RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5242
(217 letters)
>gnl|CDD|220553 pfam10075, PCI_Csn8, COP9 signalosome, subunit CSN8. This PCI_Csn8
domain is conserved from plants to humans. It is a
signature protein motif found in components of CSN (COP9
signalosome). It functions as a structural scaffold for
subunit-subunit interactions within the complex and is a
key regulator of photomorphogenic development.
Length = 144
Score = 113 bits (284), Expect = 6e-32
Identities = 44/140 (31%), Positives = 64/140 (45%), Gaps = 5/140 (3%)
Query: 64 ITSQILLKALTNFPHTDFILCKCLLSKDLCKEDP-IDQIIYLADLLESCKFTQFWSRMHT 122
+ ILLK LT DF L + + + + +P I Q++ L LL + +FW + +
Sbjct: 6 LYGLILLKLLTQNDIADFRLLLKRIPQAIKESNPEIQQLLTLGQLLWENDYAKFWQTLRS 65
Query: 123 ---IPDLFLNIEGFNDSIRKFVCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKKYGWK 179
D I G D+IR + +VG + +I L+ELL D L + KK GW
Sbjct: 66 NDWSEDYTPFIAGLEDTIRDEIAALVGKAYSSISIDDLAELLGLSSDEELEKFAKKRGWT 125
Query: 180 ELDNGYIFIANQDENIKTKN 199
+G I N E IK KN
Sbjct: 126 LDSDGRILPPN-PEEIKPKN 144
>gnl|CDD|217534 pfam03399, SAC3_GANP, SAC3/GANP/Nin1/mts3/eIF-3 p25 family. This
large family includes diverse proteins involved in large
complexes. The alignment contains one highly conserved
negatively charged residue and one highly conserved
positively charged residue that are probably important
for the function of these proteins. The family includes
the yeast nuclear export factor Sac3, and mammalian
GANP/MCM3-associated proteins, which facilitate the
nuclear localisation of MCM3, a protein that associates
with chromatin in the G1 phase of the cell-cycle. The
26S protease (or 26S proteasome) is responsible for
degrading ubiquitin conjugates. It consists of 19S
regulatory complexes associated with the ends of 20S
proteasomes. The 19S regulatory complex is composed of
about 20 different polypeptides and confers
ATP-dependence and substrate specificity to the 26S
enzyme. The conserved region occurs at the C-terminal of
the Nin1-like regulatory subunit. This family includes
several eukaryotic translation initiation factor 3
subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation
factor 3 (eIF3) is a multisubunit complex that is
required for binding of mRNA to 40 S ribosomal subunits,
stabilisation of ternary complex binding to 40 S
subunits, and dissociation of 40 and 60 S subunits.
Length = 155
Score = 94.2 bits (235), Expect = 1e-24
Identities = 35/154 (22%), Positives = 62/154 (40%), Gaps = 11/154 (7%)
Query: 19 ERYNPEHLSTLEKYVEVQCA----ENVYDLEANLAVLKLYQFHQNY------NMKITSQI 68
+ NP L L+ V A E + N + +L + + + + +
Sbjct: 1 DEPNPSDLRPLKVAVLEIGARIALEKGDLEQFNQCLSQLKELYDDLLGKSPNEAEFIAYY 60
Query: 69 LLKALTNFPHTDFILCKCLLSKDLCKEDPIDQIIYLADLLESCKFTQFWSRMHTIPDLFL 128
LL L+N P +DF LL ++ + I + L L + +F+ + P L+
Sbjct: 61 LLYLLSNNPISDFHTELELLPDEIRNDPYIQFALELEQALMEGNYHRFFRLLKKAPYLYA 120
Query: 129 NI-EGFNDSIRKFVCHVVGITFQTIDKKLLSELL 161
+ E F D IRK + +++I L+ELL
Sbjct: 121 CLLERFLDRIRKEALKAISKAYRSIPLSYLAELL 154
>gnl|CDD|191505 pfam06373, CART, Cocaine and amphetamine regulated transcript
protein (CART). This family consists of several cocaine
and amphetamine regulated transcript type I protein
(CART) sequences. Cocaine and amphetamine regulated
transcript (CART) peptide has been shown to be an
anorectic peptide that inhibits both normal and
starvation-induced feeding and completely blocks the
feeding response induced by neuropeptide Y and regulated
by leptin in the hypothalamus. The C-terminal part
containing the three disulfide bridges is the
biologically active part of the molecule affecting food
intake. The solution structure of the active part of
CART has a fold equivalent to other functionally
distinct small proteins. CART consists mainly of turns
and loops spanned by a compact framework composed by a
few small stretches of antiparallel beta-sheet common to
cystine knots.
Length = 73
Score = 28.1 bits (63), Expect = 0.89
Identities = 10/32 (31%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 150 QTIDKKL---LSELLDGVEDSTLRLWVKKYGW 178
+ +K+L L E+L+ ++ + LW KK+G
Sbjct: 4 LSEEKELLEALQEVLEKLQSKRIPLWEKKFGQ 35
>gnl|CDD|148573 pfam07037, DUF1323, Putative transcription regulator (DUF1323).
This family consists of several hypothetical
Enterobacterial proteins of around 120 residues in
length. This family appears to have an HTH domain and is
therefore likely to act as a transcriptional regulator.
Length = 122
Score = 28.6 bits (64), Expect = 1.3
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 157 LSELLDGVEDSTLRLWVKKYGWK 179
L+EL G T+ WV+K GWK
Sbjct: 6 LAELT-GYSRQTINRWVRKEGWK 27
>gnl|CDD|216148 pfam00847, AP2, AP2 domain. This 60 amino acid residue domain can
bind to DNA and is found in transcription factor
proteins.
Length = 53
Score = 26.8 bits (60), Expect = 1.4
Identities = 6/36 (16%), Positives = 14/36 (38%)
Query: 142 CHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKKYG 177
G+ + + ++E+ D E R + +G
Sbjct: 1 SGYKGVRYDKRWGRWVAEIRDPGEKKKKRFSLGTFG 36
>gnl|CDD|188774 cd09388, LIM1_LMO1_LMO3, The first LIM domain of LMO1 and LMO3
(LIM domain only protein 1 and 3). The first LIM
domain of LMO1 and LMO3 (LIM domain only protein 1 and
3): LMO1 and LMO3 are highly homologous and belong to
the LMO protein family. LMO1 and LMO3 are nuclear
protein that plays important roles in transcriptional
regulation and development. As LIM domains lack
intrinsic DNA-binding activity, nuclear LMOs are
involved in transcriptional regulation by forming
complexes with other transcription factors or
cofactors. For example, LMO1 interacts with the the
bHLH domain of bHLH transcription factor, TAL1 (T-cell
acute leukemia1)/SCL (stem cell leukemia) . LMO1
inhibits the expression of TAL1/SCL target genes. LMO3
facilitates p53 binding to its response elements, which
suggests that LMO3 acts as a co-repressor of p53,
suppressing p53-dependent transcriptional regulation.
In addition, LMO3 interacts with neuronal transcription
factor, HEN2, and acts as an oncogene in neuroblastoma.
Another binding partner of LMO3 is calcium- and
integrin-binding protein CIB, which binds via the
second LIM domain (LIM2) of LMO3. One role of the
CIB/LMO3 complex is to inhibit cell proliferation.
Although LMO1 and LMO3 are highly homologous proteins,
they play different roles in the regulation of the
pituitary glycoprotein hormone alpha-subunit (alpha
GSU) gene. Alpha GSU promoter activity was markedly
repressed by LMO1 but activated by LMO3. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 27.1 bits (60), Expect = 1.5
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 61 NMKITSQILLKALTNFPHTDFILCKC 86
N KI + LLKAL + H D + C C
Sbjct: 5 NRKIKDRYLLKALDQYWHEDCLKCAC 30
>gnl|CDD|172532 PRK14038, PRK14038, ADP-dependent glucokinase; Provisional.
Length = 453
Score = 29.0 bits (65), Expect = 1.9
Identities = 12/44 (27%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 141 VCHVVGITFQTIDKKLLSELLDGVEDSTLRLWVKKYGWKELDNG 184
+ ++G +I + +EL VE +R +++++GW EL G
Sbjct: 69 IPQLLGSILWSIRRGKAAELF--VESCEVRFYMRQWGWDELRMG 110
>gnl|CDD|133390 cd04762, HTH_MerR-trunc, Helix-Turn-Helix DNA binding domain of
truncated MerR-like proteins. Proteins in this family
mostly have a truncated helix-turn-helix (HTH) MerR-like
domain. They lack a portion of the C-terminal region,
called Wing 2 and the long dimerization helix that is
typically present in MerR-like proteins. These truncated
domains are found in response regulator receiver (REC)
domain proteins (i.e., CheY), cytosine-C5 specific DNA
methylases, IS607 transposase-like proteins, and RacA, a
bacterial protein that anchors chromosomes to cell
poles.
Length = 49
Score = 26.0 bits (58), Expect = 2.5
Identities = 12/18 (66%), Positives = 14/18 (77%), Gaps = 1/18 (5%)
Query: 158 SELLDGVEDSTLRLWVKK 175
+ELL GV STLR WVK+
Sbjct: 7 AELL-GVSPSTLRRWVKE 23
>gnl|CDD|171854 PRK13039, PRK13039, superantigen-like protein; Reviewed.
Length = 232
Score = 27.7 bits (61), Expect = 4.6
Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 2/48 (4%)
Query: 170 RLWVKKYGWKE--LDNGYIFIANQDENIKTKNITEKIEFENAATIMTS 215
+L +KKY E D G I I +DEN ++++K++FE A ++ S
Sbjct: 174 KLLIKKYKLYEGSADKGRIVINMKDENKYEIDLSDKLDFERMADVINS 221
>gnl|CDD|233098 TIGR00707, argD, transaminase, acetylornithine/succinylornithine
family. This family of proteins, for which ornithine
aminotransferases form an outgroup, consists mostly of
proteins designated acetylornithine aminotransferase.
However, the two very closely related members from E.
coli are assigned different enzymatic activities. One is
acetylornithine aminotransferase (EC 2.6.1.11), ArgD, an
enzyme of arginine biosynthesis, while another is
succinylornithine aminotransferase, an enzyme of the
arginine succinyltransferase pathway, an
ammonia-generating pathway of arginine catabolism (See
MEDLINE:98361920). Members of this family may also act
on ornithine, like ornithine aminotransferase (EC
2.6.1.13) (see MEDLINE:90337349) and on
succinyldiaminopimelate, like
N-succinyldiaminopmelate-aminotransferase (EC 2.6.1.17,
DapC, an enzyme of lysine biosynthesis) (see
MEDLINE:99175097).
Length = 379
Score = 26.9 bits (60), Expect = 9.2
Identities = 14/37 (37%), Positives = 16/37 (43%), Gaps = 4/37 (10%)
Query: 21 YNPEHLSTLEKYVEVQCAENVY----DLEANLAVLKL 53
Y EK VE A+ V+ EAN A LKL
Sbjct: 67 YTEPQEELAEKLVEHSGADRVFFCNSGAEANEAALKL 103
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
0.321 0.137 0.406
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,898,933
Number of extensions: 1020429
Number of successful extensions: 833
Number of sequences better than 10.0: 1
Number of HSP's gapped: 827
Number of HSP's successfully gapped: 21
Length of query: 217
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 124
Effective length of database: 6,812,680
Effective search space: 844772320
Effective search space used: 844772320
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (25.8 bits)