RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12694
(112 letters)
>gnl|CDD|143541 cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain of Lrh-1 like
nuclear receptor family like is composed of two C4-type
zinc fingers. The DNA-binding domain of Lrh-1 like
nuclear receptor family like is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which co-ordinates a single zinc atom.
This domain interacts with specific DNA sites upstream
of the target gene and modulates the rate of
transcriptional initiation. This nuclear receptor
family includes at least three subgroups of receptors
that function in embryo development and
differentiation, and other processes. FTZ-F1 interacts
with the cis-acting DNA motif of ftz gene, which is
required at several stages of development.
Particularly, FTZ-F1 regulated genes are strongly
linked to steroid biosynthesis and sex-determination;
LRH-1 is a regulator of bile-acid homeostasis,
steroidogenesis, reverse cholesterol transport and the
initial stages of embryonic development; SF-1 is an
essential regulator of endocrine development and
function and is considered a master regulator of
reproduction; SF-1 functions cooperatively with other
transcription factors to modulate gene expression.
Phospholipids have been identified as potential ligand
for LRH-1 and steroidogenic factor-1 (SF-1). However,
the ligand for FTZ-F1 has not yet been identified. Most
nuclear receptors function as homodimer or
heterodimers. However, LRH-1 and SF-1 bind to DNA as
monomers. Like other members of the nuclear receptor
(NR) superfamily of ligand-activated transcription
factors, receptors in this family have a central well
conserved DNA-binding domain (DBD), a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain (LBD).
Length = 93
Score = 44.8 bits (106), Expect = 2e-07
Identities = 17/18 (94%), Positives = 17/18 (94%)
Query: 1 MRGGRNKFGPMYKRDRAR 18
MRGGRNKFGPMYKRDRA
Sbjct: 76 MRGGRNKFGPMYKRDRAL 93
>gnl|CDD|227415 COG5083, SMP2, Uncharacterized protein involved in plasmid
maintenance [General function prediction only].
Length = 580
Score = 29.1 bits (65), Expect = 0.42
Identities = 16/47 (34%), Positives = 25/47 (53%)
Query: 62 IKQEIQIPQVSSLTSSPDSSPSPIASHRTEKSLYSSSYIPSDMEDDV 108
+ E+ + +SLT+SPD P I + R ++SL S S + D V
Sbjct: 92 VPYELILSPNNSLTASPDQDPELILNEREQESLGSGSDLSKLNFDIV 138
>gnl|CDD|218917 pfam06159, DUF974, Protein of unknown function (DUF974). Family
of uncharacterized eukaryotic proteins.
Length = 235
Score = 28.0 bits (63), Expect = 0.86
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 46 TLSYNPASTSPYGNLYIKQEIQIPQVSSLTSSPDSSPSPIASHRTEKSL 94
L N S+ ++ IK E+Q P S + DS +P+ + R +SL
Sbjct: 19 YLCVNNESSKEVRDVSIKAELQTP--SQRLNLSDSVDAPVETLRPGESL 65
>gnl|CDD|235012 PRK02201, PRK02201, putative inner membrane protein translocase
component YidC; Provisional.
Length = 357
Score = 25.7 bits (57), Expect = 5.9
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 30 VQTLQRASPYMIGDGVTLSYNPASTSPYGNLYIKQ 64
VQ+ S +G G+ N S + Y L+I
Sbjct: 52 VQSFVVKSSTNVGSGLEFYTNKESKNNYRYLFISS 86
>gnl|CDD|240236 PTZ00037, PTZ00037, DnaJ_C chaperone protein; Provisional.
Length = 421
Score = 25.9 bits (57), Expect = 6.1
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 12/68 (17%)
Query: 51 PASTSPY--GNLYIKQEIQIPQVSSLTSS---------PDSSPSPIASHRTEKSLYSSSY 99
P SP+ GNLY+ E+ P T+ P + TE + ++
Sbjct: 327 PTYKSPFKKGNLYVTFEVIFPVDRKFTNEEKEILKSLFPQNPEEKKDLEDTEIEVVTAQN 386
Query: 100 I-PSDMED 106
+ P +++D
Sbjct: 387 VDPEEVKD 394
>gnl|CDD|237822 PRK14819, PRK14819, NADH dehydrogenase subunit B; Provisional.
Length = 264
Score = 25.3 bits (55), Expect = 7.3
Identities = 20/62 (32%), Positives = 25/62 (40%)
Query: 22 MMRQRQIAVQTLQRASPYMIGDGVTLSYNPASTSPYGNLYIKQEIQIPQVSSLTSSPDSS 81
M Q+QI Q+L R Y GD P T L I ++ P SP +S
Sbjct: 150 MTLQKQIDAQSLGRVRWYGSGDKGQTKEFPVPTFGAHGLEIDGKLVDPVGGLPLLSPYTS 209
Query: 82 PS 83
PS
Sbjct: 210 PS 211
>gnl|CDD|176486 cd08665, APC10-CUL7, APC10-like DOC1 domain of CUL7, subunit of
the SCF-ROC1-like E3 ubiquitin ligase complex that
mediates substrate ubiquitination. This model
represents the APC10/DOC1 domain present in CUL7, a
subunit of the SCF-ROC1-like E3 Ubiquitin (Ub) ligase
complex, which mediates substrate ubiquitination (or
ubiquitylation), and is a component of the
ubiquitin-26S proteasome pathway for selective
proteolytic degradation. CUL7 is a member of the
Cullin-RING ligase family and functions as a molecular
scaffold assembling the SCF-ROC1-like E3 Ub ligase
complex consisting of the adapter protein Skp1, CUL7,
the WD40 repeat-containing F-box Fbw8 (also known as
Fbx29), and ROC1 (RING-box protein 1). CUL7 is a large
protein with a C-terminal cullin domain that binds ROC1
and additional domains, including an APC10/DOC1 domain.
While the Fbw8 protein is responsible for substrate
protein recognition, the ROC1 RING domain recruits an
Ub-charged E2 Ub-conjugating enzyme for substrate
ubiquitination. It remains to be determined how CUL7
binds to the Skp1-Fbw8 heterodimer. The CUL7 E3 Ub
ligase has been implicated in the proteasomal
degradation of the cellular proteins, cyclin D1, an
important regulator of the G1 to S-phase cell cycle
progression, and insulin receptor substrate 1, a
critical component of the signaling pathways downstream
of the insulin and insulin-like growth factor 1
receptor. CUL7 appears to be an important regulator of
placental development. Germ line mutations of CUL7 are
linked to 3-M syndrome and Yakuts short stature
syndrome.
Length = 131
Score = 24.9 bits (54), Expect = 8.0
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 50 NPASTSPYGNLYIKQEIQIPQVSSLTSSPDSSPSP 84
N ++ S Y N+++ + + I Q+ L +S DSS P
Sbjct: 31 NGSTGSHYINIHMHRGVVIRQLYMLVASEDSSYMP 65
>gnl|CDD|218632 pfam05549, Allexi_40kDa, Allexivirus 40kDa protein.
Length = 271
Score = 25.1 bits (55), Expect = 8.6
Identities = 17/77 (22%), Positives = 28/77 (36%)
Query: 14 RDRARKLQMMRQRQIAVQTLQRASPYMIGDGVTLSYNPASTSPYGNLYIKQEIQIPQVSS 73
RD R L +V+ S L + + L+ K + ++S
Sbjct: 84 RDALRTLTRTVDSIYSVEQKIELSTQTPSSSKLLKKLTSIETSLEALHAKLDELTSSLTS 143
Query: 74 LTSSPDSSPSPIASHRT 90
+ P SP+P +SH T
Sbjct: 144 TLAGPSVSPTPASSHPT 160
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
0.313 0.129 0.364
Gapped
Lambda K H
0.267 0.0617 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,527,143
Number of extensions: 439291
Number of successful extensions: 317
Number of sequences better than 10.0: 1
Number of HSP's gapped: 317
Number of HSP's successfully gapped: 20
Length of query: 112
Length of database: 10,937,602
Length adjustment: 76
Effective length of query: 36
Effective length of database: 7,566,698
Effective search space: 272401128
Effective search space used: 272401128
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: 53 (24.4 bits)