RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8226
(115 letters)
>gnl|CDD|153422 cd07973, Spt4, Transcription elongation factor Spt4. Spt4 is a
transcription elongation factor. Three
transcription-elongation factors Spt4, Spt5, and Spt6,
are conserved among eukaryotes and are essential for
transcription via the modulation of chromatin structure.
It is known that Spt4, Spt5, and Spt6 are general
transcription-elongation factors, controlling
transcription both positively and negatively in
important regulatory and developmental roles. Spt4
functions entirely in the context of the Spt4-Spt5
heterodimer and it has been found only as a complex to
Spt5 in Yeast and Human. Spt4 is a small protein that
has zinc finger at the N-terminus. Spt5 is a large
protein that has several interesting structural features
of an acidic N-terminus, a single NGN domain, five or
six KOW domains, and a set of simple C-termianl repeats.
Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not
essential for viability in yeast, however Spt4 is
critical for normal function of the Spt4-Spt5 complex.
Spt4 homolog is not found in bacteria.
Length = 98
Score = 110 bits (277), Expect = 6e-33
Identities = 35/54 (64%), Positives = 44/54 (81%)
Query: 58 TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
T DQFE DGC NC+ +L MK + + VY+CTS NF+G+IALMDP+ SWVA+WQRI
Sbjct: 14 TEDQFERDGCPNCEGYLDMKGNHERVYDCTSPNFEGIIALMDPEKSWVARWQRI 67
>gnl|CDD|203389 pfam06093, Spt4, Spt4/RpoE2 zinc finger. This family consists of
several eukaryotic transcription elongation Spt4
proteins as well as archaebacterial RpoE2. Three
transcription-elongation factors Spt4, Spt5, and Spt6
are conserved among eukaryotes and are essential for
transcription via the modulation of chromatin structure.
Spt4 and Spt5 are tightly associated in a complex, while
the physical association of the Spt4-Spt5 complex with
Spt6 is considerably weaker. It has been demonstrated
that Spt4, Spt5, and Spt6 play roles in transcription
elongation in both yeast and humans including a role in
activation by Tat. It is known that Spt4, Spt5, and Spt6
are general transcription-elongation factors,
controlling transcription both positively and negatively
in important regulatory and developmental roles. RpoE2
is one of 13 subunits in the archaeal RNA polymerase.
These proteins contain a C4-type zinc finger, and the
structure has been solved in. The structure reveals that
Spt4-Spt5 binding is governed by an acid-dipole
interaction between Spt5 and Spt4, and the complex binds
to and travels along the elongating RNA polymerase. The
Spt4-Spt5 complex is likely to be an ancient, core
component of the transcription elongation machinery.
Length = 77
Score = 97.4 bits (243), Expect = 4e-28
Identities = 35/54 (64%), Positives = 43/54 (79%), Gaps = 1/54 (1%)
Query: 58 TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
T DQFE DGC NC EFLHMK R+ V CTS NF+G++A++DP+ SWVAKWQR+
Sbjct: 12 TEDQFEDDGCPNC-EFLHMKGDRERVSECTSENFEGLVAILDPEKSWVAKWQRL 64
>gnl|CDD|227530 COG5204, SPT4, Transcription elongation factor SPT4
[Transcription].
Length = 112
Score = 64.2 bits (156), Expect = 1e-14
Identities = 28/54 (51%), Positives = 36/54 (66%), Gaps = 1/54 (1%)
Query: 58 TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
T + F DGC NC L+MK NV CTS F+G++A++ P +SWVAKWQRI
Sbjct: 20 TLNGFRKDGCPNC-PMLNMKGGVTNVEECTSPKFEGVVAMLQPTNSWVAKWQRI 72
>gnl|CDD|236146 PRK08064, PRK08064, cystathionine beta-lyase; Provisional.
Length = 390
Score = 27.8 bits (62), Expect = 1.2
Identities = 11/31 (35%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 35 HRPWTIDPIPSASAETINPRTTSTFDQFEFD 65
H + D A I STF QF+FD
Sbjct: 13 HNQYKHDKQTGAVNVPI--YHASTFHQFDFD 41
>gnl|CDD|188074 TIGR00694, thiM, hydroxyethylthiazole kinase. This model
represents the hydoxyethylthiazole kinase, ThiM, of a
number of bacteria, and C-terminal domains of
bifunctional thiamine biosynthesis proteins of
Saccharomyces cerevisiae and Schizosaccharomyces pombe,
in which the N-terminal domain corresponds to the
bacterial thiamine-phosphate pyrophosphorylase (EC
2.5.1.3), ThiE [Biosynthesis of cofactors, prosthetic
groups, and carriers, Thiamine].
Length = 249
Score = 26.9 bits (60), Expect = 2.2
Identities = 12/63 (19%), Positives = 22/63 (34%), Gaps = 7/63 (11%)
Query: 18 KPSTLAGLKVVGVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCD----NCDEF 73
K S A + NE +P +DP+ + + RT ++ + N E
Sbjct: 62 KESIEAMIAAGKSANELGKPVVLDPVGVGATKF---RTETSLELLSEGRVAAIKGNAGEI 118
Query: 74 LHM 76
+
Sbjct: 119 AAL 121
>gnl|CDD|235899 PRK06975, PRK06975, bifunctional uroporphyrinogen-III
synthetase/uroporphyrin-III C-methyltransferase;
Reviewed.
Length = 656
Score = 25.8 bits (57), Expect = 6.6
Identities = 11/39 (28%), Positives = 17/39 (43%)
Query: 11 LYYRPPPKPSTLAGLKVVGVHNEDHRPWTIDPIPSASAE 49
L+ LAG +V+ V + R W + + A AE
Sbjct: 126 LFAEIDAAFGALAGKRVLIVRGDGGREWLAERLREAGAE 164
>gnl|CDD|173733 cd07829, STKc_CDK_like, Catalytic domain of Cyclin-Dependent
protein Kinase-like Serine/Threonine Kinases.
Serine/Threonine Kinases (STKs), Cyclin-Dependent
protein Kinase (CDK)-like subfamily, catalytic (c)
domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The CDK-like subfamily
is part of a larger superfamily that includes the
catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. CDKs belong to a large family of STKs that are
regulated by their cognate cyclins. Together, they are
involved in the control of cell-cycle progression,
transcription, and neuronal function. CDKs are partly
regulated by their subcellular localization, which
defines substrate phosphorylation and the resulting
specific function. CDK1, CDK2, CDK4, and CDK6 have
well-defined functions in the cell cycle, such as the
regulation of the early G1 phase by CDK4 or CDK6, the
G1/S phase transition by CDK2, or the entry of mitosis
by CDK1. They also exhibit overlapping cyclin
specificity and functions in certain conditions.
Knockout mice with a single CDK deleted remain viable
with specific phenotypes, showing that some CDKs can
compensate for each other. For example, CDK4 can
compensate for the loss of CDK6, however, double
knockout mice with both CDK4 and CDK6 deleted die in
utero. CDK8 and CDK9 are mainly involved in
transcription while CDK5 is implicated in neuronal
function. CDK7 plays essential roles in both the cell
cycle as a CDK-Activating Kinase (CAK) and in
transcription as a component of the general
transcription factor TFIIH.
Length = 282
Score = 25.1 bits (56), Expect = 8.7
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 1 MRTIDPGLLTLYYRPP 16
+RT ++TL+YR P
Sbjct: 152 LRTYTHEVVTLWYRAP 167
>gnl|CDD|223409 COG0332, FabH, 3-oxoacyl-[acyl-carrier-protein].
Length = 323
Score = 25.3 bits (56), Expect = 9.2
Identities = 5/23 (21%), Positives = 8/23 (34%)
Query: 91 FDGMIALMDPKDSWVAKWQRIRR 113
+ +D D W+ IR
Sbjct: 20 NADLEKRVDTSDEWIETRTGIRE 42
>gnl|CDD|215153 PLN02271, PLN02271, serine hydroxymethyltransferase.
Length = 586
Score = 25.2 bits (55), Expect = 9.9
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 84 YNCTSSNFDGMIALMDPKD 102
Y+CTS+NF L+ P D
Sbjct: 221 YSCTSANFAVYTGLLLPGD 239
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
0.319 0.136 0.442
Gapped
Lambda K H
0.267 0.0688 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,950,486
Number of extensions: 473807
Number of successful extensions: 427
Number of sequences better than 10.0: 1
Number of HSP's gapped: 425
Number of HSP's successfully gapped: 12
Length of query: 115
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 36
Effective length of database: 7,433,636
Effective search space: 267610896
Effective search space used: 267610896
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: 53 (24.3 bits)