RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7447
(114 letters)
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 33.3 bits (77), Expect = 0.017
Identities = 18/56 (32%), Positives = 22/56 (39%), Gaps = 8/56 (14%)
Query: 24 FRYTCDSCGKVYKLKRSLYRHRTLECG--KEPRYQCPHCPYRGKQKVHLKTHVAIK 77
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 = 32.7 bits (75), Expect = 0.031
Identities = 15/38 (39%), Positives = 17/38 (44%), Gaps = 8/38 (21%)
Query: 25 RYTCDSCGKVYKLKRSLYRHRTLECG--KEPRYQCPHC 60
R C SCG Y +R +CG EP Y CP C
Sbjct: 667 RRRCPSCGTE------TYENRCPDCGTHTEPVYVCPDC 698
>gnl|CDD|235757 PRK06260, PRK06260, threonine synthase; Validated.
Length = 397
Score = 30.7 bits (70), Expect = 0.11
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 27/80 (33%)
Query: 23 QFRYTCDSCGK----VYKLK--------RSLYRHR----------TLECGKEPRYQCPHC 60
+ YTC CG +Y L R ++R++ +L G P Y+CP
Sbjct: 17 EIIYTCPECGGLLEVIYDLDKIFDKLRGRGVWRYKELLPVKKKIVSLNEGGTPLYRCP-- 74
Query: 61 PYRGKQKVHLKTHVAIKHQG 80
++++ +K + +KH+G
Sbjct: 75 --NLEKELGVK-ELYVKHEG 91
>gnl|CDD|225277 COG2414, COG2414, Aldehyde:ferredoxin oxidoreductase [Energy
production and conversion].
Length = 614
Score = 30.4 bits (69), Expect = 0.20
Identities = 10/31 (32%), Positives = 14/31 (45%)
Query: 52 EPRYQCPHCPYRGKQKVHLKTHVAIKHQGPE 82
+ RY C CP + V +K +GPE
Sbjct: 285 KKRYGCGSCPIGCGRVVRIKRGKGGGTEGPE 315
>gnl|CDD|222450 pfam13909, zf-H2C2_5, C2H2-type zinc-finger domain.
Length = 24
Score = 27.2 bits (61), Expect = 0.31
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 55 YQCPHCPYRGKQKVHLKTHVAIKH 78
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 = 28.6 bits (64), Expect = 0.34
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 26 YTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCP 58
Y CD C +K RS+ R+R C + + CP
Sbjct: 24 YACDGCSGFFK--RSIRRNRQYVCKSKGQGGCP 54
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 27.2 bits (61), Expect = 2.0
Identities = 13/56 (23%), Positives = 17/56 (30%), Gaps = 11/56 (19%)
Query: 15 HTLF---NPLLQFRYTCDSCGKVYKLKRSLYRHRTLECGKEPR-------YQCPHC 60
H F P L TC C +V + + LE + C HC
Sbjct: 79 HIWFFKSIPSL-LDMTCRDCERVLYFEAYVVLGTDLEKIQLLNETEYVYDSFCAHC 133
>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 = 27.0 bits (60), Expect = 2.1
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 9/38 (23%)
Query: 23 QFRYTCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHC 60
++ 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 = 26.7 bits (59), Expect = 3.1
Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 26 YTCDSCGKVYKLKRSLYRHRTLEC 49
Y C+ C K Y + SL RHR +C
Sbjct: 159 YICEFCLKYYGSQTSLVRHR-KKC 181
>gnl|CDD|222888 PHA02582, 10, baseplate wedge subunit and tail pin; Provisional.
Length = 604
Score = 26.6 bits (59), Expect = 3.5
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 7 FSEFNLPPHTLFNP 20
F+EF L P+ NP
Sbjct: 291 FAEFGLSPNEPINP 304
>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 = 3.6
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 23 QFRY--TCDSCGKVYKLKRSLYRHRTLECGKEPRYQCPHC 60
Q RY C CG+ +L+ + E + RY CPHC
Sbjct: 196 QRRYYVPCPHCGEEQELRWERLKWDKGEAPETARYVCPHC 235
>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 = 24.5 bits (53), Expect = 3.6
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 55 YQCPHCPYRGKQKVHLKTHVAIKH 78
++CP C K LK H+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>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 = 26.6 bits (59), Expect = 3.9
Identities = 11/40 (27%), Positives = 14/40 (35%), Gaps = 5/40 (12%)
Query: 33 KVYKLKRSLYRHRTLECGKEPRYQCPHCPYRGKQKVHLKT 72
VY + L H + RY+ P QK KT
Sbjct: 449 SVYNPELQLADHA-----RPVRYEMAPPPAPSTQKPDPKT 483
>gnl|CDD|224462 COG1545, COG1545, Predicted nucleic-acid-binding protein
containing a Zn-ribbon [General function prediction
only].
Length = 140
Score = 25.8 bits (57), Expect = 4.5
Identities = 8/31 (25%), Positives = 13/31 (41%), Gaps = 3/31 (9%)
Query: 41 LYRHRTLECGKE---PRYQCPHCPYRGKQKV 68
L + +CG+ PR CP C + +
Sbjct: 27 LLGTKCKKCGRVYFPPRAYCPKCGSETELEW 57
>gnl|CDD|233362 TIGR01340, aconitase_mito, aconitate hydratase, mitochondrial.
This model represents mitochondrial forms of the TCA
cycle enzyme aconitate hydratase, also known as
aconitase and citrate hydro-lyase [Energy metabolism,
TCA cycle].
Length = 745
Score = 26.4 bits (58), Expect = 4.6
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 2/35 (5%)
Query: 82 EMLSVKHQGPEMLSIKHQGPETLSIK--HQFSQDQ 114
EML G L + + + IK H S+DQ
Sbjct: 698 EMLKNGGGGEVDLRVTKKNGKVFEIKLKHTVSKDQ 732
>gnl|CDD|219537 pfam07727, RVT_2, Reverse transcriptase (RNA-dependent DNA
polymerase). A reverse transcriptase gene is usually
indicative of a mobile element such as a retrotransposon
or retrovirus. Reverse transcriptases occur in a variety
of mobile elements, including retrotransposons,
retroviruses, group II introns, bacterial msDNAs,
hepadnaviruses, and caulimoviruses. This Pfam entry
includes reverse transcriptases not recognised by the
pfam00078 model.
Length = 246
Score = 25.9 bits (58), Expect = 5.8
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 32 GKVYKLKRSLY 42
KV +LK+SLY
Sbjct: 112 NKVCRLKKSLY 122
>gnl|CDD|218998 pfam06356, DUF1064, Protein of unknown function (DUF1064). This
family consists of several phage and bacterial proteins
of unknown function.
Length = 118
Score = 24.9 bits (54), Expect = 8.6
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 33 KVYKLKRSLYRHRTLECGKEPRY 55
K +K+K L+R+R + K +Y
Sbjct: 88 KEFKIKAKLFRNRYRQSCKALKY 110
>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 = 23.9 bits (52), Expect = 9.1
Identities = 7/20 (35%), Positives = 9/20 (45%)
Query: 26 YTCDSCGKVYKLKRSLYRHR 45
+TC C V+ S Y H
Sbjct: 25 FTCSVCPTVFGPNDSYYEHE 44
>gnl|CDD|217859 pfam04045, P34-Arc, Arp2/3 complex, 34 kD subunit p34-Arc. Arp2/3
protein complex has been implicated in the control of
actin polymerisation in cells. The human complex
consists of seven subunits which include the actin
related Arp2 and Arp3, and five others referred to as
p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. This
family represents the p34-Arc subunit.
Length = 240
Score = 24.9 bits (55), Expect = 9.5
Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 9/49 (18%)
Query: 69 HLKTHV-------AIKHQGPEMLSVKHQGPEMLSIKHQGPETLSIKHQF 110
LK + A + Q L+ + +G E+ I ++ ET+ IK F
Sbjct: 62 LLKRNCMAAPFEKAFEKQ--AELAEEAEGEEVAVIHYRDDETIYIKPSF 108
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
0.323 0.138 0.444
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: 5,433,917
Number of extensions: 422328
Number of successful extensions: 498
Number of sequences better than 10.0: 1
Number of HSP's gapped: 494
Number of HSP's successfully gapped: 69
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)