RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7991
(81 letters)
>gnl|CDD|215619 PLN03185, PLN03185, phosphatidylinositol phosphate kinase;
Provisional.
Length = 765
Score = 39.8 bits (93), Expect = 3e-05
Identities = 24/62 (38%), Positives = 29/62 (46%), Gaps = 3/62 (4%)
Query: 11 GVVQHGSFKY--DDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFP 68
G V G KY DG +Y G+W RG +HG G + P Y+G F G G G
Sbjct: 17 GNVPEGPGKYLWSDGCMYEGEWR-RGMRHGNGKISWPSGATYEGEFSGGYMHGSGTYTGT 75
Query: 69 DG 70
DG
Sbjct: 76 DG 77
Score = 32.9 bits (75), Expect = 0.008
Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 6 EEEYPGVVQHGSFKY--DDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLG 63
E E+ G HGS Y DGT Y G W KHG+G+ + P+ ++G++ GL G G
Sbjct: 58 EGEFSGGYMHGSGTYTGTDGTTYKGRW-RLNLKHGLGYQRYPNGDVFEGSWIQGLQEGPG 116
Score = 27.5 bits (61), Expect = 0.75
Identities = 20/57 (35%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 16 GSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDGAK 72
G+ + G Y G W + G HG G D Y GT+ GL G GV +P G++
Sbjct: 139 GTLTWVSGDSYEGQWLD-GMMHGFGVYTWSDGGCYVGTWTRGLKDGKGVF-YPAGSR 193
Score = 26.3 bits (58), Expect = 1.7
Identities = 15/53 (28%), Positives = 21/53 (39%), Gaps = 1/53 (1%)
Query: 22 DGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDGAKAE 74
+G Y G G G D Y+G + G+ G G + +P GA E
Sbjct: 7 NGDFYSGSL-LGNVPEGPGKYLWSDGCMYEGEWRRGMRHGNGKISWPSGATYE 58
Score = 25.9 bits (57), Expect = 2.2
Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 15 HGSFKYDDGTLYIGDWNERGQKHGMG 40
G + + DG Y+G W RG K G G
Sbjct: 161 FGVYTWSDGGCYVGTWT-RGLKDGKG 185
>gnl|CDD|197832 smart00698, MORN, Possible plasma membrane-binding motif in
junctophilins, PIP-5-kinases and protein kinases.
Length = 22
Score = 33.1 bits (77), Expect = 8e-04
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 49 RYDGTFHNGLCSGLGVMRFPD 69
RY+G + NG G GV + +
Sbjct: 2 RYEGEWRNGKRHGRGVYTYAN 22
Score = 24.2 bits (54), Expect = 2.0
Identities = 7/21 (33%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 26 YIGDWNERGQKHGMGHMKLPD 46
Y G+W G++HG G +
Sbjct: 3 YEGEW-RNGKRHGRGVYTYAN 22
>gnl|CDD|202256 pfam02493, MORN, MORN repeat. The MORN (Membrane Occupation and
Recognition Nexus) repeat is found in multiple copies
in several proteins including junctophilins (See
Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat
protein has been identified in the parasite Toxoplasma
gondiis a dynamic component of cell division apparatus
in Toxoplasma gondii. It has been hypothesised to
functions as a linker protein between certain membrane
regions and the parasite's cytoskeleton.
Length = 23
Score = 31.2 bits (72), Expect = 0.005
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 50 YDGTFHNGLCSGLGVMRFPDG 70
Y+G + NG G GV +PDG
Sbjct: 1 YEGEWKNGKRHGKGVYTWPDG 21
Score = 23.9 bits (53), Expect = 2.4
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 26 YIGDWNERGQKHGMGHMKLPDHTR 49
Y G+W + G++HG G PD R
Sbjct: 1 YEGEW-KNGKRHGKGVYTWPDGDR 23
>gnl|CDD|226989 COG4642, COG4642, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 139
Score = 31.6 bits (72), Expect = 0.015
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 16 GSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDGAKAE 74
GS KYD+G +Y G + G+ +G G + Y+G F++G G G +G
Sbjct: 47 GSLKYDNGRIYTGTL-KNGKMNGQGTYTFANGDIYEGPFNSGKFRGQGTRGSFNGWLYI 104
Score = 29.3 bits (66), Expect = 0.10
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 1/55 (1%)
Query: 16 GSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDG 70
++ G + G+ G G +K + Y GT NG +G G F +G
Sbjct: 24 STYDILGCARVGGSLKQ-GKLAGKGSLKYDNGRIYTGTLKNGKMNGQGTYTFANG 77
Score = 28.2 bits (63), Expect = 0.27
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 1/66 (1%)
Query: 16 GSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDGAKAEM 75
G++ + +G +Y G +N G+ G G + Y G F G +G G + DG+
Sbjct: 70 GTYTFANGDIYEGPFNS-GKFRGQGTRGSFNGWLYIGRFTEGQANGKGFLLKEDGSVYTG 128
Query: 76 SSDEVR 81
+ R
Sbjct: 129 MFKQGR 134
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 27.4 bits (62), Expect = 0.63
Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 4/24 (16%)
Query: 47 HTRYDGTFHNGL----CSGLGVMR 66
H ++ F L CSGLGV+R
Sbjct: 314 HEKFAEKFDKILVDAPCSGLGVIR 337
>gnl|CDD|239284 cd02986, DLP, Dim1 family, Dim1-like protein (DLP) subfamily; DLP
is a novel protein which shares 38% sequence identity
to Dim1. Like Dim1, it is also implicated in pre-mRNA
splicing and cell cycle progression. DLP is located in
the nucleus and has been shown to interact with the U5
small nuclear ribonucleoprotein particle
(snRNP)-specific 102kD protein (or Prp6). Dim1 protein,
also known as U5 snRNP-specific 15kD protein is a
component of U5 snRNP, which pre-assembles with U4/U6
snRNPs to form a [U4/U6:U5] tri-snRNP complex required
for pre-mRNA splicing. Dim1 adopts a thioredoxin fold
but does not contain the redox active CXXC motif.
Length = 114
Score = 25.9 bits (57), Expect = 1.5
Identities = 9/19 (47%), Positives = 13/19 (68%), Gaps = 4/19 (21%)
Query: 41 HMKL----PDHTRYDGTFH 55
HMK+ PDHT++ G+F
Sbjct: 80 HMKVDYGSPDHTKFVGSFK 98
>gnl|CDD|181509 PRK08629, PRK08629, coproporphyrinogen III oxidase; Provisional.
Length = 433
Score = 26.2 bits (58), Expect = 2.2
Identities = 13/27 (48%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 5 DEEEYPGVVQHGSFKYDDGTLYIGDWN 31
D +EY GV GSF + DGTLY+ ++
Sbjct: 294 DYDEYLGV-GSGSFSFLDGTLYVNTFS 319
>gnl|CDD|199834 cd10276, BamB_YfgL, Beta-barrel assembly machinery (Bam) complex
component B and related proteins. BamB (YflG) is a
non-essential component of the beta-barrel assembly
machinery (Bam), a multi-subunit complex that inserts
proteins with beta-barrel topology into the outer
membrane. BamB has been found to interact with BamA,
which in turn binds and stabilizes pre-folded
beta-barrel proteins; it has been suggested that BamB
participates in the stabilization.
Length = 358
Score = 25.4 bits (56), Expect = 3.3
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 19 KYDDGTLYIGDWNER 33
Y DG +Y+G + R
Sbjct: 118 TYADGKIYVGTGDGR 132
>gnl|CDD|239525 cd03441, R_hydratase_like, (R)-hydratase [(R)-specific enoyl-CoA
hydratase]. Catalyzes the hydration of trans-2-enoyl
CoA to (R)-3-hydroxyacyl-CoA as part of the PHA
(polyhydroxyalkanoate) biosynthetic pathway. The
structure of the monomer includes a five-strand
antiparallel beta-sheet wrapped around a central alpha
helix, referred to as a hot dog fold. The active site
lies within a substrate-binding tunnel formed by the
homodimer. Other enzymes with this fold include MaoC
dehydratase, Hydratase-Dehydrogenase-Epimerase protein
(HDE), and the fatty acid synthase beta subunit.
Length = 127
Score = 24.9 bits (55), Expect = 3.6
Identities = 18/60 (30%), Positives = 20/60 (33%), Gaps = 12/60 (20%)
Query: 28 GDWN------ERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDGAKAEMSSDEVR 81
GD N E + G G H G L SGL V P A + S VR
Sbjct: 23 GDPNPIHVDPEYAKAAGFG--GRIAH----GMLTLSLASGLLVQWLPGTDGANLGSQSVR 76
>gnl|CDD|180315 PRK05933, PRK05933, type III secretion system protein; Validated.
Length = 372
Score = 25.2 bits (55), Expect = 5.1
Identities = 16/41 (39%), Positives = 19/41 (46%), Gaps = 6/41 (14%)
Query: 2 SQKDEEEYPGVVQHGSFKYDDGTLYIGDWNERG-----QKH 37
Q +EE+ VV GSF D LY D E G Q+H
Sbjct: 224 CQLTQEEWHQVV-PGSFILLDSCLYDPDTEESGALLTIQRH 263
>gnl|CDD|217376 pfam03122, Herpes_MCP, Herpes virus major capsid protein. This
family represents the major capsid protein (MCP) of
herpes viruses. The capsid shell consists of 150 MCP
hexamers and 12 MCP pentamers. One pentamer is found at
each of the 12 apices of the icosahedral shell, and the
hexamers form the edges and 20 faces.
Length = 1352
Score = 24.9 bits (55), Expect = 5.8
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 10/37 (27%)
Query: 34 GQKHGMGHMKLPDHTR-YDGTFHNGLCSGLGVMRFPD 69
GQ+ G + R DG +NGLC +M +P
Sbjct: 886 GQRTGS-----TRNFRSLDGVLYNGLC----LMAYPK 913
>gnl|CDD|197753 smart00481, POLIIIAc, DNA polymerase alpha chain like domain.
DNA polymerase alpha chain like domain, incl. family of
hypothetical proteins.
Length = 67
Score = 23.8 bits (52), Expect = 6.4
Identities = 9/38 (23%), Positives = 17/38 (44%)
Query: 15 HGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDG 52
H + DG L + +R ++ G+ + + DH G
Sbjct: 5 HSDYSLLDGALSPEELVKRAKELGLKAIAITDHGNLFG 42
>gnl|CDD|224437 COG1520, COG1520, FOG: WD40-like repeat [Function unknown].
Length = 370
Score = 24.5 bits (53), Expect = 8.0
Identities = 5/12 (41%), Positives = 8/12 (66%)
Query: 20 YDDGTLYIGDWN 31
DG +Y+G W+
Sbjct: 109 GSDGKIYVGSWD 120
>gnl|CDD|217668 pfam03676, UPF0183, Uncharacterized protein family (UPF0183). This
family of proteins includes Lin-10 from C. elegans.
Length = 395
Score = 24.3 bits (53), Expect = 8.7
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 49 RYDGTFHNGLCSGLGVMRFPDGA 71
D + G GLG ++FPDGA
Sbjct: 127 PIDSKYTPGFGHGLGSLKFPDGA 149
>gnl|CDD|240581 cd12946, NOPS_p54nrb_PSF_PSPC1, NOPS domain, including C-terminal
coiled-coil region, in p54nrb/PSF/PSPC1 family
proteins. The family contains a DBHS domain (for
Drosophila behavior, human splicing), which comprises
two conserved RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction NOPS (NONA and PSP1)
domain. This model corresponds to the NOPS domain, with
a long helical C-terminal extension, found in the
p54nrb/PSF/PSPC1 proteins. The NOPS domain specifically
binds to the second RNA recognition motif (RRM2) domain
of the partner DBHS protein via a substantial
interaction surface. Its highly conserved C-terminal
residues are critical for functional DBHS dimerization
while the highly conserved C-terminal helical
extension, forming a right-handed antiparallel
heterodimeric coiled-coil, is essential for
localization of these proteins to subnuclear bodies.
Members in the family include 54 kDa nuclear RNA- and
DNA-binding protein (p54nrb), polypyrimidine
tract-binding protein (PTB)-associated-splicing factor
(PSF) and paraspeckle protein component 1 (PSPC1 or
PSP1), which are ubiquitously expressed and are
conserved in vertebrates. p54nrb, also termed NONO or
NMT55, is a multi-functional protein involved in
numerous nuclear processes including transcriptional
regulation, splicing, DNA unwinding, nuclear retention
of hyperedited double-stranded RNA, viral RNA
processing, control of cell proliferation, and
circadian rhythm maintenance. PSF, also termed POMp100,
is a multi-functional protein that binds RNA,
single-stranded DNA (ssDNA), double-stranded DNA
(dsDNA) and many factors, and mediates diverse
activities in the cell. PSPC1 is a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. The cellular function
of PSPC1 remains unknown currently. PSF has an
additional large N-terminal domain that differentiates
it from other family members.
Length = 93
Score = 23.9 bits (51), Expect = 9.8
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 1 MSQKDEEEYPGVVQHGSFKYD 21
K+ E+ P Q G+F+Y+
Sbjct: 28 QYHKEREQPPRFAQPGTFEYE 48
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
0.316 0.138 0.434
Gapped
Lambda K H
0.267 0.0933 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,185,574
Number of extensions: 317962
Number of successful extensions: 174
Number of sequences better than 10.0: 1
Number of HSP's gapped: 172
Number of HSP's successfully gapped: 26
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (23.8 bits)