-C interacts with receptors.
Length = 149
Score = 215 bits (549), Expect = 8e-69
Identities = 74/149 (49%), Positives = 106/149 (71%), Gaps = 7/149 (4%)
Query: 302 GTLIWKITDYSLKCQES-----IELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYI 356
G LIWKI DYS K QE+ L SP FYTS++GYKL + L+LNG+G G+GTH+S+++
Sbjct: 1 GVLIWKIKDYSRKLQEAVAGSNTVLYSPPFYTSRYGYKLCLRLYLNGDGTGKGTHLSLFV 60
Query: 357 KLLPGEYDALLKWPFSHSVSFTLFDQSE--KPVNVVESFVPDPTWENFQRPSKQPDSLGF 414
++ GEYDALL+WPF ++ TL DQS+ K ++ E+F+PDP FQRP +++GF
Sbjct: 61 HVMKGEYDALLEWPFRGKITLTLLDQSDDSKRKHITETFMPDPNSSAFQRPPTGENNIGF 120
Query: 415 GFPRFVSLDTIRKRQFLKDDAIFIRVKVD 443
G+P FV L+ + R ++KDD +FI+V+VD
Sbjct: 121 GYPEFVPLEKLESRGYVKDDTLFIKVEVD 149
>gnl|CDD|239746 cd03777, MATH_TRAF3, Tumor Necrosis Factor Receptor
(TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily,
TRAF domain; TRAF molecules serve as adapter proteins
that link TNFRs and downstream kinase cascades resulting
in the activation of transcription factors and the
regulation of cell survival, proliferation and stress
responses. TRAF3 was first described as a molecule that
binds the cytoplasmic tail of CD40. However, it is not
required for CD40 signaling. More recently, TRAF3 has
been identified as a key regulator of type I interferon
(IFN) production and the mammalian innate antiviral
immunity. It mediates IFN responses in Toll-like
receptor (TLR)-dependent as well as TLR-independent
viral recognition pathways. It is also a key element in
immunological homeostasis through its regulation of the
anti-inflammatory cytokine interleukin-10. TRAF3
contains a RING finger domain, five zinc finger domains,
and a TRAF domain. The TRAF domain can be divided into a
more divergent N-terminal alpha helical region (TRAF-N),
and a highly conserved C-terminal MATH subdomain
(TRAF-C) with an eight-stranded beta-sandwich structure.
TRAF-N mediates trimerization while TRAF-C interacts
with receptors.
Length = 186
Score = 145 bits (368), Expect = 1e-41
Identities = 64/154 (41%), Positives = 96/154 (62%), Gaps = 6/154 (3%)
Query: 297 TLNYSGTLIWKITDYSLKCQE-----SIELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTH 351
T +Y+G LIWKI DY + QE ++ L S FYT FGYK+ ++LNG+G G+GTH
Sbjct: 34 TASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTH 93
Query: 352 VSVYIKLLPGEYDALLKWPFSHSVSFTLFDQSEKPVNVVESFVPDPTWENFQRPSKQPDS 411
+S++ ++ GEYDALL WPF V+ L DQ ++ ++F PDP +F++P+ + +
Sbjct: 94 LSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMN- 152
Query: 412 LGFGFPRFVSLDTIRKRQFLKDDAIFIRVKVDPS 445
+ G P FV+ + ++KDD IFI+V VD S
Sbjct: 153 IASGCPVFVAQTVLENGTYIKDDTIFIKVIVDTS 186
>gnl|CDD|239749 cd03780, MATH_TRAF5, Tumor Necrosis Factor Receptor
(TNFR)-Associated Factor (TRAF) family, TRAF5 subfamily,
TRAF domain, C-terminal MATH subdomain; TRAF molecules
serve as adapter proteins that link TNFRs and downstream
kinase cascades resulting in the activation of
transcription factors and the regulation of cell
survival, proliferation and stress responses. TRAF5 was
identified as an activator of nuclear factor-kappaB and
a regulator of lymphotoxin-beta receptor and CD40
signaling. Its interaction with CD40 is indirect,
involving hetero-oligomerization with TRAF3. In
addition, TRAF5 has been shown to associate with other
TNFRs including CD27, CD30, OX40 and GITR
(glucocorticoid-induced TNFR). It plays a role in
modulating Th2 immune responses (driven by OX40
costimulation) and T-cell activation (triggered by
GITR). It is also involved in osteoclastogenesis. TRAF5
contains a RING finger domain, five zinc finger domains,
and a TRAF domain. The TRAF domain can be divided into a
more divergent N-terminal alpha helical region (TRAF-N),
and a highly conserved C-terminal MATH subdomain
(TRAF-C) with an eight-stranded beta-sandwich structure.
TRAF-N mediates trimerization while TRAF-C interacts
with receptors.
Length = 148
Score = 140 bits (354), Expect = 5e-40
Identities = 62/149 (41%), Positives = 99/149 (66%), Gaps = 8/149 (5%)
Query: 302 GTLIWKITDYSLKCQESIE-----LLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYI 356
G LIWK+TDY +K +E+++ + S FYTS+ GY+L +LNG+G+G+GTH+S+Y
Sbjct: 1 GKLIWKVTDYKMKKKEAVDGHTVSIFSQPFYTSRCGYRLCARAYLNGDGSGKGTHLSLYF 60
Query: 357 KLLPGEYDALLKWPFSHSVSFTLFDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGF 416
++ GE+D+LL+WPF V+ L DQS K +++E+F DP +F+RP + + + G
Sbjct: 61 VVMRGEFDSLLQWPFRQRVTLMLLDQSGKKNHIMETFKADPNSSSFKRPDGEMN-IASGC 119
Query: 417 PRFVSLDTIR--KRQFLKDDAIFIRVKVD 443
PRFV+ + K ++KDD +F++V VD
Sbjct: 120 PRFVAHSVLENAKNTYIKDDTLFLKVAVD 148
>gnl|CDD|239747 cd03778, MATH_TRAF2, Tumor Necrosis Factor Receptor (TNFR)
Associated Factor (TRAF) family, TRAF2 subfamily, TRAF
domain; TRAF molecules serve as adapter proteins that
link TNFRs and downstream kinase cascades resulting in
the activation of transcription factors and the
regulation of cell survival, proliferation and stress
responses. TRAF2 associates with the receptors TNFR-1,
TNFR-2, RANK (which mediates differentiation and
maturation of osteoclasts) and CD40 (which is important
for the proliferation and activation of B cells), among
others. It regulates distinct pathways that lead to the
activation of nuclear factor-kappaB and Jun NH2-terminal
kinases. TRAF2 also indirectly associates with death
receptors through its interaction with TRADD
(TNFR-associated death domain protein). It is involved
in regulating oxidative stress or ROS-induced cell death
and in the preconditioning of cells by sublethal stress
for protection from subsequent injury. TRAF2 contains a
RING finger domain, five zinc finger domains, and a TRAF
domain. The TRAF domain can be divided into a more
divergent N-terminal alpha helical region (TRAF-N), and
a highly conserved C-terminal MATH subdomain (TRAF-C)
with an eight-stranded beta-sandwich structure. TRAF-N
mediates trimerization while TRAF-C interacts with
receptors.
Length = 164
Score = 135 bits (340), Expect = 8e-38
Identities = 61/150 (40%), Positives = 97/150 (64%), Gaps = 8/150 (5%)
Query: 300 YSGTLIWKITDYSLKCQESIE-----LLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSV 354
Y G IWKI+D++ K QE++ + SP+FYTS++GYK+ + ++LNG+G G GTH+S+
Sbjct: 17 YDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSL 76
Query: 355 YIKLLPGEYDALLKWPFSHSVSFTLFDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGF 414
+ ++ G DALL+WPF+ V+ L DQ+ + +V+++F PD T +FQRP + +
Sbjct: 77 FFVVMKGPNDALLRWPFNQKVTLMLLDQNNRE-HVIDAFRPDVTSSSFQRPVNDMN-IAS 134
Query: 415 GFPRFVSLDTIR-KRQFLKDDAIFIRVKVD 443
G P F + K +++DDAIFI+ VD
Sbjct: 135 GCPLFCPVSKXEAKNSYVRDDAIFIKAIVD 164
>gnl|CDD|239748 cd03779, MATH_TRAF1, Tumor Necrosis Factor Receptor (TNFR)
Associated Factor (TRAF) family, TRAF1 subfamily, TRAF
domain, C-terminal MATH subdomain; TRAF molecules serve
as adapter proteins that link TNFRs and downstream
kinase cascades resulting in the activation of
transcription factors and the regulation of cell
survival, proliferation and stress responses. TRAF1
expression is the most restricted among the TRAFs. It is
found exclusively in activated lymphocytes, dendritic
cells and certain epithelia. TRAF1 associates, directly
or indirectly through heterodimerization with TRAF2,
with the TNFR family receptors TNFR-2, CD30, RANK, CD40
and LMP1, among others. It also binds the intracellular
proteins TRADD, TANK, TRIP, RIP1, RIP2 and FLIP. TRAF1
is unique among the TRAFs in that it lacks a RING
domain, which is critical for the activation of nuclear
factor-kappaB and Jun NH2-terminal kinase. Studies on
TRAF1-deficient mice suggest that TRAF1 has a negative
regulatory role in TNFR-mediated signaling events. TRAF1
contains one zinc finger and one TRAF domain. The TRAF
domain can be divided into a more divergent N-terminal
alpha helical region (TRAF-N), and a highly conserved
C-terminal MATH subdomain (TRAF-C) with an
eight-stranded beta-sandwich structure. TRAF-N mediates
trimerization while TRAF-C interacts with receptors.
Length = 147
Score = 132 bits (334), Expect = 4e-37
Identities = 67/149 (44%), Positives = 100/149 (67%), Gaps = 9/149 (6%)
Query: 302 GTLIWKITDYSLKCQES-----IELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYI 356
GT +WKITD S K +ES + L SP+FYT+++GYK+ + L+LNG+GAG+GTH+S++
Sbjct: 1 GTFLWKITDVSQKQRESSHGRDVSLCSPAFYTAKYGYKVCLRLYLNGDGAGKGTHISLFF 60
Query: 357 KLLPGEYDALLKWPFSHSVSFTLFDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGF 416
++ GEYDALL WPF H V+F L DQ+ + +V+++F PD + +FQRP + + G
Sbjct: 61 VIMKGEYDALLPWPFRHKVTFMLLDQNNRE-HVIDAFRPDLSSASFQRPVSDMN-VASGC 118
Query: 417 PRFVSLDTIR--KRQFLKDDAIFIRVKVD 443
P F L ++ K + KDD I+I+ VD
Sbjct: 119 PLFFPLKKLQSPKHAYCKDDTIYIKCVVD 147
>gnl|CDD|239745 cd03776, MATH_TRAF6, Tumor Necrosis Factor Receptor
(TNFR)-Associated Factor (TRAF) family, TRAF6 subfamily,
TRAF domain, C-terminal MATH subdomain; composed of
proteins with similarity to human TRAF6, including the
Drosophila protein DTRAF2. TRAF molecules serve as
adapter proteins that link TNFRs and downstream kinase
cascades resulting in the activation of transcription
factors and the regulation of cell survival,
proliferation and stress responses. TRAF6 is the most
divergent in its TRAF domain among the mammalian TRAFs.
In addition to mediating TNFR family signaling, it is
also an essential signaling molecule of the
interleukin-1/Toll-like receptor superfamily. Whereas
other TRAF molecules display similar and overlapping
TNFR-binding specificities, TRAF6 binds completely
different sites on receptors such as CD40 and RANK.
TRAF6 serves as a molecular bridge between innate and
adaptive immunity and plays a central role in
osteoimmunology. DTRAF2, as an activator of nuclear
factor-kappaB, plays a pivotal role in Drosophila
development and innate immunity. TRAF6 contains a RING
finger domain, five zinc finger domains, and a TRAF
domain. The TRAF domain can be divided into a more
divergent N-terminal alpha helical region (TRAF-N), and
a highly conserved C-terminal MATH subdomain (TRAF-C)
with an eight-stranded beta-sandwich structure. TRAF-N
mediates trimerization while TRAF-C interacts with
receptors.
Length = 147
Score = 122 bits (307), Expect = 4e-33
Identities = 51/146 (34%), Positives = 85/146 (58%), Gaps = 5/146 (3%)
Query: 302 GTLIWKITDYS--LKCQES---IELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYI 356
G +WKI ++S + E+ + + SP FYTS GYKL L L+ A ++S+++
Sbjct: 1 GIYVWKIKNFSNLRRSMEAGSPVVIHSPGFYTSPPGYKLCARLNLSLPEARCPNYISLFV 60
Query: 357 KLLPGEYDALLKWPFSHSVSFTLFDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGF 416
L+ GE D+ L WPF +++ TL DQSE N+ E+ + P FQRP+ + GFG+
Sbjct: 61 HLMQGENDSHLDWPFQGTITLTLLDQSEPRQNIHETMMSKPELLAFQRPTTDRNPKGFGY 120
Query: 417 PRFVSLDTIRKRQFLKDDAIFIRVKV 442
F ++ + +R F+K+D + I+++V
Sbjct: 121 VEFAHIEDLLQRGFVKNDTLLIKIEV 146
>gnl|CDD|238068 cd00121, MATH, MATH (meprin and TRAF-C homology) domain; an
independent folding unit with an eight-stranded
beta-sandwich structure found in meprins, TRAFs and
other proteins. Meprins comprise a class of
extracellular metalloproteases which are anchored to the
membrane and are capable of cleaving growth factors,
extracellular matrix proteins, and biologically active
peptides. TRAF molecules serve as adapter proteins that
link cell surface receptors of the Tumor Necrosis Factor
and 1nterleukin-1/Toll-like families to downstream
kinase cascades, which results in the activation of
transcription factors and the regulation of cell
survival, proliferation and stress responses in the
immune and inflammatory systems. Other members include
the ubiquitin ligases, TRIM37 and SPOP, and the
ubiquitin-specific proteases, HAUSP and Ubp21p. A large
number of uncharacterized members mostly from
lineage-specific expansions in C. elegans and rice
contain MATH and BTB domains, similar to SPOP. The MATH
domain has been shown to bind peptide/protein substrates
in TRAFs and HAUSP. It is possible that the MATH domain
in other members of this superfamily also interacts with
various protein substrates. The TRAF domain may also be
involved in the trimerization of TRAFs. Based on
homology, it is postulated that the MATH domain in
meprins may be involved in its tetramer assembly and
that the MATH domain, in general, may take part in
diverse modular arrangements defined by adjacent
multimerization domains.
Length = 126
Score = 89.7 bits (223), Expect = 1e-21
Identities = 45/142 (31%), Positives = 71/142 (50%), Gaps = 16/142 (11%)
Query: 302 GTLIWKITDYSLKCQESIELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPG 361
G WKI ++S ESI SP F GYK ++ ++ NG+G G ++S+Y++L G
Sbjct: 1 GKHTWKIVNFSELEGESIY--SPPFEV--GGYKWRIRIYPNGDGES-GDYLSLYLELDKG 55
Query: 362 EYDALLKWPFSHSVSFTLFDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFVS 421
E D L KW + L +Q+ ++ +SF E G+GFP+F+S
Sbjct: 56 ESD-LEKWSVRAEFTLKLVNQNGGK-SLSKSFTHVFFSEK---------GSGWGFPKFIS 104
Query: 422 LDTIRKRQFLKDDAIFIRVKVD 443
D + +L DD++ I V+V
Sbjct: 105 WDDLEDSYYLVDDSLTIEVEVK 126
>gnl|CDD|216189 pfam00917, MATH, MATH domain. This motif has been called the
Meprin And TRAF-Homology (MATH) domain. This domain is
hugely expanded in the nematode C. elegans.
Length = 116
Score = 71.9 bits (177), Expect = 2e-15
Identities = 32/136 (23%), Positives = 57/136 (41%), Gaps = 21/136 (15%)
Query: 308 ITDYSLKCQESIELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALL 367
I ++S K +E E S Y +FG ++ ++ NG + +Y+ GE D LL
Sbjct: 1 IKNFS-KIKEG-ENYYTSPYEERFGIPWRLRIYRNGG------FLGLYLHCEKGEKDELL 52
Query: 368 KWPFSHSVSFTLFDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFVSLDTIRK 427
W + L + K + F +P+ G+G+ +F+S D + +
Sbjct: 53 GWSIETEFTLKLVSDNGKSLTK------RNKSHVFTKPT------GYGWGKFISWDDL-E 99
Query: 428 RQFLKDDAIFIRVKVD 443
++ DD I I +V
Sbjct: 100 NDYVVDDTIIIEAEVK 115
>gnl|CDD|239740 cd03771, MATH_Meprin, Meprin family, MATH domain; Meprins are
multidomain, highly glycosylated extracellular
metalloproteases, which are either anchored to the
membrane or secreted into extracellular spaces. They are
expressed in renal and intestinal brush border
membranes, leukocytes, and cancer cells, and are capable
of cleaving growth factors, cytokines, extracellular
matrix proteins, and biologically active peptides.
Meprin proteases are composed of two related subunits,
alpha and beta, which form homo- or hetro-complexes
where the basic unit is a disulfide-linked dimer.
Despite their similarity, the two subunits differ in
their ability to self-associate, in proteolytic
processing during biosynthesis and in substrate
specificity. Both subunits are synthesized as membrane
spanning proteins, however, the alpha subunit is cleaved
during biosynthesis and loses its transmembrane domain.
Meprin beta forms homodimers or heterotetramers while
meprin alpha oligomerizes into large complexes
containing 10-100 subunits. Both alpha and beta subunits
contain a catalytic astacin (M12 family) protease domain
followed by the adhesion or interaction domains MAM,
MATH and AM. The MATH and MAM domains provide
symmetrical intersubunit disulfide bonds necessary for
the dimerization of meprin subunits. The MATH domain may
also be required for folding of an activable zymogen.
Length = 167
Score = 67.0 bits (164), Expect = 3e-13
Identities = 46/168 (27%), Positives = 79/168 (47%), Gaps = 34/168 (20%)
Query: 305 IWKITDYSLKCQES---IELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPG 361
+W++ ++S + + ++ SP FY+ + GY QV L+ NG + +Y L G
Sbjct: 5 VWRVRNFSQLLETTPKGTKIYSPRFYSPE-GYAFQVGLYPNGT-ESYPGYTGLYFHLCSG 62
Query: 362 EYDALLKWP-FSHSVSFTLFDQS---EKPVNVVESFVPDPT----------WENFQRPSK 407
E D +L+WP + + TL DQ ++ ++ SF DP+ W+ RPSK
Sbjct: 63 ENDDVLEWPCPNRQATMTLLDQDPDIQQRMSNQRSFTTDPSMTSSDNGEYFWD---RPSK 119
Query: 408 --QPDS----------LGFGFPRFVSLDTIRKRQFLKDDAIFIRVKVD 443
D+ G+G+ F+S +R+R FLK D + I + +
Sbjct: 120 VGSYDTDTNGCTCYRGPGYGWSTFISHSRLRRRDFLKGDDLIILLDFE 167
>gnl|CDD|190233 pfam02176, zf-TRAF, TRAF-type zinc finger.
Length = 60
Score = 60.5 bits (147), Expect = 4e-12
Identities = 24/61 (39%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 203 HQTKCTRAPIPCPNQCEMVALPREELDVHIKEHCNSLLVSCVFKDAGCRFKGMRGETMEK 262
H C AP+PCPN C + RE++ H++E C V C FK GC+ M E ++K
Sbjct: 1 HLKTCPFAPVPCPNGCCKKKILREDVPDHLEEDCPKREVPCPFKPYGCKVD-MPREALQK 59
Query: 263 H 263
H
Sbjct: 60 H 60
Score = 40.9 bits (96), Expect = 5e-05
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 96 HLQTCKYDAIPC--NKCLAAIPKTLMEDHSKFTCPERITTCQY----CLESFSGMEMEDH 149
HL+TC + +PC C I + + DH + CP+R C + C ++ H
Sbjct: 1 HLKTCPFAPVPCPNGCCKKKILREDVPDHLEEDCPKREVPCPFKPYGCKVDMPREALQKH 60
Score = 35.1 bits (81), Expect = 0.005
Identities = 16/43 (37%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 149 HTGHCSYEMVYCENKCGHK-IQRRLMAKHRANDCYKRLVACRY 190
H C + V C N C K I R + H DC KR V C +
Sbjct: 1 HLKTCPFAPVPCPNGCCKKKILREDVPDHLEEDCPKREVPCPF 43
>gnl|CDD|239752 cd03783, MATH_Meprin_Alpha, Meprin family, Alpha subunit, MATH
domain; Meprins are multidomain extracellular
metalloproteases capable of cleaving growth factors,
cytokines, extracellular matrix proteins, and
biologically active peptides. They are composed of two
related subunits, alpha and beta, which form homo- or
hetro-complexes where the basic unit is a
disulfide-linked dimer. The alpha subunit is synthesized
as a membrane spanning protein, however, it is cleaved
during biosynthesis and loses its transmembrane domain.
It oligomerizes into large complexes, containing 10-100
subunits (dimers that associate noncovalently), which
are secreted as latent proteases and can move through
extracellular spaces in a nondestructive manner. This
allows delivery of the concentrated protease to sites
containing activating enzymes, such as sites of
inflammation, infection or cancerous growth. Meprin
alpha shows preference for small or hydrophobic residues
at the P1 and P1' sites of its substrate. Both alpha and
beta subunits contain a catalytic astacin (M12 family)
protease domain followed by the adhesion or interaction
domains MAM, MATH and AM. The MATH and MAM domains
provide symmetrical intersubunit disulfide bonds
necessary for the dimerization of meprin subunits. The
MATH domain may also be required for folding of an
activable zymogen.
Length = 167
Score = 54.5 bits (131), Expect = 7e-09
Identities = 45/169 (26%), Positives = 74/169 (43%), Gaps = 32/169 (18%)
Query: 303 TLIWKITDYSL---KCQESIELLSPSFYTSQFGYKLQVSLFLNGNGAGE-GTHVSVYIKL 358
+W++ ++S + L SP FY+ + GY VSL+ N + G + +Y L
Sbjct: 3 NAVWRVRNFSQILENTTKGDVLQSPRFYSPE-GYGYGVSLYPLSNESDYSGNYTGLYFHL 61
Query: 359 LPGEYDALLKWP-FSHSVSFTLFDQS---EKPVNVVESFVPDPT-----------WENFQ 403
GE DA+L+WP + T+ DQ ++ SF D + W+
Sbjct: 62 CSGENDAVLEWPALNRQAIITVLDQDPDVRLRMSSSRSFTTDKSQTSSAINGTLRWD--- 118
Query: 404 RPSK----QPD-----SLGFGFPRFVSLDTIRKRQFLKDDAIFIRVKVD 443
RPS+ + FG+ F+S +R+R FLK+D + I V +
Sbjct: 119 RPSRVGTYDTSCDCFRGIDFGWSTFISHSQLRRRSFLKNDDLIIFVDFE 167
>gnl|CDD|239751 cd03782, MATH_Meprin_Beta, Meprin family, Beta subunit, MATH
domain; Meprins are multidomain extracellular
metalloproteases capable of cleaving growth factors,
cytokines, extracellular matrix proteins, and
biologically active peptides. They are composed of two
related subunits, alpha and beta, which form homo- or
hetro-complexes where the basic unit is a
disulfide-linked dimer. The beta subunit is a type I
membrane protein, which forms homodimers or
heterotetramers (alpha2beta2 or alpha3beta). Meprin beta
shows preference for acidic residues at the P1 and P1'
sites of its substrate. Among its best substrates are
growth factors and chemokines such as gastrin and
osteopontin. Both alpha and beta subunits contain a
catalytic astacin (M12 family) protease domain followed
by the adhesion or interaction domains MAM, MATH and AM.
The MATH and MAM domains provide symmetrical
intersubunit disulfide bonds necessary for the
dimerization of meprin subunits. The MATH domain may
also be required for folding of an activable zymogen.
Length = 167
Score = 51.0 bits (122), Expect = 1e-07
Identities = 38/144 (26%), Positives = 58/144 (40%), Gaps = 31/144 (21%)
Query: 321 LLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALLKWPFS-HSVSFTL 379
+ SP F +S GY QV L+LNG G ++++Y+ L G D L+WP + L
Sbjct: 24 IYSPPFLSST-GYSFQVGLYLNGTDDYPG-NLAIYLHLTSGPNDDQLQWPCPWQQATMML 81
Query: 380 FDQS---EKPVNVVESFVPDPT----------WENFQRPSK------QPDSL------GF 414
DQ + ++ S DP W+ P K D G+
Sbjct: 82 LDQHPDIRQRMSNQRSVTTDPNMTSTDSDEYFWD---DPRKVGSEVTDTDGSTFYRGPGY 138
Query: 415 GFPRFVSLDTIRKRQFLKDDAIFI 438
G F++ +R R F+K D +
Sbjct: 139 GTSAFITHLRLRSRDFIKGDDVIF 162
>gnl|CDD|214496 smart00061, MATH, meprin and TRAF homology.
Length = 95
Score = 46.9 bits (112), Expect = 6e-07
Identities = 23/117 (19%), Positives = 42/117 (35%), Gaps = 23/117 (19%)
Query: 304 LIWKITDYSLKCQESIELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEY 363
L + S + +E SPS F ++ ++ +S+Y+ E
Sbjct: 2 LSHTFKNVS-RLEEGESYFSPSEEH--FNIPWRLKIYRKNG------FLSLYLHCEKEEC 52
Query: 364 DALLKWPFSHSVSFTLFDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFV 420
D+ KW + L Q+ K + F++PS G+GF +F+
Sbjct: 53 DSR-KWSIEAEFTLKLVSQNGKS-------LSKKDKHVFEKPS------GWGFSKFI 95
>gnl|CDD|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional.
Length = 567
Score = 48.3 bits (115), Expect = 6e-06
Identities = 39/161 (24%), Positives = 66/161 (40%), Gaps = 27/161 (16%)
Query: 84 CKWYDELKSLKGHLQTCKYDAIPCNK--CLAAIPKTLMEDHSKFTCPERITTCQYCLESF 141
CK Y +S+ H C + C C + ++H C+ C ++F
Sbjct: 413 CKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNH---------VHCEKCGQAF 463
Query: 142 SGMEMEDHTGHCSYEMVYCENKCGHKIQRRLMAKHRANDCYKRLVACRYC-----SKSYV 196
EME H +E + C CG +++ M +H+A+ C RL+ CR+C +
Sbjct: 464 QQGEMEKHM-KVFHEPLQC--PCGVVLEKEQMVQHQASTCPLRLITCRFCGDMVQAGGSA 520
Query: 197 ADT------LVTHQTKCTRAPIPCPNQCEMVALPREELDVH 231
D + H++ C PC + V L +E+D+H
Sbjct: 521 MDVRDRLRGMSEHESICGSRTAPCDSCGRSVML--KEMDIH 559
Score = 33.7 bits (77), Expect = 0.19
Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 14/80 (17%)
Query: 186 VACRYCSKSYVADTLVTHQTKCTRAPIPCPNQCEMVALPREELDVHIKEHCNSLLVSCVF 245
V CR C + ++ H+ C+R + CP+ + L EE H+ HC
Sbjct: 408 VECRNCKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHV--HCEK------- 458
Query: 246 KDAGCRFKGMRGETMEKHIE 265
C +GE MEKH++
Sbjct: 459 ----CGQAFQQGE-MEKHMK 473
>gnl|CDD|239742 cd03773, MATH_TRIM37, Tripartite motif containing protein 37
(TRIM37) family, MATH domain; TRIM37 is a peroxisomal
protein and is a member of the tripartite motif (TRIM)
protein subfamily, also known as the
RING-B-box-coiled-coil (RBCC) subfamily of zinc-finger
proteins. Mutations in the human TRIM37 gene (also known
as MUL) cause Mulibrey (muscle-liver-brain-eye) nanism,
a rare growth disorder of prenatal onset characterized
by dysmorphic features, pericardial constriction and
hepatomegaly. TRIM37, similar to other TRIMs, contains a
cysteine-rich, zinc-binding RING-finger domain followed
by another cysteine-rich zinc-binding domain, the B-box,
and a coiled-coil domain. TRIM37 is autoubiquitinated in
a RING domain-dependent manner, indicating that it
functions as an ubiquitin E3 ligase. In addition to the
tripartite motif, TRIM37 also contains a MATH domain
C-terminal to the coiled-coil domain. The MATH domain of
TRIM37 has been shown to interact with the TRAF domain
of six known TRAFs in vitro, however, it is unclear
whether this is physiologically relevant. Eleven TRIM37
mutations have been associated with Mulibrey nanism so
far. One mutation, Gly322Val, is located in the MATH
domain and is the only mutation that does not affect the
length of the protein. It results in the incorrect
subcellular localization of TRIM37.
Length = 132
Score = 42.0 bits (99), Expect = 8e-05
Identities = 29/140 (20%), Positives = 54/140 (38%), Gaps = 20/140 (14%)
Query: 307 KITDYSLKCQESIELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDAL 366
+ ++S Q + + S ++L+V + +GNG G +SV+++L G
Sbjct: 10 TLENFSTLRQSADPVYSDPLNVDGLCWRLKV--YPDGNGEVRGNFLSVFLELCSG----- 62
Query: 367 LKWPFSHSVSFTLFDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFVSLDTIR 426
L + + Q+ N+ F D F+ +G+ RF LD +
Sbjct: 63 LGEASKYEYRVEMVHQANPTKNIKREFASD-----FEV------GECWGYNRFFRLDLLI 111
Query: 427 KRQFLKD--DAIFIRVKVDP 444
+L D + +R V P
Sbjct: 112 NEGYLLPENDTLILRFSVRP 131
>gnl|CDD|236709 PRK10531, PRK10531, acyl-CoA thioesterase; Provisional.
Length = 422
Score = 34.0 bits (78), Expect = 0.16
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 354 VYIKLLPGEYDALLKWPFSHSVSFTLFDQSEKPVNVVESFVPD 396
YI ++PG Y + P + + TL+ EKP++V D
Sbjct: 113 QYIAVMPGTYQGTVYVP-AAAPPITLYGTGEKPIDVKIGLALD 154
>gnl|CDD|214606 smart00301, DM, Doublesex DNA-binding motif.
Length = 54
Score = 29.6 bits (67), Expect = 0.39
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 84 CKWYDELKSLKGHLQTCKYDAIPCNKC 110
C+ + LKGH C + C KC
Sbjct: 8 CENHGVKVPLKGHKPECPFRDCECEKC 34
>gnl|CDD|152058 pfam11622, DUF3251, Protein of unknown function (DUF3251). This
family of proteins with unknown function appears to be
restricted to Enterobacteriaceae. Some members if this
family are annotated as putative lipoprotein YajI
however this cannot be confirmed.
Length = 156
Score = 30.6 bits (69), Expect = 0.87
Identities = 38/155 (24%), Positives = 59/155 (38%), Gaps = 23/155 (14%)
Query: 275 MCSLVSKQQQQISTLKSALNKVTLNYSGTLIWKITDYSLKCQESIELL----SPSFYTSQ 330
S V + Q +STL L TLN I + + K + LL +P+ SQ
Sbjct: 2 QQSEVPQLHQSVSTLNQELT--TLNQQTVKIEQQNALNAKSTSGVYLLPGANTPARLESQ 59
Query: 331 FGYKLQVSLFLNGNGAGEGTHVSVYI-----KLLPGEYDALLKW----PFSHSVSFTLFD 381
G +L+VSL N GT ++ I LP + A ++W + + +
Sbjct: 60 IG-RLRVSL-RNITPEANGTRATLRIQGESAAPLPA-FKATVEWGQLDGTTGNYQEV--N 114
Query: 382 QSEKPVNVVESFVPDPTWENFQRPSK--QPDSLGF 414
+ S +P P+ + PD LGF
Sbjct: 115 TQSQLFVAPASLLP-PSDVSIPLRLSGVTPDQLGF 148
>gnl|CDD|144376 pfam00751, DM, DM DNA binding domain. The DM domain is named after
dsx and mab-3. dsx contains a single amino-terminal DM
domain, whereas mab-3 contains two amino-terminal
domains. The DM domain has a pattern of conserved zinc
chelating residues C2H2C4. The dsx DM domain has been
shown to dimerise and bind palindromic DNA.
Length = 46
Score = 26.9 bits (60), Expect = 2.5
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 93 LKGHLQTCKYDAIPCNKC 110
LKGH + C Y C KC
Sbjct: 16 LKGHKRYCPYRDCTCEKC 33
>gnl|CDD|132832 cd07299, PX_TCGAP, The phosphoinositide binding Phox Homology
domain of Tc10/Cdc42 GTPase-activating protein. The PX
domain is a phosphoinositide (PI) binding module present
in many proteins with diverse functions such as cell
signaling, vesicular trafficking, protein sorting, and
lipid modification, among others. TCGAP (Tc10/Cdc42
GTPase-activating protein) contains N-terminal PX and
Src Homology 3 (SH3) domains, a central Rho GAP domain,
and C-terminal proline-rich regions. It is widely
expressed in the brain where it is involved in
regulating the outgrowth of axons and dendrites and is
regulated by the protein tyrosine kinase Fyn. It
interacts with cdc42 and TC10beta through its GAP domain
and with phosphatidylinositol-(4,5)-bisphosphate
[PI(4,5)P2] through its PX domain. It is translocated to
the plasma membrane in adipocytes in response to insulin
and may be involved in the regulation of
insulin-stimulated glucose transport. TCGAP has also
been named sorting nexins 26 (SNX26). SNXs make up the
largest group among PX domain containing proteins. They
are involved in regulating membrane traffic and protein
sorting in the endosomal system. The PX domain of SNXs
binds PIs and targets the protein to PI-enriched
membranes. SNXs differ from each other in PI-binding
specificity and affinity, and the presence of other
protein-protein interaction domains, which help
determine subcellular localization and specific function
in the endocytic pathway. It is unknown whether TCGAP
also functions as a SNX.
Length = 113
Score = 28.7 bits (64), Expect = 2.6
Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 6/53 (11%)
Query: 57 LSLTPDVSDSEKDTMGSLIHCIHYK-EGCKW-----YDELKSLKGHLQTCKYD 103
L L+ + SD + L+ + +G W Y++ ++L HL C +D
Sbjct: 9 LQLSNERSDWTSSSEKDLVFLVQVTCQGRSWMVLRSYEDFRTLDAHLHRCIFD 61
>gnl|CDD|130324 TIGR01257, rim_protein, retinal-specific rim ABC transporter. This
model describes the photoreceptor protein (rim protein)
in eukaryotes. It is the member of ABC transporter
superfamily. Rim protein is a membrane glycoprotein
which is localized in the photoreceptor outer segment
discs. Mutation/s in its genetic loci is implicated in
the recessive Stargardt's disease [Transport and binding
proteins, Other].
Length = 2272
Score = 30.4 bits (68), Expect = 3.0
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 333 YKLQVSLFLNGNGAGEGTHVSVYIKLLP 360
Y+ Q++ FL NGAG+ T +S+ LLP
Sbjct: 954 YENQITAFLGHNGAGKTTTLSILTGLLP 981
>gnl|CDD|184471 PRK14039, PRK14039, ADP-dependent glucokinase; Provisional.
Length = 453
Score = 29.8 bits (67), Expect = 3.7
Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 7/40 (17%)
Query: 61 PDVSDSEKDTMGSLIHCIHYKEGCKW-------YDELKSL 93
P S D + LIHC+ G +W ++ LK+
Sbjct: 42 PGKILSLSDFVAGLIHCMKNGCGAEWLVFEQSVFEFLKNR 81
>gnl|CDD|221419 pfam12097, DUF3573, Protein of unknown function (DUF3573). This
family of proteins is functionally uncharacterized. This
protein is found in bacteria. Proteins in this family
are typically between 372 to 530 amino acids in length.
Length = 375
Score = 29.1 bits (65), Expect = 4.6
Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 3/80 (3%)
Query: 266 ENVNQHMLLMCSLVSKQQQQISTLKSALNKVTLNYSGTLIWKITDYSLKCQESIEL---L 322
+ +SK Q+QI +L++ +N + + L + YS K +S
Sbjct: 31 IQQTDSNQIDKKDISKLQKQIKSLQAQINHLEEQTNSNLSSQFATYSSKVNDSTLTGNGE 90
Query: 323 SPSFYTSQFGYKLQVSLFLN 342
+ Q + + N
Sbjct: 91 TKVLSLGQRNNNIASDIMSN 110
>gnl|CDD|206084 pfam13913, zf-C2HC_2, zinc-finger of a C2HC-type. This family
contains a number of divergent C2H2 type zinc fingers.
Length = 25
Score = 25.6 bits (57), Expect = 4.6
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 185 LVACRYCSKSYVADTLVTHQTKCT 208
LV C C + + D L H+ C
Sbjct: 2 LVPCPICGRKFAPDRLAKHEKVCK 25
>gnl|CDD|190261 pfam02257, RFX_DNA_binding, RFX DNA-binding domain. RFX is a
regulatory factor which binds to the X box of MHC class
II genes and is essential for their expression. The
DNA-binding domain of RFX is the central domain of the
protein and binds ssDNA as either a monomer or
homodimer.
Length = 73
Score = 27.1 bits (61), Expect = 4.7
Identities = 15/54 (27%), Positives = 20/54 (37%), Gaps = 12/54 (22%)
Query: 218 CEMVALPREELDVHIKEHCNSL------------LVSCVFKDAGCRFKGMRGET 259
E +LPR + H HC L L+ VF R G RG++
Sbjct: 19 SEGSSLPRNRVYAHYVSHCAELGLKPLSAASFGKLIRSVFPGLKTRRLGTRGQS 72
>gnl|CDD|212108 cd10796, GH57N_APU, N-terminal catalytic domain of thermoactive
amylopullulanases; glycoside hydrolase family 57 (GH57).
Pullulanases (EC 3.2.1.41) are capable of hydrolyzing
the alpha-1,6 glucosidic bonds of pullulan, producing
maltotriose. Amylopullulanases (APU, E.C 3.2.1.1/41)
are type II pullulanases which can also degrade both the
alpha-1,6 and alpha-1,4 glucosidic bonds of starch,
producing oligosaccharides. This subfamily includes GH57
archaeal thermoactive APUs, which show both
pullulanolytic and amylolytic activities. They have an
acid pH optimum and the presence of Ca2+ might increase
their activity, thermostability, and substrate affinity.
Besides GH57 thermoactive APUs, all mesophilic and some
thermoactive APUs belong to glycoside hydrolase family
13 with catalytic features distinct from GH57. This
subfamily also includes many uncharacterized proteins
found in bacteria and archaea.
Length = 313
Score = 29.1 bits (66), Expect = 5.0
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 7/40 (17%)
Query: 295 KVTLNYSGTLIWKITDYSL-----KCQES--IELLSPSFY 327
KVT N S +L+ ++ DY + + E IEL + +Y
Sbjct: 47 KVTFNLSPSLLEQLEDYGIIPLYRELAEEGQIELSTTPYY 86
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
0.320 0.132 0.411
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,406,020
Number of extensions: 1941036
Number of successful extensions: 1396
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1361
Number of HSP's successfully gapped: 36
Length of query: 450
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 350
Effective length of database: 6,502,202
Effective search space: 2275770700
Effective search space used: 2275770700
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: 61 (27.3 bits)