RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6945
(61 letters)
>gnl|CDD|197331 cd09097, Deadenylase_CCR4, C-terminal deadenylase domain of CCR4
and related domains. This subfamily contains the
C-terminal catalytic domain of the deadenylases,
Saccharomyces cerevisiae Ccr4p and two vertebrate
homologs (CCR4a and CCR4b), and related domains. CCR4
belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. CCR4 is the major deadenylase subunit of the
CCR4-NOT transcription complex, which contains two
deadenylase subunits and several noncatalytic subunits.
The other deadenylase subunit, Caf1 (called Pop2 in
yeast), is a DEDD-type protein and does not belong in
this superfamily. Saccharomyces cerevisiae CCR4 (or
Ccr4p) is a 3'-5' poly(A) RNA and ssDNA exonuclease. It
is the catalytic subunit of the yeast mRNA deadenylase
(Ccr4p/Pop2p/Not complex). This complex participates in
various ways in mRNA metabolism, including transcription
initiation and elongation, and mRNA degradation. Ccr4p
degrades both poly(A) and single-stranded DNA. There are
two vertebrate homologs of Ccr4p, CCR4a (also called
CCR4-NOT transcription complex subunit 6 or CNOT6) and
CCR4b (also called CNOT6-like or CNOT6L), which
independently associate with other components to form
distinct CCR4-NOT multisubunit complexes. The nuclease
domain of CNOT6 and CNOT6L exhibits Mg2+-dependent
deadenylase activity, with specificity for poly (A) RNA
as substrate. CCR4a is a component of P-bodies and is
necessary for foci formation. CCR4b regulates p27/Kip1
mRNA levels, thereby influencing cell cycle progression.
They both contribute to the prevention of cell death by
regulating insulin-like growth factor-binding protein 5.
Length = 329
Score = 62.7 bits (153), Expect = 1e-13
Identities = 27/61 (44%), Positives = 35/61 (57%), Gaps = 8/61 (13%)
Query: 1 VIEFLSTGRVTSDHQDFKDLPYKSVLNKICQNDKSNDFTHSFKLASAYSED-IMPYTNYT 59
V E LS G V+ +H DFK+ PY L ++ THSFKL SAY+ +P+TNYT
Sbjct: 221 VYELLSNGSVSPNHPDFKEDPYGEYL-------TASGLTHSFKLKSAYANLGELPFTNYT 273
Query: 60 Y 60
Sbjct: 274 P 274
>gnl|CDD|197339 cd10312, Deadenylase_CCR4b, C-terminal deadenylase domain of CCR4b,
also known as CCR4-NOT transcription complex subunit
6-like. This subfamily contains the C-terminal
catalytic domain of the deadenylase, CCR4b, also known
as CCR4-NOT transcription complex subunit 6-like
(CNOT6L). CCR4 belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. CCR4 is the major deadenylase subunit of the
CCR4-NOT transcription complex, which contains two
deadenylase subunits and several noncatalytic subunits.
The other deadenylase subunit, Caf1, is a DEDD-type
protein and does not belong in this superfamily. There
are two vertebrate CCR4 proteins, CCR4a (also called
CCR4-NOT transcription complex subunit 6 or CNOT6) and
CCR4b. CCR4b associates with other components, such as
CNOT1-3 and Caf1, to form a CCR4-NOT multisubunit
complex, which regulates transcription and mRNA
degradation. The nuclease domain of CCR4b exhibits
Mg2+-dependent deadenylase activity with strict
specificity for poly (A) RNA as substrate. CCR4b is
mainly localized in the cytoplasm. It regulates cell
growth and influences cell cycle progression by
regulating p27/Kip1 mRNA levels. It contributes to the
prevention of cell death by regulating insulin-like
growth factor-binding protein 5.
Length = 348
Score = 62.0 bits (150), Expect = 2e-13
Identities = 29/64 (45%), Positives = 39/64 (60%), Gaps = 4/64 (6%)
Query: 1 VIEFLSTGRVTSDHQDFKDLPYKSVLNKICQNDKSND----FTHSFKLASAYSEDIMPYT 56
V+E+LS G V +H+DFK+L Y L N K+ TH F+L SAY ++MPYT
Sbjct: 229 VVEYLSNGGVADNHKDFKELRYNECLMNFSCNGKNGSSEGRITHGFQLKSAYENNLMPYT 288
Query: 57 NYTY 60
NYT+
Sbjct: 289 NYTF 292
>gnl|CDD|197340 cd10313, Deadenylase_CCR4a, C-terminal deadenylase domain of CCR4a,
also known as CCR4-NOT transcription complex subunit 6.
This subfamily contains the C-terminal catalytic domain
of the deadenylase, CCR4a, also known as CCR4-NOT
transcription complex subunit 6 (CNOT6). CCR4 belongs to
the large EEP (exonuclease/endonuclease/phosphatase)
superfamily that contains functionally diverse enzymes
that share a common catalytic mechanism of cleaving
phosphodiester bonds. CCR4 is the major deadenylase
subunit of the CCR4-NOT transcription complex, which
contains two deadenylase subunits and several
noncatalytic subunits. The other deadenylase subunit,
Caf1, is a DEDD-type protein and does not belong in this
superfamily. There are two vertebrate CCR4 proteins,
CCR4a and CCR4b (also called CNOT6-like or CNOT6L).
CCR4a associates with other components, such as CNOT1-3
and Caf1, to form a CCR4-NOT multisubunit complex, which
regulates transcription and mRNA degradation. The
nuclease domain of CCR4a exhibits Mg2+-dependent
deadenylase activity with specificity for poly (A) RNA
as substrate. CCR4a is a component of P-bodies and is
necessary for foci formation of various P-body
components. It also plays a role in cellular responses
to DNA damage, by regulating Chk2 activity.
Length = 350
Score = 61.2 bits (148), Expect = 4e-13
Identities = 33/64 (51%), Positives = 45/64 (70%), Gaps = 4/64 (6%)
Query: 1 VIEFLSTGRVTSDHQDFKDLPY-KSVLNKIC--QNDKSND-FTHSFKLASAYSEDIMPYT 56
V+E+LSTG V ++H+DFK+L Y +S+ N C +N +N TH FKL SAY +MPYT
Sbjct: 231 VVEYLSTGGVETNHKDFKELRYNESLTNFSCNGKNGTTNGRITHGFKLKSAYENGLMPYT 290
Query: 57 NYTY 60
NYT+
Sbjct: 291 NYTF 294
>gnl|CDD|178689 PLN03144, PLN03144, Carbon catabolite repressor protein 4 homolog;
Provisional.
Length = 606
Score = 26.2 bits (58), Expect = 0.83
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 7/46 (15%)
Query: 4 FLSTGRVTSDHQDFKDLPYKSVLNKICQNDKSNDFTHSFKLASAYS 49
L+TG+V H D P +L ++ TH L SAYS
Sbjct: 475 LLATGKVDPLHPDLAVDPL-GILR------PASKLTHQLPLVSAYS 513
>gnl|CDD|227564 COG5239, CCR4, mRNA deadenylase, exonuclease subunit and related
nucleases [RNA processing and modification].
Length = 378
Score = 25.1 bits (55), Expect = 2.3
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 10/60 (16%)
Query: 1 VIEFLSTGRVTS-DHQDFKDLPYKSVLNKICQNDKSNDFTHSFKLASAYSEDIMPYTNYT 59
V +FL T ++ + + +D SV K F H L S S+ + +TN+T
Sbjct: 259 VYKFLVTSQIQLHESLNGRDFSLYSVGYK---------FVHPENLKSDNSKGELGFTNWT 309
>gnl|CDD|227464 COG5135, COG5135, Uncharacterized conserved protein [Function
unknown].
Length = 245
Score = 24.2 bits (52), Expect = 4.3
Identities = 6/34 (17%), Positives = 14/34 (41%)
Query: 21 PYKSVLNKICQNDKSNDFTHSFKLASAYSEDIMP 54
P+ + + +N+ + F+LA+ P
Sbjct: 5 PWIPMFIQSLKNNTDVEPFVYFQLATVDELTNKP 38
>gnl|CDD|206345 pfam14177, YkyB, YkyB-like protein. The YkyB-like protein family
includes the B. subtilis YkyB protein, which is
functionally uncharacterized. This family of proteins
is found in bacteria. Proteins in this family are
approximately 150 amino acids in length. There are two
conserved sequence motifs: NRHAKTA and HLG.
Length = 141
Score = 23.9 bits (52), Expect = 5.9
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 13 DHQDFKDLPYKSVLNKICQNDKSN 36
+DFK+LP+ L++ +N K
Sbjct: 76 TKEDFKNLPHLGKLDQSYRNPKVR 99
>gnl|CDD|185384 PRK15487, PRK15487, O-antigen ligase RfaL; Provisional.
Length = 400
Score = 23.5 bits (51), Expect = 9.2
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 38 FTHSFKLASAYSEDIMPYTNY 58
+ Y++ IMP+TNY
Sbjct: 136 LSELILYIKDYNQGIMPFTNY 156
>gnl|CDD|197306 cd08372, EEP, Exonuclease-Endonuclease-Phosphatase (EEP) domain
superfamily. This large superfamily includes the
catalytic domain (exonuclease/endonuclease/phosphatase
or EEP domain) of a diverse set of proteins including
the ExoIII family of apurinic/apyrimidinic (AP)
endonucleases, inositol polyphosphate 5-phosphatases
(INPP5), neutral sphingomyelinases (nSMases),
deadenylases (such as the vertebrate circadian-clock
regulated nocturnin), bacterial cytolethal distending
toxin B (CdtB), deoxyribonuclease 1 (DNase1), the
endonuclease domain of the non-LTR retrotransposon
LINE-1, and related domains. These diverse enzymes share
a common catalytic mechanism of cleaving phosphodiester
bonds; their substrates range from nucleic acids to
phospholipids and perhaps proteins.
Length = 241
Score = 23.6 bits (51), Expect = 9.3
Identities = 5/27 (18%), Positives = 8/27 (29%)
Query: 34 KSNDFTHSFKLASAYSEDIMPYTNYTY 60
+ L ++ YT TY
Sbjct: 169 SMLRLFVALNLVDSFETLPHAYTFDTY 195
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
0.317 0.132 0.384
Gapped
Lambda K H
0.267 0.0676 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 2,848,519
Number of extensions: 177330
Number of successful extensions: 153
Number of sequences better than 10.0: 1
Number of HSP's gapped: 148
Number of HSP's successfully gapped: 13
Length of query: 61
Length of database: 10,937,602
Length adjustment: 32
Effective length of query: 29
Effective length of database: 9,518,274
Effective search space: 276029946
Effective search space used: 276029946
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: 41 (21.7 bits)
S2: 53 (24.3 bits)