RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16005
(248 letters)
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 79.3 bits (196), Expect = 2e-17
Identities = 47/202 (23%), Positives = 85/202 (42%), Gaps = 27/202 (13%)
Query: 51 SDIYTEHSCAVNVAKYSPSGFYIASGDISGKVRIWDTVNKEHILKNEFHPIGGPIKDIAW 110
H+ V +SP G +A+G G +++WD E + + H GP++D+A
Sbjct: 2 RRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHT--GPVRDVAA 59
Query: 111 SPDNQRMIS----------IVENGAKVSSL-----PIDYEPSSISLDHEHGLVAVGGADS 155
S D + S +E G V +L + SS++ + +++ D
Sbjct: 60 SADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYV----SSVAFSPDGRILSSSSRDK 115
Query: 156 KISI--VENGAKVSSLP-IDYEPSSISLDHEHGLVAVGGADSKVHIYELNNKSLSPKAEL 212
I + VE G +++L +S++ + VA D + +++L + A L
Sbjct: 116 TIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLR--TGKCVATL 173
Query: 213 -DHLGPVTDCSFSPSNEYLVAS 233
H G V +FSP E L++S
Sbjct: 174 TGHTGEVNSVAFSPDGEKLLSS 195
Score = 70.1 bits (172), Expect = 3e-14
Identities = 31/211 (14%), Positives = 69/211 (32%), Gaps = 39/211 (18%)
Query: 38 NSVIIRNIENPAISDIYTEHSCAVNVAKYSPSGFYIASGDISGKVRIWDTVNKEHILKNE 97
++ + ++E T H+ V+ +SP G ++S +++WD +
Sbjct: 73 KTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGK--CLTT 130
Query: 98 FHPIGGPIKDIAWSPDNQRMISIVENGAKVSSLPIDYEPSSISLDHEHGLVAVGGADSKI 157
+ +A+SPD VA D I
Sbjct: 131 LRGHTDWVNSVAFSPDGT-------------------------------FVASSSQDGTI 159
Query: 158 SI--VENGAKVSSLPIDYEP-SSISLDHEHGLVAVGGADSKVHIYELNNKSLSPKAELD- 213
+ + G V++L +S++ + + +D + +++L+ L
Sbjct: 160 KLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKC--LGTLRG 217
Query: 214 HLGPVTDCSFSPSNEYLVASDAHRKVVLYRV 244
H V +FSP L + + ++ +
Sbjct: 218 HENGVNSVAFSPDGYLLASGSEDGTIRVWDL 248
Score = 63.9 bits (156), Expect = 5e-12
Identities = 35/198 (17%), Positives = 75/198 (37%), Gaps = 37/198 (18%)
Query: 38 NSVIIRNIENPAISDIYTEHSCAVNVAKYSPSGFYIASGDISGKVRIWDTVNKEHILKNE 97
++ + ++E H+ VN +SP G ++AS G +++WD + +
Sbjct: 115 KTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLT 174
Query: 98 FHPIGGPIKDIAWSPDNQRMISIVENGAKVSSLPIDYEPSSISLDHEHGLVAVGGADSKI 157
H G + +A+SPD ++++S +D I
Sbjct: 175 GHT--GEVNSVAFSPDGEKLLS-------------------------------SSSDGTI 201
Query: 158 SIVE--NGAKVSSLPI-DYEPSSISLDHEHGLVAVGGADSKVHIYELNNKSLSPKAELDH 214
+ + G + +L + +S++ + L+A G D + +++L H
Sbjct: 202 KLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSG-H 260
Query: 215 LGPVTDCSFSPSNEYLVA 232
VT ++SP + L +
Sbjct: 261 TNSVTSLAWSPDGKRLAS 278
Score = 46.6 bits (111), Expect = 4e-06
Identities = 22/116 (18%), Positives = 48/116 (41%), Gaps = 6/116 (5%)
Query: 137 SSISLDHEHGLVAVGGADSKISI--VENGAKVSSLPIDYEP-SSISLDHEHGLVAVGGAD 193
+ ++ + L+A G D I + +E G + +L P ++ + +A G +D
Sbjct: 13 TCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSD 72
Query: 194 SKVHIYELNNKSLSPKAEL-DHLGPVTDCSFSPSNEYLVASDAHRKVVLYRVPDFE 248
+ +++L L H V+ +FSP L +S + + ++ V +
Sbjct: 73 KTIRLWDLETGECV--RTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGK 126
Score = 28.5 bits (64), Expect = 3.1
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 214 HLGPVTDCSFSPSNEYLVASDAHRKVVLYRVPDFE 248
H G VT +FSP + L + ++ + E
Sbjct: 8 HTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGE 42
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 55.1 bits (131), Expect = 8e-09
Identities = 38/196 (19%), Positives = 71/196 (36%), Gaps = 29/196 (14%)
Query: 53 IYTEHSCAVNVAKYSPSGFYIASGDISGKVRIWDTVNKEHILKNEFHPIGGPIKDIAWSP 112
+ HS +V +SP G +ASG G VR+WD + + GP+ +++SP
Sbjct: 279 TLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSP 338
Query: 113 DNQRMISIVENGAKVSSLPIDYEPSSISLDHEHGLVAVGGADSKISIVENGAKVSSLPID 172
D ++S + + + +L+ +
Sbjct: 339 DGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHSNV------------------------- 373
Query: 173 YEPSSISLDHEHGLVAVGGADSKVHIYELNNKSLSPKAELDHLGPVTDCSFSPSNEYLVA 232
S+S + +V+ G D V +++L+ SL H VT FSP + L +
Sbjct: 374 ---LSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRN-LDGHTSRVTSLDFSPDGKSLAS 429
Query: 233 SDAHRKVVLYRVPDFE 248
+ + L+ +
Sbjct: 430 GSSDNTIRLWDLKTSL 445
Score = 49.3 bits (116), Expect = 6e-07
Identities = 45/247 (18%), Positives = 88/247 (35%), Gaps = 23/247 (9%)
Query: 20 PIVLGGDPKGKNFLYTNGNSVIIRNIENPAISDIYTEHSCAVNVAKYSPSGFYIASGDIS 79
++ G + L + ++ + S + H ++ +SP G + SG
Sbjct: 29 SLLSLGSSESGILLLALLSDSLVSLPD--LSSLLLRGHEDSITSIAFSPDGELLLSGSSD 86
Query: 80 GKVRIWDTVNKEHILKNEFHPIGGPIKDIAW-SPDNQRMISIVENG---AKVSSLPIDYE 135
G +++WD N E ++K+ + +A SPD ++ + K+ L +
Sbjct: 87 GTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNSILLASSSLDGTVKLWDLSTPGK 146
Query: 136 PSSISLDHEHG------------LVAVGGADSKISI--VENGAKVSSLPIDYEPSSISLD 181
H L + D I + + G +S+L +P S
Sbjct: 147 LIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAF 206
Query: 182 HEHG--LVAVGGADSKVHIYELNNKSLSPKAELDHLGPVTDCSFSPSNEYLVASDAHRKV 239
G L+A G +D + +++L+ L H V SFSP L + + +
Sbjct: 207 SPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSV-VSSFSPDGSLLASGSSDGTI 265
Query: 240 VLYRVPD 246
L+ +
Sbjct: 266 RLWDLRS 272
Score = 47.8 bits (112), Expect = 2e-06
Identities = 45/216 (20%), Positives = 82/216 (37%), Gaps = 40/216 (18%)
Query: 26 DPKGKNFLYTNG---NSVIIRNIENPA-ISDIYTEHSCAVNVAKYSPSGFYIASG-DISG 80
P G + L + +V + ++ P + HS +V +SP G +ASG + G
Sbjct: 119 SPDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDG 178
Query: 81 KVRIWDTVNKEHILKNEFHPIGGPIKDIAWSPDNQRMISIVENGAKVSSLPIDYEPSSIS 140
+++WD + + H P+ +A+SPD +I
Sbjct: 179 TIKLWDLRTGKPLSTLAGHT--DPVSSLAFSPDGGLLI---------------------- 214
Query: 141 LDHEHGLVAVGGADSKISI--VENGAKVSSLPIDYEPSSISLDHEHG-LVAVGGADSKVH 197
A G +D I + + G + S + S +S G L+A G +D +
Sbjct: 215 --------ASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIR 266
Query: 198 IYELNNKSLSPKAELDHLGPVTDCSFSPSNEYLVAS 233
+++L + S + H V +FSP + L +
Sbjct: 267 LWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASG 302
Score = 31.6 bits (70), Expect = 0.37
Identities = 12/58 (20%), Positives = 24/58 (41%)
Query: 38 NSVIIRNIENPAISDIYTEHSCAVNVAKYSPSGFYIASGDISGKVRIWDTVNKEHILK 95
+V + ++ ++ H+ V +SP G +ASG +R+WD +
Sbjct: 392 GTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDLKTSLKSVS 449
>gnl|CDD|197651 smart00320, WD40, WD40 repeats. Note that these repeats are
permuted with respect to the structural repeats
(blades) of the beta propeller domain.
Length = 40
Score = 39.2 bits (92), Expect = 5e-05
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 53 IYTEHSCAVNVAKYSPSGFYIASGDISGKVRIWD 86
H+ V +SP G Y+ASG G +++WD
Sbjct: 7 TLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 30.0 bits (68), Expect = 0.10
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 214 HLGPVTDCSFSPSNEYLVASDAHRKVVLY 242
H GPVT +FSP +YL + + L+
Sbjct: 11 HTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
Score = 25.0 bits (55), Expect = 7.1
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 94 LKNEFHPIGGPIKDIAWSPDNQRMIS 119
L GP+ +A+SPD + + S
Sbjct: 4 LLKTLKGHTGPVTSVAFSPDGKYLAS 29
>gnl|CDD|149648 pfam08662, eIF2A, Eukaryotic translation initiation factor eIF2A.
This is a family of eukaryotic translation initiation
factors.
Length = 194
Score = 41.1 bits (97), Expect = 1e-04
Identities = 27/111 (24%), Positives = 44/111 (39%), Gaps = 14/111 (12%)
Query: 27 PKGKNFLYTNGNSVIIRNIENPAISDIYTEHSCAVNVAKYSPSGFYIAS---GDISGKVR 83
P GK F G + + I++ N +SP G + G+++G++
Sbjct: 69 PNGKEFAVIYGYMPAKITFFDLKGNVIHSLGEQPRNTIFWSPFGRLVLLAGFGNLAGQIE 128
Query: 84 IWDTVNKEHILKNEFHPIGGPIKDIAWSPDNQRMISI-------VENGAKV 127
WD NK+ I E D WSPD + ++ V+NG K+
Sbjct: 129 FWDVKNKKKIATAE-ASNA---TDCEWSPDGRYFLTATTSPRLRVDNGFKI 175
Score = 26.8 bits (60), Expect = 7.9
Identities = 27/136 (19%), Positives = 48/136 (35%), Gaps = 39/136 (28%)
Query: 103 GPIKDIAWSPDNQRMISIVENGAKVSSLPIDYEPSSISLDHEHGLVAVGGADSKISIVEN 162
GPI D AWSP N + +++ Y P+ I+ +
Sbjct: 60 GPIHDFAWSP-NGKEFAVIYG----------YMPAKITF-FDL----------------K 91
Query: 163 GAKVSSLPIDYEPSSISLDHEHGLVAVGGADS---KVHIYELNNKSL--SPKAELDHLGP 217
G + SL + LV + G + ++ +++ NK + +A
Sbjct: 92 GNVIHSLGEQPRNTIFWSPFGR-LVLLAGFGNLAGQIEFWDVKNKKKIATAEASN----- 145
Query: 218 VTDCSFSPSNEYLVAS 233
TDC +SP Y + +
Sbjct: 146 ATDCEWSPDGRYFLTA 161
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 37.7 bits (88), Expect = 2e-04
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 53 IYTEHSCAVNVAKYSPSGFYIASGDISGKVRIWD 86
H+ V +SP G +ASG G VR+WD
Sbjct: 6 TLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 30.4 bits (69), Expect = 0.063
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 214 HLGPVTDCSFSPSNEYLVASDAHRKVVLY 242
H GPVT +FSP L + V ++
Sbjct: 10 HTGPVTSVAFSPDGNLLASGSDDGTVRVW 38
>gnl|CDD|217409 pfam03178, CPSF_A, CPSF A subunit region. This family includes a
region that lies towards the C-terminus of the cleavage
and polyadenylation specificity factor (CPSF) A (160
kDa) subunit. CPSF is involved in mRNA polyadenylation
and binds the AAUAAA conserved sequence in pre-mRNA.
CPSF has also been found to be necessary for splicing of
single-intron pre-mRNAs. The function of the aligned
region is unknown but may be involved in RNA/DNA
binding.
Length = 318
Score = 34.1 bits (79), Expect = 0.049
Identities = 15/77 (19%), Positives = 25/77 (32%), Gaps = 4/77 (5%)
Query: 165 KVSSLPIDYEPSSISLDHEHGLVAVGGADSKVHIYELNNKSLSPKAELDHLGPVTDCSFS 224
V + +++ L G K+ +Y+L L PKA LD S
Sbjct: 79 LVHKTEVKGAVTALCEFQGRLLAGQG---QKLRVYDLGKDKLLPKAFLD-TPITYVVSLK 134
Query: 225 PSNEYLVASDAHRKVVL 241
++ D + V
Sbjct: 135 VFGNRIIVGDLMKSVTF 151
>gnl|CDD|218251 pfam04762, IKI3, IKI3 family. Members of this family are
components of the elongator multi-subunit component of a
novel RNA polymerase II holoenzyme for transcriptional
elongation. This region contains WD40 like repeats.
Length = 903
Score = 31.9 bits (73), Expect = 0.33
Identities = 24/110 (21%), Positives = 42/110 (38%), Gaps = 14/110 (12%)
Query: 142 DHEHGL-VAVGGADSKISIVENGAKVSSLPIDYEPSSISLDHEHGLVAVGGAD-SKVHIY 199
D E L + V +I IV+ S +++G VAV D S + +
Sbjct: 342 DPEKPLTLHVLTESGQILIVD-------FAWTVARSPTLSPNDNGTVAV--IDGSTLLLT 392
Query: 200 ELNNKSLSP---KAELDHLGPVTDCSFSPSNEYLVASDAHRKVVLYRVPD 246
L ++ P EL+ + D +FS SN + + + +Y +
Sbjct: 393 PLRLANVPPPMSARELELPSNINDVAFSKSNSCVAVLTSDGDISIYELSL 442
>gnl|CDD|240468 cd12888, SPRY_PRY_TRIM7_like, PRY/SPRY domain in tripartite
motif-binding protein 7 (TRIM7)-like, including TRIM7,
TRIM10, TRIM15, TRIM26, TRIM39, TRIM41. This domain,
consisting of the distinct N-terminal PRY subdomain
followed by the SPRY subdomain, is found at the
C-terminus of several tripartite motif-containing (TRIM)
proteins, including TRIM7 (also referred to as
glycogenin-interacting protein, RING finger protein 90
or RNF90), TRIM10, TRIM15, TRIM26, TRIM39 and TRIM41.
TRIM7 or GNIP interacts with glycogenin and stimulates
its self-glucosylating activity via its SPRY domain.
TRIM10 (also known as hematopoietic RING finger 1
(HERF1) or TRIM10/HERF1) plays a key role in definitive
erythroid development; downregulation of the Spi-1/PU.1
oncogene induces the expression of TRIM10/HERF1, a key
factor required for terminal erythroid cell
differentiation and survival. Antiviral activity of
TRIM15 is dependent on the ability of its B-box to
interact with the MLV Gag precursor protein;
downregulation of TRIM15, along with TRIM11, enhances
virus release suggesting that these proteins contribute
to the endogenous restriction of retroviruses in cells.
Tripartite motif-containing 26 (TRIM26) function is as
yet unknown; however, since it is localized in the human
histocompatibility complex (MHC) class I region, TRIM26
may play a role in immune response although studies show
no association between TRIM26 polymorphisms and the risk
of aspirin-exacerbated respiratory disease. TRIM39 is a
MOAP-1 (Modulator of Apoptosis)-binding protein that
stabilizes MOAP-1 through inhibition of its
poly-ubiquitination process. TRIM41 (also known as RING
finger-interacting protein with C kinase or RINCK)
functions as an E3 ligase that catalyzes the
ubiquitin-mediated degradation of protein kinase C.
Length = 171
Score = 30.2 bits (69), Expect = 0.61
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 3/65 (4%)
Query: 138 SISLDHEHGLVAVGGADSKISIVENGAKVSSLPIDYEPSSI--SLDHEHGLVAVGGADSK 195
+S E G+ AVG + + + L + EP I LD+E G VA AD++
Sbjct: 81 EVSFSPEEGIWAVGKWGGQYWALTSPETRLPLSLC-EPRRIRVYLDYEAGQVAFYDADTQ 139
Query: 196 VHIYE 200
HI+
Sbjct: 140 AHIFT 144
>gnl|CDD|240485 cd12905, SPRY_PRY_TRIM_Bty_69_NF7, PRY/SPRY domain in tripartite
motif-containing protein 69 (TRIM69), Bloodthirsty (bty)
and NF7. This domain, consisting of the distinct
N-terminal PRY subdomain followed by the SPRY subdomain,
is found at the C-terminus of TRIM69 and TRIM proteins
NF7 and bloodthirsty (bty). TRIM69 is a novel testis E3
ubiquitin ligase that may function to ubiquitinate its
particular substrates during spermatogenesis. In humans,
TRIM69 localizes in the cytoplasm and nucleus, and
requires an intact RING finger domain to function. TRIM
protein NF7, which also contains a chromodomain (CHD) at
the N-terminus and an RFP (Ret finger protein)-like
domain at the C-terminus, is required for its
association with transcriptional units of RNA polymerase
II which is mediated by a trimeric B box. In Xenopus
oocyte, xNF7 has been identified as a nuclear
microtubule-associated protein (MAP) whose
microtubule-bundling activity, but not E3-ligase
activity, contributes to microtubule organization and
spindle integrity. Bloodthirsty (bty) is a novel gene
identified in zebrafish and has been shown to likely
play a role in in regulation of the terminal steps of
erythropoiesis.
Length = 176
Score = 29.2 bits (66), Expect = 1.5
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 177 SISLDHEHGLVAVGGADSKVHIY 199
+ LD+E G V+ AD+ HIY
Sbjct: 123 GVFLDYEGGQVSFYDADTMTHIY 145
>gnl|CDD|219547 pfam07741, BRF1, Brf1-like TBP-binding domain. This region
covers both the Brf homology II and III regions. This
region is involved in binding TATA binding protein.
Length = 95
Score = 28.0 bits (63), Expect = 1.7
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 81 KVRIWDTVNKEHILKNE 97
K RIWD +NK+++ + E
Sbjct: 17 KERIWDELNKDYLEEQE 33
>gnl|CDD|132862 cd07223, Pat_PNPLA5-mammals, Patatin-like phospholipase domain
containing protein 5. PNPLA5, also known as GS2L
(GS2-like), plays a role in regulation of adipocyte
differentiation. PNPLA5 is expressed in brain tissue in
high mRNA levels and low levels in liver tissue. There
is no concrete evidence in support of the enzymatic
activity of GS2L. This family includes patatin-like
proteins: GS2L (GS2-like) and PNPLA5 (Patatin-like
phospholipase domain-containing protein 5) reported
exclusively in mammals.
Length = 405
Score = 29.1 bits (65), Expect = 2.0
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 6/79 (7%)
Query: 162 NGAKVSSLPIDYEPSSISLDHEHGLVAVGGADSKVHIYELN--NKSLSPKAELDHLGPVT 219
+GA ++LP PS+I++ HG V + + +++ELN N S LG
Sbjct: 168 DGALSNNLPFSDCPSTITVSPFHGTVDICPQSTSANLHELNAFNASFQISTRNFFLG--L 225
Query: 220 DCSFSPSNEYLVASDAHRK 238
C P E V +D R+
Sbjct: 226 KCLIPPKPE--VVADNCRQ 242
>gnl|CDD|240492 cd13734, SPRY_PRY_C-I, PRY/SPRY domain in tripartite
motif-containing proteins 1, 9, 18, 36, 46, 67,76
(TRIM1, TRIM9, TRIM18, TRIM36, TRIM46, TRIM67, TRIM76).
This domain, consisting of the distinct N-terminal PRY
subdomain followed by the SPRY subdomain, is found at
the C-terminus of several Class I TRIM proteins,
including TRIM1, TRIM9, TRIM18, TRIM36, TRIM46, TRIM67
and TRIM76. TRIM1 (also known as MID2) and its close
homolog, TRIM18 (also known as MID1), both contain a
B30.2-like domain at their C-terminus and a single
fibronectin type III (FN3) motif between it and their
N-terminal RBCC domain. Their coiled-coil motifs mediate
both homo- and heterodimerization, a prerequisite for
association of the rapamycin-sensitive PP2A regulatory
subunit Alpha 4 with microtubules. Mutations in TRIM18
have shown to cause Opitz syndrome, a disorder causing
congenital anomalies such as cleft lip and palate as
well as heart defects. TRIM9 is expressed mainly in the
cerebral cortex, and functions as an E3 ubiquitin
ligase. Its immunoreactivity is severely decreased in
affected brain areas in Parkinson's disease and dementia
with Lewy bodies, possibly playing an important role in
the regulation of neuronal function and participating in
pathological process of Lewy body disease through its
ligase. TRIM36 interacts with centromere protein-H, one
of the kinetochore proteins and possibly associates with
chromosome segregation; an excess of TRIM36 may cause
chromosomal instability. TRIM46 has not yet been
characterized. TRIM67 negatively regulates Ras activity
via degradation of 80K-H, leading to neural
differentiation, including neuritogenesis. TRIM76 (also
known as cardiomyopathy-associated protein 5 or CMYA5)
is a muscle-specific member of the TRIM superfamily, but
lacks the RING domain. It is possibly involved in
protein kinase A signaling as well as vesicular
trafficking. It has also been implicated in Duchenne
muscular dystrophy and cardiac disease.
Length = 169
Score = 28.4 bits (64), Expect = 2.4
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 165 KVSSLPIDYEPSSIS--LDHEHGLVAVGGADSKVHIYELNNK 204
KV L + P I LD++ G ++ A+SK H++ +
Sbjct: 107 KVVDLTVTPHPRRIGVLLDYDRGTLSFYDAESKQHLHTFHVD 148
>gnl|CDD|119350 cd02871, GH18_chitinase_D-like, GH18 domain of Chitinase D (ChiD).
ChiD, a chitinase found in Bacillus circulans,
hydrolyzes the 1,4-beta-linkages of N-acetylglucosamine
in chitin and chitodextrins. The domain architecture of
ChiD includes a catalytic glycosyl hydrolase family 18
(GH18) domain, a chitin-binding domain, and a
fibronectin type III domain. The chitin-binding and
fibronectin type III domains are located either
N-terminal or C-terminal to the catalytic domain. This
family includes exochitinase Chi36 from Bacillus cereus.
Length = 312
Score = 28.5 bits (64), Expect = 3.7
Identities = 11/58 (18%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 147 LVAVGGADSKISIVENGAK---VSSL-PI--DYEPSSISLDHEHGLVAVGGADSKVHI 198
L+++GGA+ + + + V S+ I +Y + +D E G + ++
Sbjct: 77 LISIGGANGHVDLNHTAQEDNFVDSIVAIIKEYGFDGLDIDLESGSNPLNATPVITNL 134
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 28.5 bits (63), Expect = 4.3
Identities = 38/173 (21%), Positives = 65/173 (37%), Gaps = 36/173 (20%)
Query: 73 IASGDISGKVRIWDTVNKEHILKNEFHPIGGPIKDIAWSPDNQRMISIVENGAKVSSLPI 132
+AS + G V++WD + + + + H + WS I
Sbjct: 548 VASSNFEGVVQVWDVARSQLVTEMKEH------EKRVWS--------------------I 581
Query: 133 DYEPSSISLDHEHGLVAVGGADS--KISIVENGAKVSSLPIDYEPSSISLDHEHGL-VAV 189
DY + +L +A G D K+ + G + ++ + E G +A
Sbjct: 582 DYSSADPTL------LASGSDDGSVKLWSINQGVSIGTIKTKANICCVQFPSESGRSLAF 635
Query: 190 GGADSKVHIYELNNKSLSPKAELDHLGPVTDCSFSPSNEYLVASDAHRKVVLY 242
G AD KV+ Y+L N L + H V+ F S+ LV+S + L+
Sbjct: 636 GSADHKVYYYDLRNPKLPLCTMIGHSKTVSYVRFVDSST-LVSSSTDNTLKLW 687
>gnl|CDD|181555 PRK08780, PRK08780, DNA topoisomerase I; Provisional.
Length = 780
Score = 28.2 bits (63), Expect = 5.0
Identities = 20/87 (22%), Positives = 36/87 (41%), Gaps = 19/87 (21%)
Query: 121 VENGAKVSSLPIDYEPSSISLDHEHGLVAVGG-----------ADSKISI--------VE 161
V+ G+K +SL + +P +I L L+ S I + +
Sbjct: 672 VKRGSKYASLKKEDDPYTIDLARALFLIEEKEEIARNRVIKDFEGSGIQVLNGRYGPYIT 731
Query: 162 NGAKVSSLPIDYEPSSISLDHEHGLVA 188
+G +P D EP+S++L+ L+A
Sbjct: 732 DGKLNGKIPKDREPASLTLEEVQQLLA 758
>gnl|CDD|179655 PRK03822, lplA, lipoate-protein ligase A; Provisional.
Length = 338
Score = 27.7 bits (62), Expect = 5.3
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 12/41 (29%)
Query: 8 IFATLPRTQRGQPIVLGGDPKGKNFLYTNGNSVIIRNIENP 48
IF +P TQR VL FL+ N ++V+I +NP
Sbjct: 24 IFRQMPATQR----VL--------FLWRNADTVVIGRAQNP 52
>gnl|CDD|227657 COG5354, COG5354, Uncharacterized protein, contains Trp-Asp (WD)
repeat [General function prediction only].
Length = 561
Score = 27.9 bits (62), Expect = 6.2
Identities = 39/208 (18%), Positives = 70/208 (33%), Gaps = 37/208 (17%)
Query: 32 FLYTNGNSV-IIRNIENPAISDIYTEHSCAVNVAKYSPSGFYIASGDISGKVRIWDTVNK 90
F + + N ++ I + + V SP G Y+ S +G V W
Sbjct: 5 FPLDYSAVISVFWNSQSEVIHTRFESENWPVAYVSESPLGTYLFSEHAAG-VECW----- 58
Query: 91 EHILKNEFHPIGGPIKD-IAWSPDNQ-RMISIVENGAKVSSLPIDYEPSSISLDHEHGLV 148
GGP K + + + N + + EP ++ E +
Sbjct: 59 -----------GGPSKAKLVRFRHPDVKYLDFSPNEKYLVTW--SREP---IIEPEIEIS 102
Query: 149 AVGGADS-KISIVENGAKVSSLPIDYEPSSI------SLDHEHGLVAVGGADSKVHIYEL 201
++ + + +G V S +P S+D ++ VG S ++I+E+
Sbjct: 103 PFTSKNNVFVWDIASGMIVFSFNGISQPYLGWPVLKFSIDDKYVARVVG---SSLYIHEI 159
Query: 202 N-NKSLSPKAELDHLGPVTDCSFSPSNE 228
N P L +G + D S SP
Sbjct: 160 TDNIEEHPFKNLRPVG-ILDFSISPEGN 186
>gnl|CDD|220674 pfam10282, Lactonase, Lactonase, 7-bladed beta-propeller. This
entry contains bacterial 6-phosphogluconolactonases
(6PGL)YbhE-type (EC:3.1.1.31) which hydrolyse
6-phosphogluconolactone to 6-phosphogluconate. The entry
also contains the fungal muconate lactonising enzyme
carboxy-cis,cis-muconate cyclase (EC:5.5.1.5) and
muconate cycloisomerase (EC:5.5.1.1), which convert
cis,cis-muconates to muconolactones and vice versa as
part of the microbial beta-ketoadipate pathway.
Structures of proteins in this family have revealed a
7-bladed beta-propeller fold.
Length = 344
Score = 27.6 bits (62), Expect = 7.5
Identities = 30/143 (20%), Positives = 52/143 (36%), Gaps = 39/143 (27%)
Query: 108 IAWSPDNQRMISIVENGAK--VSSLPIDYEPSSISLDHEHGLVAVGGADSKISIVENGAK 165
+A SPD + + ++ E G VS+ ID + ++L V GGA
Sbjct: 42 LAVSPDGKTLYAVNETGEDGGVSAFRIDPDTGKLTL---LNQVPTGGAS----------- 87
Query: 166 VSSLPIDYEPSSISLDHEHGLVAVGG-ADSKVHIYELNNK-SLSPKAELDHL---GPVTD 220
P +S+D + + V V +Y L+ SL +++ GP +
Sbjct: 88 ---------PCHLSVDPDGRFLFVANYGGGSVSVYPLDADGSLGEASQVVQHEGSGPNPE 138
Query: 221 ---------CSFSPSNEYLVASD 234
+P ++LV D
Sbjct: 139 RQEGPHAHSVVLTPDGKFLVVPD 161
>gnl|CDD|240359 PTZ00324, PTZ00324, glutamate dehydrogenase 2; Provisional.
Length = 1002
Score = 27.5 bits (61), Expect = 8.3
Identities = 12/38 (31%), Positives = 18/38 (47%)
Query: 62 NVAKYSPSGFYIASGDISGKVRIWDTVNKEHILKNEFH 99
+ +K SP GF + + D K+ V +NEFH
Sbjct: 723 DESKLSPQGFLVLTDDRDVKLPDGTIVESGLRFRNEFH 760
>gnl|CDD|227498 COG5170, CDC55, Serine/threonine protein phosphatase 2A, regulatory
subunit [Signal transduction mechanisms].
Length = 460
Score = 27.3 bits (60), Expect = 8.7
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 46 ENPAISDIYTEHSCAVNVAKYSPSGFYIASGDISGKVRIWDTVNKEHILK 95
+ D + E +++ K+S +G YI S D V+IWD ++ +K
Sbjct: 268 IDGVDVDFFEEIVSSISDFKFSDNGRYILSRDYL-TVKIWDVNMAKNPIK 316
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
0.314 0.134 0.393
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,631,169
Number of extensions: 1181163
Number of successful extensions: 775
Number of sequences better than 10.0: 1
Number of HSP's gapped: 742
Number of HSP's successfully gapped: 43
Length of query: 248
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 154
Effective length of database: 6,768,326
Effective search space: 1042322204
Effective search space used: 1042322204
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.1 bits)