RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7450
(161 letters)
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 33.0 bits (76), Expect = 0.064
Identities = 18/56 (32%), Positives = 22/56 (39%), Gaps = 8/56 (14%)
Query: 19 FRYTCDSCGKVYKLKRSLYRHRTLECG--KEPRYQCPHCPYRGKQKVHLKTHVAIK 72
R C SCGK + YR R CG EP Y+CP C ++ K
Sbjct: 625 GRRKCPSCGKE-----TFYR-RCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPT 674
>gnl|CDD|237798 PRK14714, PRK14714, DNA polymerase II large subunit; Provisional.
Length = 1337
Score = 32.4 bits (74), Expect = 0.10
Identities = 15/38 (39%), Positives = 17/38 (44%), Gaps = 8/38 (21%)
Query: 20 RYTCDSCGKVYKLKRSLYRHRTLECG--KEPRYQCPHC 55
R C SCG Y +R +CG EP Y CP C
Sbjct: 667 RRRCPSCGTE------TYENRCPDCGTHTEPVYVCPDC 698
>gnl|CDD|222450 pfam13909, zf-H2C2_5, C2H2-type zinc-finger domain.
Length = 24
Score = 28.4 bits (64), Expect = 0.20
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 50 YQCPHCPYRGKQKVHLKTHVAIKH 73
Y+C HCPY K L+ H+ + H
Sbjct: 1 YKCSHCPYSSTPK-KLERHLKLHH 23
>gnl|CDD|143537 cd07163, NR_DBD_TLX, DNA-binding domain of Tailless (TLX) is
composed of two C4-type zinc fingers. DNA-binding
domain of Tailless (TLX) 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. TLX
interacts with specific DNA sites upstream of the
target gene and modulates the rate of transcriptional
initiation. TLX is an orphan receptor that is
expressed by neural stem/progenitor cells in the adult
brain of the subventricular zone (SVZ) and the dentate
gyrus (DG). It plays a key role in neural development
by promoting cell cycle progression and preventing
apoptosis in the developing brain. Like other members
of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, TLX has 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 = 92
Score = 29.0 bits (65), Expect = 0.35
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 21 YTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCP 53
Y CD C +K RS+ R+R C + + CP
Sbjct: 24 YACDGCSGFFK--RSIRRNRQYVCKSKGQGGCP 54
>gnl|CDD|235757 PRK06260, PRK06260, threonine synthase; Validated.
Length = 397
Score = 29.9 bits (68), Expect = 0.49
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 27/80 (33%)
Query: 18 QFRYTCDSCGK----VYKLK--------RSLYRHR----------TLECGKEPRYQCPHC 55
+ YTC CG +Y L R ++R++ +L G P Y+CP
Sbjct: 17 EIIYTCPECGGLLEVIYDLDKIFDKLRGRGVWRYKELLPVKKKIVSLNEGGTPLYRCP-- 74
Query: 56 PYRGKQKVHLKTHVAIKHQG 75
++++ +K + +KH+G
Sbjct: 75 --NLEKELGVK-ELYVKHEG 91
>gnl|CDD|225277 COG2414, COG2414, Aldehyde:ferredoxin oxidoreductase [Energy
production and conversion].
Length = 614
Score = 29.6 bits (67), Expect = 0.67
Identities = 10/31 (32%), Positives = 14/31 (45%)
Query: 47 EPRYQCPHCPYRGKQKVHLKTHVAIKHQGPE 77
+ RY C CP + V +K +GPE
Sbjct: 285 KKRYGCGSCPIGCGRVVRIKRGKGGGTEGPE 315
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family
contains a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 25.7 bits (56), Expect = 2.1
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 50 YQCPHCPYRGKQKVHLKTHVAIKH 73
++CP C K LK H+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|220661 pfam10263, SprT-like, SprT-like family. This family represents a
domain found in eukaryotes and prokaryotes. The domain
contains a characteristic motif of the zinc
metallopeptidases. This family includes the bacterial
SprT protein.
Length = 153
Score = 27.3 bits (61), Expect = 2.3
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 9/38 (23%)
Query: 18 QFRYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHC 55
++ Y C SCG++Y KR + RH +Y+C C
Sbjct: 117 RYIYRCGSCGQLYPRKRRIRRH---------KYRCGRC 145
>gnl|CDD|227360 COG5027, SAS2, Histone acetyltransferase (MYST family) [Chromatin
structure and dynamics].
Length = 395
Score = 27.0 bits (60), Expect = 5.1
Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 21 YTCDSCGKVYKLKRSLYRHRTLEC 44
Y C+ C K Y + SL RHR +C
Sbjct: 159 YICEFCLKYYGSQTSLVRHR-KKC 181
>gnl|CDD|224462 COG1545, COG1545, Predicted nucleic-acid-binding protein
containing a Zn-ribbon [General function prediction
only].
Length = 140
Score = 26.2 bits (58), Expect = 5.5
Identities = 8/31 (25%), Positives = 13/31 (41%), Gaps = 3/31 (9%)
Query: 36 LYRHRTLECGKE---PRYQCPHCPYRGKQKV 63
L + +CG+ PR CP C + +
Sbjct: 27 LLGTKCKKCGRVYFPPRAYCPKCGSETELEW 57
>gnl|CDD|188778 cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM
and RhoGap domain containing protein. The second LIM
domain of Lrg1p, a LIM and RhoGap domain containing
protein: The members of this family contain three
tandem repeats of LIM domains and a Rho-type GTPase
activating protein (RhoGap) domain. Lrg1p is a Rho1
GTPase-activating protein required for efficient cell
fusion in yeast. Lrg1p-GAP domain strongly and
specifically stimulates the GTPase activity of Rho1p, a
regulator of beta (1-3)-glucan synthase in vitro. The
LIM domain is 50-60 amino acids in size and shares 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.
Length = 53
Score = 25.0 bits (55), Expect = 6.0
Identities = 7/20 (35%), Positives = 9/20 (45%)
Query: 21 YTCDSCGKVYKLKRSLYRHR 40
+TC C V+ S Y H
Sbjct: 25 FTCSVCPTVFGPNDSYYEHE 44
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 26.4 bits (58), Expect = 7.9
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 12/87 (13%)
Query: 75 GPEMLSVKHQGPEML-SIKHQGPETLSIKHQVSEMLSIKHQGPETLSIKHQGPEMLSIKH 133
G + ++V+ + ++L SIK E SI+ + E+ S+K++ + H E I H
Sbjct: 60 GQQQINVEDEKRKILQSIK--KEENSSIEDVLKEVKSLKNE------LAH-KKE--EINH 108
Query: 134 QGPESAFDLRRNNQAHLNGRKDMMERL 160
D+ R N + KD+ E +
Sbjct: 109 PTILKIEDILRENDFSESYIKDINEFI 135
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 24.0 bits (52), Expect = 7.9
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 50 YQCPHCPYRGKQKVHLKTHVAI 71
Y+CP C K K L+ H+
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
>gnl|CDD|213980 TIGR04367, HpnR_B12_rSAM, hopanoid C-3 methylase HpnR. Members of
this are family are a B12-binding domain/radical SAM
domain protein required for 3-methylhopanoid production.
Activity was confirmed by mutant phenotype by disrupting
this gene in Methylococcus capsulatus strain Bath. This
protein family should only occur in genomes that encode
a squalene-hopene cyclase (see TIGR01507) [Fatty acid
and phospholipid metabolism, Biosynthesis].
Length = 490
Score = 26.2 bits (58), Expect = 8.2
Identities = 11/40 (27%), Positives = 14/40 (35%), Gaps = 5/40 (12%)
Query: 28 KVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKT 67
VY + L H + RY+ P QK KT
Sbjct: 449 SVYNPELQLADHA-----RPVRYEMAPPPAPSTQKPDPKT 483
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 26.4 bits (59), Expect = 8.3
Identities = 13/56 (23%), Positives = 17/56 (30%), Gaps = 11/56 (19%)
Query: 10 HTLF---NPLLQFRYTCDSCGKVYKLKRSLYRHRTLECGKEPR-------YQCPHC 55
H F P L TC C +V + + LE + C HC
Sbjct: 79 HIWFFKSIPSL-LDMTCRDCERVLYFEAYVVLGTDLEKIQLLNETEYVYDSFCAHC 133
>gnl|CDD|218790 pfam05876, Terminase_GpA, Phage terminase large subunit (GpA).
This family consists of several phage terminase large
subunit proteins as well as related sequences from
several bacterial species. The DNA packaging enzyme of
bacteriophage lambda, terminase, is a heteromultimer
composed of a small subunit, gpNu1, and a large subunit,
gpA, products of the Nu1 and A genes, respectively.
Terminase is involved in the site-specific binding and
cutting of the DNA in the initial stages of packaging.
It is now known that gpA is actively involved in late
stages of packaging, including DNA translocation, and
that this enzyme contains separate functional domains
for its early and late packaging activities.
Length = 552
Score = 26.4 bits (59), Expect = 8.3
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 18 QFRY--TCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHC 55
Q RY C CG+ +L+ + E + RY CPHC
Sbjct: 196 QRRYYVPCPHCGEEQELRWERLKWDKGEAPETARYVCPHC 235
>gnl|CDD|143512 cd06916, NR_DBD_like, DNA-binding domain of nuclear receptors is
composed of two C4-type zinc fingers. DNA-binding
domain of nuclear receptors 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. It
interacts with a specific DNA site upstream of the
target gene and modulates the rate of transcriptional
initiation. Nuclear receptors form a superfamily of
ligand-activated transcription regulators, which
regulate various physiological functions, from
development, reproduction, to homeostasis and
metabolism in animals (metazoans). The family contains
not only receptors for known ligands but also orphan
receptors for which ligands do not exist or have not
been identified. NRs share a common structural
organization with a central well conserved DNA binding
domain (DBD), a variable N-terminal domain, a flexible
hinge and a C-terminal ligand binding domain (LBD).
Most nuclear receptors bind as homodimers or
heterodimers to their target sites, which consist of
two hexameric half-sites. Specificity is determined by
the half-site sequence, the relative orientation of the
half-sites and the number of spacer nucleotides between
the half-sites. However, a growing number of nuclear
receptors have been reported to bind to DNA as
monomers.
Length = 72
Score = 24.8 bits (55), Expect = 8.4
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 10/46 (21%)
Query: 21 YTCDSCGKVYKLKRSLYRHRTLEC--------GKEPRYQCPHCPYR 58
TC+ C K + +RS+ R+ C K R +C C +
Sbjct: 16 LTCEGC-KGF-FRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLK 59
>gnl|CDD|234003 TIGR02768, TraA_Ti, Ti-type conjugative transfer relaxase TraA.
This protein contains domains distinctive of a single
strand exonuclease (N-terminus, MobA/MobL, pfam03389) as
well as a helicase domain (central region, homologous to
the corresponding region of the F-type relaxase TraI,
TIGR02760). This protein likely fills the same role as
TraI(F), nicking (at the oriT site) and unwinding the
coiled plasmid prior to conjugative transfer.
Length = 744
Score = 26.3 bits (58), Expect = 8.7
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 5/46 (10%)
Query: 120 SIKHQGPEMLSIKHQGPESAFDLRRNNQA-----HLNGRKDMMERL 160
S QG +++ KH G + RR A +L R++ ER+
Sbjct: 201 SYAEQGIDLIPTKHIGVHAKAMERRGEAAERLPENLAIRQENAERI 246
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
0.320 0.136 0.422
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,765,569
Number of extensions: 644087
Number of successful extensions: 636
Number of sequences better than 10.0: 1
Number of HSP's gapped: 632
Number of HSP's successfully gapped: 48
Length of query: 161
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 72
Effective length of database: 6,990,096
Effective search space: 503286912
Effective search space used: 503286912
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 (21.8 bits)
S2: 55 (25.0 bits)