RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7814
(460 letters)
>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 = 134 bits (339), Expect = 9e-38
Identities = 58/151 (38%), Positives = 84/151 (55%), Gaps = 9/151 (5%)
Query: 311 GVYFWKMYNFPAKLKEMK-EINRYFYSACFYSSCFGYRFCTRVNISR---EDAQYLSLFI 366
G+Y WK+ NF + M+ +S FY+S GY+ C R+N+S Y+SLF+
Sbjct: 1 GIYVWKIKNFSNLRRSMEAGSPVVIHSPGFYTSPPGYKLCARLNLSLPEARCPNYISLFV 60
Query: 367 HLVQGENDDILDWPFVGRIRFTALNTSSEF-SITDEIQSDKNFDSFKRPVNFFLNKKAFG 425
HL+QGEND LDWPF G I T L+ S +I + + S +F+RP N K FG
Sbjct: 61 HLMQGENDSHLDWPFQGTITLTLLDQSEPRQNIHETMMSKPELLAFQRPTT-DRNPKGFG 119
Query: 426 FNNFIRVADVLDPGRGFLMEDDTFVIKTQVT 456
+ F + D+L RGF+ ++DT +IK +V
Sbjct: 120 YVEFAHIEDLLQ--RGFV-KNDTLLIKIEVN 147
>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 = 113 bits (286), Expect = 5e-30
Identities = 53/152 (34%), Positives = 84/152 (55%), Gaps = 11/152 (7%)
Query: 311 GVYFWKMYNFPAKLKEMK-EINRYFYSACFYSSCFGYRFCTRVNISRE---DAQYLSLFI 366
GV WK+ ++ KL+E N YS FY+S +GY+ C R+ ++ + +LSLF+
Sbjct: 1 GVLIWKIKDYSRKLQEAVAGSNTVLYSPPFYTSRYGYKLCLRLYLNGDGTGKGTHLSLFV 60
Query: 367 HLVQGENDDILDWPFVGRIRFTAL---NTSSEFSITDEIQSDKNFDSFKRPVNFFLNKKA 423
H+++GE D +L+WPF G+I T L + S IT+ D N +F+RP N
Sbjct: 61 HVMKGEYDALLEWPFRGKITLTLLDQSDDSKRKHITETFMPDPNSSAFQRPPT-GENNIG 119
Query: 424 FGFNNFIRVADVLDPGRGFLMEDDTFVIKTQV 455
FG+ F+ + + RG++ +DDT IK +V
Sbjct: 120 FGYPEFVPLEKLES--RGYV-KDDTLFIKVEV 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 = 71.6 bits (175), Expect = 1e-14
Identities = 46/167 (27%), Positives = 80/167 (47%), Gaps = 11/167 (6%)
Query: 296 QTEEIEDNVV-LKLC--NGVYFWKMYNFPAKLKE-MKEINRYFYSACFYSSCFGYRFCTR 351
++E V+ + +GV+ WK+ +F K +E + +S FY+S +GY+ C R
Sbjct: 1 AXADLEQKVLEXEASTYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLR 60
Query: 352 VNISRED---AQYLSLFIHLVQGENDDILDWPFVGRIRFTALNTSSEFSITDEIQSDKNF 408
+ ++ + +LSLF +++G ND +L WPF ++ L+ ++ + D + D
Sbjct: 61 IYLNGDGTGRGTHLSLFFVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTS 120
Query: 409 DSFKRPVNFFLNKKAFGFNNFIRVADVLDPGRGFLMEDDTFVIKTQV 455
SF+RPVN A G F V+ + + DD IK V
Sbjct: 121 SSFQRPVNDM--NIASGCPLFCPVSKX--EAKNSYVRDDAIFIKAIV 163
>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 = 67.1 bits (164), Expect = 2e-13
Identities = 46/157 (29%), Positives = 79/157 (50%), Gaps = 16/157 (10%)
Query: 311 GVYFWKMYNFPAKLKEMKEINRY-FYSACFYSSCFGYRFCTRV----NISREDAQYLSLF 365
G WK+ ++ KL+E K + +S FY+ +GY+ N S E + +LS++
Sbjct: 1 GTLLWKITDYSRKLQEAKGRDNLELFSPPFYTHRYGYKLQVSAFLNGNGSGEGS-HLSVY 59
Query: 366 IHLVQGENDDILDWPFVGRIRFTALNTSSEFS-----ITDEIQSDKNFDSFKRPVNFFLN 420
I ++ GE D++L+WPF RI FT L+ S IT+ D + +F++P L+
Sbjct: 60 IRVLPGEYDNLLEWPFSHRITFTLLDQSDPSLSKPQHITETFTPDPTWKNFQKPSASRLD 119
Query: 421 KK--AFGFNNFIRVADVLDPGRGFLMEDDTFVIKTQV 455
+ FG+ FI D+ R ++ +DD ++ V
Sbjct: 120 ESTLGFGYPKFISHEDLKK--RNYI-KDDAIFLRASV 153
>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 = 66.8 bits (163), Expect = 3e-13
Identities = 32/111 (28%), Positives = 60/111 (54%), Gaps = 6/111 (5%)
Query: 311 GVYFWKMYNFPAKLKE--MKEINRYFYSACFYSSCFGYRFCTRVNISREDA---QYLSLF 365
G + WK+ + K +E A FY++ +GY+ C R+ ++ + A ++SLF
Sbjct: 1 GTFLWKITDVSQKQRESSHGRDVSLCSPA-FYTAKYGYKVCLRLYLNGDGAGKGTHISLF 59
Query: 366 IHLVQGENDDILDWPFVGRIRFTALNTSSEFSITDEIQSDKNFDSFKRPVN 416
+++GE D +L WPF ++ F L+ ++ + D + D + SF+RPV+
Sbjct: 60 FVIMKGEYDALLPWPFRHKVTFMLLDQNNREHVIDAFRPDLSSASFQRPVS 110
>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 = 61.6 bits (149), Expect = 2e-11
Identities = 46/153 (30%), Positives = 77/153 (50%), Gaps = 14/153 (9%)
Query: 311 GVYFWKMYNFPAKLKEMKEINRY-FYSACFYSSCFGYRFCTRVNISREDA---QYLSLFI 366
G WK+ ++ K KE + + +S FY+S GYR C R ++ + + +LSL+
Sbjct: 1 GKLIWKVTDYKMKKKEAVDGHTVSIFSQPFYTSRCGYRLCARAYLNGDGSGKGTHLSLYF 60
Query: 367 HLVQGENDDILDWPFVGRIRFTALN-TSSEFSITDEIQSDKNFDSFKRP---VNFFLNKK 422
+++GE D +L WPF R+ L+ + + I + ++D N SFKRP +N
Sbjct: 61 VVMRGEFDSLLQWPFRQRVTLMLLDQSGKKNHIMETFKADPNSSSFKRPDGEMNI----- 115
Query: 423 AFGFNNFIRVADVLDPGRGFLMEDDTFVIKTQV 455
A G F+ VL+ + ++DDT +K V
Sbjct: 116 ASGCPRFV-AHSVLENAKNTYIKDDTLFLKVAV 147
>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 = 62.3 bits (151), Expect = 2e-11
Identities = 40/148 (27%), Positives = 76/148 (51%), Gaps = 14/148 (9%)
Query: 279 SMLEQKIKVNNFELNLKQTEEIEDNVVLKLC-----NGVYFWKMYNFPAKLKEM---KEI 330
+LE ++ ++ L++ + ++ ++ NGV WK+ ++ + +E K +
Sbjct: 2 GLLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTL 61
Query: 331 NRYFYSACFYSSCFGYRFCTRVNISRE---DAQYLSLFIHLVQGENDDILDWPFVGRIRF 387
+ YS FY+ FGY+ C RV ++ + +LSLF +++GE D +L WPF ++
Sbjct: 62 S--LYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTL 119
Query: 388 TALNT-SSEFSITDEIQSDKNFDSFKRP 414
++ SS + D + D N SFK+P
Sbjct: 120 MLMDQGSSRRHLGDAFKPDPNSSSFKKP 147
>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 = 58.5 bits (142), Expect = 1e-10
Identities = 36/148 (24%), Positives = 56/148 (37%), Gaps = 24/148 (16%)
Query: 311 GVYFWKMYNFPAKLKEMKEINRYFYSACFYSSCFGYRFCTRV--NISREDAQYLSLFIHL 368
G + WK+ NF + YS F GY++ R+ N E YLSL++ L
Sbjct: 1 GKHTWKIVNF------SELEGESIYSPPFEV--GGYKWRIRIYPNGDGESGDYLSLYLEL 52
Query: 369 VQGENDDILDWPFVGRIRFTALNTSSEFSITDEIQSDKNFDSFKRPVNFFLNKKAFGFNN 428
+GE+D W +N + K+ V F +GF
Sbjct: 53 DKGESDL-EKWSVRAEFTLKLVNQNGG----------KSLSKSFTHVFFSEKGSGWGFPK 101
Query: 429 FIRVADVLDPGRGFLMEDDTFVIKTQVT 456
FI D+ D + + DD+ I+ +V
Sbjct: 102 FISWDDLEDS---YYLVDDSLTIEVEVK 126
>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain,
a specialized type of Zn-finger of 40 to 60 residues
that binds two atoms of zinc; defined by the
'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)-
H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved
in mediating protein-protein interactions; identified
in a proteins with a wide range of functions such as
viral replication, signal transduction, and
development; has two variants, the C3HC4-type and a
C3H2C3-type (RING-H2 finger), which have different
cysteine/histidine pattern; a subset of RINGs are
associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
Length = 45
Score = 52.1 bits (125), Expect = 4e-09
Identities = 21/41 (51%), Positives = 27/41 (65%), Gaps = 2/41 (4%)
Query: 18 ECSICLEYLKDAI-LTSCGHKFCAACIDSWIDVKGKNYCPI 57
EC ICLE ++ + L CGH FC +CID W+ GKN CP+
Sbjct: 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLK-SGKNTCPL 40
>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 = 53.2 bits (128), Expect = 2e-08
Identities = 42/165 (25%), Positives = 63/165 (38%), Gaps = 37/165 (22%)
Query: 315 WKMYNFPAKLKEMKEINRYFYSACFYSSCFGYRFCTRVNI-SREDAQ-YLSLFIHLVQGE 372
W++ NF ++L E YS FYS GY F + E Y L+ HL GE
Sbjct: 6 WRVRNF-SQLLETTPKGTKIYSPRFYSPE-GYAFQVGLYPNGTESYPGYTGLYFHLCSGE 63
Query: 373 NDDILDWPFVGR------------IRFTALNTSSEFSIT---DEIQSDK----------- 406
NDD+L+WP R I+ S++ S T SD
Sbjct: 64 NDDVLEWPCPNRQATMTLLDQDPDIQ---QRMSNQRSFTTDPSMTSSDNGEYFWDRPSKV 120
Query: 407 -NFDSFKRPVNFFLNKKAFGFNNFIRVADVLDPGRGFLMEDDTFV 450
++D+ + +G++ FI + + R FL DD +
Sbjct: 121 GSYDTDTNGCTCY-RGPGYGWSTFISHSRLRR--RDFLKGDDLII 162
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 48.3 bits (115), Expect = 7e-08
Identities = 21/44 (47%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 15 PRFECSICLEYLKDA-ILTSCGHKFCAACIDSWIDVKGKNYCPI 57
EC ICL+ L+D +LT CGH FC CI ++ K K CPI
Sbjct: 1 EELECPICLDLLRDPVVLTPCGHVFCRECILRYLKKKSK--CPI 42
>gnl|CDD|214546 smart00184, RING, Ring finger. E3 ubiquitin-protein ligase
activity is intrinsic to the RING domain of c-Cbl and
is likely to be a general function of this domain;
Various RING fingers exhibit binding activity towards
E2 ubiquitin-conjugating enzymes (Ubc' s).
Length = 40
Score = 47.9 bits (114), Expect = 9e-08
Identities = 22/40 (55%), Positives = 27/40 (67%), Gaps = 2/40 (5%)
Query: 19 CSICLE-YLKDAILTSCGHKFCAACIDSWIDVKGKNYCPI 57
C ICLE YLKD ++ CGH FC +CI W++ G N CPI
Sbjct: 1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLE-SGNNTCPI 39
>gnl|CDD|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger). The
C3HC4 type zinc-finger (RING finger) is a cysteine-rich
domain of 40 to 60 residues that coordinates two zinc
ions, and has the consensus sequence:
C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C
where X is any amino acid. Many proteins containing a
RING finger play a key role in the ubiquitination
pathway.
Length = 40
Score = 46.7 bits (111), Expect = 2e-07
Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 19 CSICLEYLKDA-ILTSCGHKFCAACIDSWIDVKGKNYCPI 57
C ICLE KD + CGH FC+ CI SW++ CP+
Sbjct: 1 CPICLEEPKDPVTILPCGHLFCSKCILSWLESGNV-TCPL 39
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 46.2 bits (110), Expect = 3e-07
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 17 FECSICLEYLKD---AILTSCGHKFCAACIDSWIDVKGKNYCPI 57
EC ICL+ + ++ CGH F C+D W+ CP+
Sbjct: 1 DECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNT--CPL 42
>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 = 46.1 bits (110), Expect = 2e-06
Identities = 30/130 (23%), Positives = 53/130 (40%), Gaps = 21/130 (16%)
Query: 327 MKEINRYFYSACFYSSCFGYRFCTRVNISREDAQYLSLFIHLVQGENDDILDWPFVGRIR 386
+KE Y+ S Y FG + + I R +L L++H +GE D++L W
Sbjct: 7 IKEGENYYTS--PYEERFGIPWR--LRIYRNGG-FLGLYLHCEKGEKDELLGWSIETEFT 61
Query: 387 FTALNTSSEFSITDEIQSDKNFDSFKRPVNFFLNKKAFGFNNFIRVADVLDPGRGFLMED 446
++ + S+T +S F +G+ FI D+ + + D
Sbjct: 62 LKLVS-DNGKSLTKRNKSHV-----------FTKPTGYGWGKFISWDDLEND----YVVD 105
Query: 447 DTFVIKTQVT 456
DT +I+ +V
Sbjct: 106 DTIIIEAEVK 115
>gnl|CDD|239743 cd03774, MATH_SPOP, Speckle-type POZ protein (SPOP) family, MATH
domain; composed of proteins with similarity to human
SPOP. SPOP was isolated as a novel antigen recognized by
serum from a scleroderma patient, whose overexpression
in COS cells results in a discrete speckled pattern in
the nuclei. It contains an N-terminal MATH domain and a
C-terminal BTB (also called POZ) domain. Together with
Cul3, SPOP constitutes an ubiquitin E3 ligase which is
able to ubiquitinate the PcG protein BMI1, the variant
histone macroH2A1 and the death domain-associated
protein Daxx. Therefore, SPOP may be involved in the
regulation of these proteins and may play a role in
transcriptional regulation, apoptosis and X-chromosome
inactivation. Cul3 binds to the BTB domain of SPOP
whereas Daxx and the macroH2A1 nonhistone region have
been shown to bind to the MATH domain. Both MATH and BTB
domains are necessary for the nuclear speckled
accumulation of SPOP. There are many proteins, mostly
uncharacterized, containing both MATH and BTB domains
from C. elegans and plants which are excluded from this
family.
Length = 139
Score = 46.0 bits (109), Expect = 4e-06
Identities = 44/156 (28%), Positives = 66/156 (42%), Gaps = 26/156 (16%)
Query: 305 VLKLCNGVYFWKMYNFPAKLKEMKEINRYFYSACFYSSCFG-YRFCTRVN---ISREDAQ 360
V+K C Y W + NF +EM E S+ F S ++C RVN + E
Sbjct: 2 VVKFC---YMWTISNFSFCREEMGE---VIKSSTFSSGANDKLKWCLRVNPKGLDEESKD 55
Query: 361 YLSLFIHLVQGENDDILDWPFVGRIRFTALNTSSEFSITDEIQSDKNFDSFKRPVNFFLN 420
YLSL++ LV ++ + +F+ LN E + E Q F+
Sbjct: 56 YLSLYLLLVSCPKSEV--R---AKFKFSILNAKGEETKAMESQR----------AYRFVQ 100
Query: 421 KKAFGFNNFIRVADVLDPGRGFLMEDDTFVIKTQVT 456
K +GF FIR +LD G L+ DD + +V+
Sbjct: 101 GKDWGFKKFIRRDFLLDEANG-LLPDDKLTLFCEVS 135
>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 = 46.0 bits (109), Expect = 6e-06
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 315 WKMYNFPAKLKEMKEINRYFYSACFYSSCFGYRFCTRV----NISREDAQYLSLFIHLVQ 370
W++ NF +++ E S FYS GY + + N S Y L+ HL
Sbjct: 6 WRVRNF-SQILENTTKGDVLQSPRFYSP-EGYGYGVSLYPLSNESDYSGNYTGLYFHLCS 63
Query: 371 GENDDILDWPFVGR 384
GEND +L+WP + R
Sbjct: 64 GENDAVLEWPALNR 77
>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18. All proteins in this
family for which functions are known are involved in
nucleotide excision repair.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 397
Score = 47.7 bits (113), Expect = 7e-06
Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 13 LDPRFECSICLEYLKDAILTSCGHKFCAACIDSWIDVKGKNYCP 56
LD C IC ++ +LTSC H FC+ CI + + K CP
Sbjct: 23 LDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPK--CP 64
>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 = 45.2 bits (107), Expect = 1e-05
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 4/70 (5%)
Query: 313 YFWKMYNFPAKLKEMKEINRYFYSACFYSSCFGYRFCTRVNISREDAQ--YLSLFIHLVQ 370
+ W + NF +L N YS F SS GY F + ++ D L++++HL
Sbjct: 4 HIWHIRNF-TQLLATTPPNGKIYSPPFLSST-GYSFQVGLYLNGTDDYPGNLAIYLHLTS 61
Query: 371 GENDDILDWP 380
G NDD L WP
Sbjct: 62 GPNDDQLQWP 71
>gnl|CDD|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2;
Provisional.
Length = 193
Score = 44.3 bits (104), Expect = 3e-05
Identities = 15/30 (50%), Positives = 22/30 (73%)
Query: 17 FECSICLEYLKDAILTSCGHKFCAACIDSW 46
F+C+ICL+ ++D ++T CGH FC CI W
Sbjct: 19 FDCNICLDQVRDPVVTLCGHLFCWPCIHKW 48
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 37.7 bits (88), Expect = 5e-04
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 4/43 (9%)
Query: 16 RFECSICLEYLKDAILTSCGHK-FCAACIDSWIDVKGKNYCPI 57
C ICLE ++ + CGH C C ++ K CPI
Sbjct: 2 DDLCVICLERPRNVVFLPCGHLCLCEEC---AKRLRSKKKCPI 41
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 40.9 bits (96), Expect = 7e-04
Identities = 21/48 (43%), Positives = 27/48 (56%), Gaps = 10/48 (20%)
Query: 18 ECSICLEYLKD--------AILTSCGHKFCAACIDSWIDVKGKNYCPI 57
EC+IC+E + D IL++C H FC CID W K KN CP+
Sbjct: 176 ECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIW--KKEKNTCPV 221
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase
[Signal transduction mechanisms].
Length = 391
Score = 40.8 bits (95), Expect = 0.001
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 13 LDPRFECSICLEYLKDAILTSCGHKFCAACIDSWIDVKGKNYCPI 57
LD C IC + T+CGH FC+ CI + + +CP+
Sbjct: 22 LDSMLRCRICDCRISIPCETTCGHTFCSLCIRRHL--GTQPFCPV 64
>gnl|CDD|222135 pfam13445, zf-RING_LisH, RING-type zinc-finger, LisH dimerisation
motif. This zinc-finger is the dimerisation motif for
LisH proteins, and is also a typical RING-type of plant
ubiquitin ligases.
Length = 55
Score = 36.5 bits (85), Expect = 0.001
Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 4/53 (7%)
Query: 9 NKLNLDPRFECSICLEYLKDA----ILTSCGHKFCAACIDSWIDVKGKNYCPI 57
+ F C I E + D ++ CGH + ++ GK CP
Sbjct: 3 YAHHFHSIFVCPISKEVMTDEENPPVMLPCGHVYSRKALEKLAKNGGKFKCPY 55
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 39.9 bits (93), Expect = 0.001
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 17 FECSICLEYLKDAILTSCGHKFCAACIDSWIDVKGKNYCPI-DEKVLTKDDI 67
++C +CLE + T CGH FC +C+ K +CP+ KV K I
Sbjct: 216 YKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKVI 267
>gnl|CDD|227481 COG5152, COG5152, Uncharacterized conserved protein, contains RING
and CCCH-type Zn-fingers [General function prediction
only].
Length = 259
Score = 37.0 bits (85), Expect = 0.012
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 2 EHQPVANNKLNLDPRFECSICLEYLKDAILTSCGHKFCAAC 42
E PV + P F C IC + + ++T CGH FC+ C
Sbjct: 183 EEAPVISGPGEKIP-FLCGICKKDYESPVVTECGHSFCSLC 222
>gnl|CDD|221705 pfam12678, zf-rbx1, RING-H2 zinc finger. There are 8 cysteine/
histidine residues which are proposed to be the
conserved residues involved in zinc binding. The
protein, of which this domain is the conserved region,
participates in diverse functions relevant to
chromosome metabolism and cell cycle control.
Length = 73
Score = 33.9 bits (78), Expect = 0.017
Identities = 14/53 (26%), Positives = 20/53 (37%), Gaps = 15/53 (28%)
Query: 19 CSICLEYLKDA-------------ILTSCGHKFCAACIDSWIDVKGKNYCPID 58
C+IC + + CGH F CI W+ K +N CP+
Sbjct: 22 CAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWL--KTRNTCPLC 72
>gnl|CDD|239741 cd03772, MATH_HAUSP, Herpesvirus-associated ubiquitin-specific
protease (HAUSP, also known as USP7) family, N-terminal
MATH (TRAF-like) domain; composed of proteins similar to
human HAUSP, an enzyme that specifically catalyzes the
deubiquitylation of p53 and MDM2, hence playing an
important role in the p53-MDM2 pathway. It contains an
N-terminal TRAF-like domain and a C-terminal catalytic
protease (C19 family) domain. The tumor suppressor p53
protein is a transcription factor that responds to many
cellular stress signals and is regulated primarily
through ubiquitylation and subsequent degradation. MDM2
is a RING-finger E3 ubiquitin ligase that promotes p53
ubiquitinylation. p53 and MDM2 bind to the same site in
the N-terminal TRAF-like domain of HAUSP in a mutually
exclusive manner. HAUSP also interacts with the
Epstein-Barr nuclear antigen 1 (EBNA1) protein of the
Epstein-Barr virus (EBV), which efficiently immortalizes
infected cells predisposing the host to a variety of
cancers. EBNA1 plays several important roles in EBV
latent infection and cellular transformation. It binds
the same pocket as p53 in the HAUSP TRAF-like domain.
Through interactions with p53, MDM2 and EBNA1, HAUSP
plays a role in cell proliferation, apoptosis and
EBV-mediated immortalization.
Length = 137
Score = 34.4 bits (79), Expect = 0.040
Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 402 IQSDKNFDSFKRPVN--FFLNKKAFGFNNFIRVADVLDPGRGFLMEDDTFVIKTQVT 456
I + SF R ++ FF + +GF+NF+ ++V DP +GF+ EDDT ++ V
Sbjct: 76 INYKDDEPSFSRRISHLFFSKENDWGFSNFMTWSEVTDPEKGFI-EDDTITLEVYVQ 131
>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 374
Score = 35.4 bits (81), Expect = 0.056
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 18 ECSICLE-YLKD--AILTSCGHKFCAACIDSWIDVKGKNYCPI 57
EC+IC+ ++K+ + C H+F C+D W+ + N CP+
Sbjct: 325 ECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWL-LGYSNKCPV 366
>gnl|CDD|128780 smart00504, Ubox, Modified RING finger domain. Modified RING
finger domain, without the full complement of
Zn2+-binding ligands. Probable involvement in
E2-dependent ubiquitination.
Length = 63
Score = 32.2 bits (74), Expect = 0.057
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 17 FECSICLEYLKDAILTSCGHKFCAACIDSWIDVKGKNYCPIDEKVLTKDDIFIDNYTRRE 76
F C I LE +KD ++ G + + I+ W+ G P+ + LT +D+ I N +
Sbjct: 2 FLCPISLEVMKDPVILPSGQTYERSAIEKWLLSHGT--DPVTGQPLTHEDL-IPNLALKS 58
>gnl|CDD|201191 pfam00378, ECH, Enoyl-CoA hydratase/isomerase family. This
family contains a diverse set of enzymes including:
Enoyl-CoA hydratase. Napthoate synthase. Carnitate
racemase. 3-hydoxybutyryl-CoA dehydratase.
Dodecanoyl-CoA delta-isomerase.
Length = 245
Score = 32.7 bits (75), Expect = 0.29
Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 6/44 (13%)
Query: 3 HQPVANNKLNLDPRFECSICLEYLKD------AILTSCGHKFCA 40
+P A N L+ + E LE L+ +LT F A
Sbjct: 14 DRPEAVNALSAELLTELIQALEKLEQDPSVKAIVLTGGPGAFSA 57
>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 1525
Score = 33.1 bits (75), Expect = 0.37
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 11/59 (18%)
Query: 10 KLNLDPRF----ECSICLEYLK--DAILTS-----CGHKFCAACIDSWIDVKGKNYCPI 57
K N+D +F EC+IC L D L S C +KF C+ W ++ CP+
Sbjct: 1459 KKNIDEKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPL 1517
>gnl|CDD|203049 pfam04564, U-box, U-box domain. This domain is related to the
Ring finger pfam00097 but lacks the zinc binding
residues.
Length = 73
Score = 30.0 bits (68), Expect = 0.43
Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 2/63 (3%)
Query: 17 FECSICLEYLKDAILTSCGHKFCAACIDSWIDVKGKNYCPIDEKVLTKDDIFIDNYTRRE 76
F I LE +KD ++ G + + I+ + P + LT D + I N +E
Sbjct: 5 FLDPITLELMKDPVILPSGITYDRSTIERHLL-SVDPTDPFTREPLTHDQL-IPNLELKE 62
Query: 77 ILE 79
++
Sbjct: 63 KID 65
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 32.3 bits (73), Expect = 0.52
Identities = 16/67 (23%), Positives = 23/67 (34%), Gaps = 4/67 (5%)
Query: 19 CSICLEYLKDAILTSCGHKFCAACIDSWIDVKGKNYCPI----DEKVLTKDDIFIDNYTR 74
C IC + CGH+ C AC + + CP+ E V+ D R
Sbjct: 64 CQICAGSTTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTETEAVVFTASSPADITDR 123
Query: 75 REILENN 81
R+
Sbjct: 124 RQWKGRE 130
>gnl|CDD|227521 COG5194, APC11, Component of SCF ubiquitin ligase and
anaphase-promoting complex [Posttranslational
modification, protein turnover, chaperones / Cell
division and chromosome partitioning].
Length = 88
Score = 29.8 bits (67), Expect = 0.74
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 34 CGHKFCAACIDSWIDVKGKNYCPIDEK 60
C H F CI W+D KG CP+D +
Sbjct: 54 CNHAFHDHCIYRWLDTKGV--CPLDRQ 78
>gnl|CDD|206613 pfam14447, Prok-RING_4, Prokaryotic RING finger family 4. RING
finger family domain found sporadically in bacteria.
The finger is fused to an N-terminal alpha-helical
domain, ROT/Trove-like repeats and a C-terminal TerD
domain. The architecture suggests a possible role in an
RNA-processing complex.
Length = 55
Score = 28.5 bits (64), Expect = 0.85
Identities = 13/58 (22%), Positives = 14/58 (24%), Gaps = 8/58 (13%)
Query: 13 LDPRFECSICLEYLKDAILTSCGHKFCAACIDSWIDVKGKNY--CPIDEKVLTKDDIF 68
P C C +L CGH D Y CP D F
Sbjct: 4 QQPEQPCLFCGTVGTKGVLLPCGHLIPDGTFDGE------RYNGCPFCGTPFEPDSPF 55
>gnl|CDD|193335 pfam12861, zf-Apc11, Anaphase-promoting complex subunit 11
RING-H2 finger. Apc11 is one of the subunits of the
anaphase-promoting complex or cyclosome. The APC
subunits are cullin family proteins with ubiquitin
ligase activity. Polyubiquitination marks proteins for
degradation by the 26S proteasome and is carried out by
a cascade of enzymes that includes ubiquitin-activating
enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and
ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and
is responsible for recruiting E2s to the APC and for
mediating the subsequent transfer of ubiquitin to APC
substrates in vivo. In Saccharomyces cerevisiae this
RING-H2 finger protein defines the minimal ubiquitin
ligase activity of the APC, and the integrity of the
RING-H2 finger is essential for budding yeast cell
viability.
Length = 85
Score = 29.4 bits (66), Expect = 0.87
Identities = 9/35 (25%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 30 ILTSCGHKFCAACIDSWIDVKG-KNYCPIDEKVLT 63
+ C H F CI W+ + K CP+ +
Sbjct: 48 VWGKCKHNFHMHCILKWLATETSKGLCPMCRQTFV 82
>gnl|CDD|214496 smart00061, MATH, meprin and TRAF homology.
Length = 95
Score = 29.2 bits (66), Expect = 1.3
Identities = 22/109 (20%), Positives = 38/109 (34%), Gaps = 22/109 (20%)
Query: 323 KLKEMKEINRYFYSACFYSSCFGYRFCTRVNISREDAQYLSLFIHLVQGENDDILDWPFV 382
+ ++E YF S F + R+ I R++ +LSL++H + E D W
Sbjct: 8 NVSRLEEGESYF-SPSEE--HFNIPW--RLKIYRKN-GFLSLYLHCEKEECDS-RKWSIE 60
Query: 383 GRIRFTALNTSSEFSITDEIQSDKNFDSFKRPVNF-FLNKKAFGFNNFI 430
++ N S + F +GF+ FI
Sbjct: 61 AEFTLKLVSQ--------------NGKSLSKKDKHVFEKPSGWGFSKFI 95
>gnl|CDD|222981 PHA03096, PHA03096, p28-like protein; Provisional.
Length = 284
Score = 30.9 bits (70), Expect = 1.3
Identities = 27/110 (24%), Positives = 42/110 (38%), Gaps = 16/110 (14%)
Query: 9 NKLNLDPRFECSICLEYLK--------DAILTSCGHKFCAACIDSWIDVK-GKNYCPIDE 59
+L L C ICLE +K IL+ H+F CI W+ K P +
Sbjct: 171 YQLRLLLSKICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENR 230
Query: 60 KVLTKDDIFIDNYTRREILENNLTCPY----KQCSSQLSIPEYESHVNTC 105
++ T + + E L+NN+ Y K + LS + H+
Sbjct: 231 RLNT---VIVFIEKINEDLKNNIPSRYWIDDKYDKNLLSFRYKKMHIRKV 277
>gnl|CDD|165237 PHA02926, PHA02926, zinc finger-like protein; Provisional.
Length = 242
Score = 30.0 bits (67), Expect = 2.4
Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 13/53 (24%)
Query: 18 ECSICLEYLKD---------AILTSCGHKFCAACIDSWIDVK----GKNYCPI 57
EC IC E + +L SC H FC CI+ W + + CPI
Sbjct: 172 ECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPI 224
>gnl|CDD|233064 TIGR00633, xth, exodeoxyribonuclease III (xth). All proteins in
this family for which functions are known are 5' AP
endonucleases that funciton in base excision repair and
the repair of abasic sites in DNA.This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 255
Score = 28.8 bits (65), Expect = 5.2
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 28 DAILTSCGHKFCAACIDSWID--VKGKNYCPI 57
D L S +DS+ID ++G ++CPI
Sbjct: 221 DYFLVS--EPLAERVVDSYIDSEIRGSDHCPI 250
>gnl|CDD|233368 TIGR01350, lipoamide_DH, dihydrolipoamide dehydrogenase. This
model describes dihydrolipoamide dehydrogenase, a
flavoprotein that acts in a number of ways. It is the E3
component of dehydrogenase complexes for pyruvate,
2-oxoglutarate, 2-oxoisovalerate, and acetoin. It can
also serve as the L protein of the glycine cleavage
system. This family includes a few members known to have
distinct functions (ferric leghemoglobin reductase and
NADH:ferredoxin oxidoreductase) but that may be
predicted by homology to act as dihydrolipoamide
dehydrogenase as well. The motif GGXCXXXGCXP near the
N-terminus contains a redox-active disulfide.
Length = 460
Score = 28.4 bits (64), Expect = 8.3
Identities = 9/30 (30%), Positives = 18/30 (60%)
Query: 285 IKVNNFELNLKQTEEIEDNVVLKLCNGVYF 314
I+V N ++ ++ ++ ++ VV KL GV
Sbjct: 68 IEVENVSVDWEKMQKRKNKVVKKLVGGVSG 97
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are
components of TFIIH, a complex that is involved in
nucleotide excision repair and transcription
initiation. Also known as MAT1 (menage a trois 1). This
family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and
repair].
Length = 309
Score = 28.2 bits (63), Expect = 8.6
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 34 CGHKFCAACIDSWIDVKGKNYCPIDEKVLTKDD----IFIDNYTRREI 77
CGH C +C+D + V+G CP + L K++ +F D +E+
Sbjct: 26 CGHTLCESCVDL-LFVRGSGSCPECDTPLRKNNFRVQLFEDPTVEKEV 72
>gnl|CDD|173109 PRK14646, PRK14646, hypothetical protein; Provisional.
Length = 155
Score = 27.6 bits (61), Expect = 9.1
Identities = 19/52 (36%), Positives = 32/52 (61%), Gaps = 9/52 (17%)
Query: 372 ENDDILDWPFVGRIRFTALNTSSEFSITDEIQSDKNFDSFKR-PVNFFLNKK 422
EN ++L+ +V L SS+ ++DE+ S+++F +FK PVN LN+K
Sbjct: 67 ENSNLLNCSYV-------LEISSQ-GVSDELTSERDFKTFKGFPVNVELNQK 110
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 0.135 0.410
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,548,762
Number of extensions: 2103616
Number of successful extensions: 1599
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1572
Number of HSP's successfully gapped: 57
Length of query: 460
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 360
Effective length of database: 6,502,202
Effective search space: 2340792720
Effective search space used: 2340792720
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)