RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16459
(143 letters)
>gnl|CDD|173623 cd00180, PKc, Catalytic domain of Protein Kinases. Protein Kinases
(PKs), catalytic (c) domain. PKs catalyze the transfer
of the gamma-phosphoryl group from ATP to
serine/threonine or tyrosine residues on protein
substrates. The PK family is part of a larger
superfamily that includes the catalytic domains of RIO
kinases, aminoglycoside phosphotransferase, choline
kinase, phosphoinositide 3-kinase (PI3K), and
actin-fragmin kinase. PKs make up a large family of
serine/threonine kinases, protein tyrosine kinases
(PTKs), and dual-specificity PKs that phosphorylate both
serine/threonine and tyrosine residues of target
proteins. Majority of protein phosphorylation, about
95%, occurs on serine residues while only 1% occurs on
tyrosine residues. Protein phosphorylation is a
mechanism by which a wide variety of cellular proteins,
such as enzymes and membrane channels, are reversibly
regulated in response to certain stimuli. PKs often
function as components of signal transduction pathways
in which one kinase activates a second kinase, which in
turn, may act on other kinases; this sequential action
transmits a signal from the cell surface to target
proteins, which results in cellular responses. The PK
family is one of the largest known protein families with
more than 100 homologous yeast enzymes and 550 human
proteins. A fraction of PK family members are
pseudokinases that lack crucial residues for catalytic
activity. The mutiplicity of kinases allows for specific
regulation according to substrate, tissue distribution,
and cellular localization. PKs regulate many cellular
processes including proliferation, division,
differentiation, motility, survival, metabolism,
cell-cycle progression, cytoskeletal rearrangement,
immunity, and neuronal functions. Many kinases are
implicated in the development of various human diseases
including different types of cancer.
Length = 215
Score = 35.7 bits (83), Expect = 0.004
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 76 SLKTVLMIAQQLQSNKGIPEVYYFGPCGKYNALVMELL-GPSLEDLFDLCNRKFTLKTVL 134
L + I ++L + I ++Y + LVME G SL+DL K + +L
Sbjct: 37 ELLREIEILKKLN-HPNIVKLYGVFEDENHLYLVMEYCEGGSLKDLLKENEGKLSEDEIL 95
Query: 135 MIAIQL 140
I +Q+
Sbjct: 96 RILLQI 101
>gnl|CDD|225023 COG2112, COG2112, Predicted Ser/Thr protein kinase [Signal
transduction mechanisms].
Length = 201
Score = 31.2 bits (71), Expect = 0.13
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 5/62 (8%)
Query: 73 FRFSLKTVLMIAQQLQSNKGIPEVYYFGPCGKYNALVME-LLGPSLEDLFDLCNRKFTLK 131
R +L+ I + L PEVY++G + + ME + G L L +RK L+
Sbjct: 58 PRRNLEKEAKILEILAGEGVTPEVYFYG----EDFIRMEYIDGRPLGKLEIGGDRKHLLR 113
Query: 132 TV 133
+
Sbjct: 114 VL 115
>gnl|CDD|240159 cd05120, APH_ChoK_like, Aminoglycoside 3'-phosphotransferase (APH)
and Choline Kinase (ChoK) family. The APH/ChoK family is
part of a larger superfamily that includes the catalytic
domains of other kinases, such as the typical
serine/threonine/tyrosine protein kinases (PKs), RIO
kinases, actin-fragmin kinase (AFK), and
phosphoinositide 3-kinase (PI3K). The family is composed
of APH, ChoK, ethanolamine kinase (ETNK), macrolide
2'-phosphotransferase (MPH2'), an unusual homoserine
kinase, and uncharacterized proteins with similarity to
the N-terminal domain of acyl-CoA dehydrogenase 10
(ACAD10). The members of this family catalyze the
transfer of the gamma-phosphoryl group from ATP (or CTP)
to small molecule substrates such as aminoglycosides,
macrolides, choline, ethanolamine, and homoserine.
Phosphorylation of the antibiotics, aminoglycosides and
macrolides, leads to their inactivation and to bacterial
antibiotic resistance. Phosphorylation of choline,
ethanolamine, and homoserine serves as precursors to the
synthesis of important biological compounds, such as the
major phospholipids, phosphatidylcholine and
phosphatidylethanolamine and the amino acids, threonine,
methionine, and isoleucine.
Length = 155
Score = 29.3 bits (66), Expect = 0.52
Identities = 11/40 (27%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 83 IAQQLQSNKG-IPEVYYFGPCGKYNALVMELL-GPSLEDL 120
I Q L +P+V G ++ L+ME + G +L+++
Sbjct: 44 ILQLLARKGLPVPKVLASGESDGWSYLLMEWIEGETLDEV 83
>gnl|CDD|223624 COG0550, TopA, Topoisomerase IA [DNA replication, recombination,
and repair].
Length = 570
Score = 28.3 bits (64), Expect = 1.6
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 73 FRFSLKTVLMIAQQL 87
FS K + IAQ+L
Sbjct: 273 LGFSAKKTMDIAQKL 287
>gnl|CDD|128673 smart00391, MBD, Methyl-CpG binding domain. Methyl-CpG binding
domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1)
domain.
Length = 77
Score = 26.2 bits (58), Expect = 2.5
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 5/35 (14%)
Query: 70 LCGFRFSLKTVLMIAQQLQSNKGIPEVYYFGPCGK 104
CG+R K ++ + G +VYY PCGK
Sbjct: 9 PCGWRRETKQ-----RKSGRSAGKFDVYYISPCGK 38
>gnl|CDD|238691 cd01397, HAT_MBD, Methyl-CpG binding domains (MBD) present in
putative chromatin remodelling factor such as BAZ2A;
BAZ2A contains a MBD, DDT, PHD-type zinc finger and
Bromo domain suggesting that BAZ2A might be associated
with histone acetyltransferase (HAT) activity. The
Drosophila melanogaster toutatis protein, a putative
subunit of the chromatin-remodeling complex, and other
such proteins in this group share a similar domain
architecture with BAZ2A, as does the Caenorhabditis
elegans flectin homolog.
Length = 73
Score = 26.2 bits (58), Expect = 2.6
Identities = 7/10 (70%), Positives = 8/10 (80%)
Query: 95 EVYYFGPCGK 104
EV Y+ PCGK
Sbjct: 26 EVAYYAPCGK 35
>gnl|CDD|237528 PRK13840, PRK13840, sucrose phosphorylase; Provisional.
Length = 495
Score = 27.7 bits (62), Expect = 2.6
Identities = 12/22 (54%), Positives = 13/22 (59%), Gaps = 2/22 (9%)
Query: 92 GIPEVYYFGPCGKYNALVMELL 113
GIP+VYY G N MELL
Sbjct: 372 GIPQVYYVGLLAGPND--MELL 391
>gnl|CDD|236843 PRK11092, PRK11092, bifunctional (p)ppGpp synthetase II/
guanosine-3',5'-bis pyrophosphate
3'-pyrophosphohydrolase; Provisional.
Length = 702
Score = 27.4 bits (61), Expect = 3.4
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 38 GKVMDKTDKPSGGGYQALVLSLLGP 62
G+V D P GYQ+L S++GP
Sbjct: 289 GRVKDYIAIPKANGYQSLHTSMIGP 313
>gnl|CDD|130763 TIGR01702, CO_DH_cata, carbon-monoxide dehydrogenase, catalytic
subunit. This model represents the carbon-monoxide
dehydrogenase catalytic subunit. This protein is related
to prismane (also called hybrid cluster protein), a
complex whose activity is not yet fully described; the
two share similar sets of ligands to unusual
metal-containing clusters.
Length = 621
Score = 27.0 bits (60), Expect = 3.8
Identities = 24/79 (30%), Positives = 28/79 (35%), Gaps = 18/79 (22%)
Query: 49 GGGYQAL-VLSLLGPSLQDLFELCGFRFSLKTVLMIAQQLQSNKGIPEVYYFGPC---GK 104
G AL L+ P EL G LK V GIP V +FG C G+
Sbjct: 470 GCSNGALEKAGLMTPE--AAEELAGE--GLKGVC-------KALGIPPVLHFGSCVDNGR 518
Query: 105 YNALVMEL---LGPSLEDL 120
L L LG + L
Sbjct: 519 AVDLATALAEDLGVDIPQL 537
>gnl|CDD|238896 cd01915, CODH, Carbon monoxide dehydrogenase (CODH) is found in
acetogenic and methanogenic organisms and is responsible
for the synthesis and breakdown of acetyl-CoA,
respectively. CODH has two types of metal clusters, a
cubane [Fe4-S4] center (B-cluster) similar to that of
hybrid cluster protein (HCP) and a Ni-Fe-S center
(C-cluster) where carbon monoxide oxidation occurs.
Bifunctional CODH forms a heterotetramer with acetyl-CoA
synthase (ACS) consisting of two CODH and two ACS
subunits while monofunctional CODH forms a homodimer.
Bifunctional CODH reduces carbon dioxide to carbon
monoxide and ACS then synthesizes acetyl-CoA from carbon
monoxide, CoA, and a methyl group donated by another
protein (CoFeSP), while monofunctional CODH oxidizes
carbon monoxide to carbon dioxide. CODH and ACS each
have a metal cluster referred to as the C- and
A-clusters, respectively.
Length = 613
Score = 26.8 bits (60), Expect = 4.4
Identities = 19/58 (32%), Positives = 23/58 (39%), Gaps = 15/58 (25%)
Query: 69 ELCGFRFSLKTVLMIAQQLQSNKGIPEVYYFGPC---GKYNALVMEL---LGPSLEDL 120
EL G LK V + L GIP V + G C + L L LG + DL
Sbjct: 481 ELAGD--GLKAVC---KAL----GIPPVLHMGSCVDNSRIVDLATALANELGVDIPDL 529
>gnl|CDD|222728 pfam14390, DUF4420, Domain of unknown function (DUF4420). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria and
archaea. Proteins in this family are typically between
310 and 334 amino acids in length.
Length = 305
Score = 26.9 bits (60), Expect = 4.5
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 6/59 (10%)
Query: 14 KCQFSLEGMEDDPPPHGFPRVYFFGKVMDKTDKPSGGGYQALVLSLLGPSLQDLF-ELC 71
+ + P P G + +T SG G LVLSL L+++F LC
Sbjct: 41 DPELLVVLKAVRRLPSKLPS--LKGIEVSRT---SGKGKTILVLSLQDSDLEEVFATLC 94
>gnl|CDD|238110 cd00186, TOP1Ac, DNA Topoisomerase, subtype IA; DNA-binding,
ATP-binding and catalytic domain of bacterial DNA
topoisomerases I and III, and eukaryotic DNA
topoisomerase III and eubacterial and archael reverse
gyrases. Topoisomerases clevage single or double
stranded DNA and then rejoin the broken phosphodiester
backbone. Proposed catalytic mechanism of single
stranded DNA cleavage is by phosphoryl transfer through
a tyrosine nucleophile using acid/base catalysis. Tyr is
activated by a nearby group (not yet identified) acting
as a general base for nucleophilic attack on the 5'
phosphate of the scissile bond. Arg and Lys stabilize
the pentavalent transition state. Glu then acts as a
proton donor for the leaving 3'-oxygen, upon cleavage of
the scissile strand.
Length = 381
Score = 26.4 bits (59), Expect = 5.9
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 73 FRFSLKTVLMIAQQL 87
FS K + IAQ+L
Sbjct: 100 LGFSAKKTMQIAQKL 114
>gnl|CDD|216497 pfam01429, MBD, Methyl-CpG binding domain. The Methyl-CpG binding
domain (MBD) binds to DNA that contains one or more
symmetrically methylated CpGs. DNA methylation in
animals is associated with alterations in chromatin
structure and silencing of gene expression. MBD has
negligible non-specific affinity for DNA. In vitro
foot-printing with MeCP2 showed the MBD can protect a 12
nucleotide region surrounding a methyl CpG pair. MBDs
are found in several Methyl-CpG binding proteins and
also DNA demethylase.
Length = 75
Score = 25.0 bits (55), Expect = 6.8
Identities = 6/10 (60%), Positives = 8/10 (80%)
Query: 95 EVYYFGPCGK 104
+VYY+ P GK
Sbjct: 31 DVYYYSPTGK 40
>gnl|CDD|214663 smart00437, TOP1Ac, Bacterial DNA topoisomerase I DNA-binding
domain. Bacterial DNA topoisomerase I and III,
Eukaryotic DNA topoisomeraes III, reverse gyrase alpha
subunit.
Length = 259
Score = 26.1 bits (58), Expect = 7.1
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 73 FRFSLKTVLMIAQQL 87
FS K + IAQ+L
Sbjct: 26 LGFSAKKTMQIAQKL 40
>gnl|CDD|240168 cd05145, RIO1_like, RIO kinase family; RIO1, RIO3 and similar
proteins, catalytic domain. The RIO kinase catalytic
domain family is part of a larger superfamily, that
includes the catalytic domains of other kinases such as
the typical serine/threonine/tyrosine protein kinases
(PKs), aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase (PI3K). RIO
kinases are atypical protein serine kinases containing a
kinase catalytic signature, but otherwise show very
little sequence similarity to typical PKs. Serine
kinases catalyze the transfer of the gamma-phosphoryl
group from ATP to serine residues in protein substrates.
The RIO catalytic domain is truncated compared to the
catalytic domains of typical PKs, with deletions of the
loops responsible for substrate binding. RIO1 is present
in archaea, bacteria and eukaryotes. In addition, RIO3
is present in multicellular eukaryotes. RIO1 is
essential for survival and is required for 18S rRNA
processing, proper cell cycle progression and chromosome
maintenance. The biological substrates for RIO1 are
unknown. The function of RIO3 is also unknown.
Length = 190
Score = 25.9 bits (58), Expect = 7.2
Identities = 9/21 (42%), Positives = 10/21 (47%), Gaps = 4/21 (19%)
Query: 94 PEVYYFGPCGKYNALVMELLG 114
PE K N LVME +G
Sbjct: 84 PEPILL----KKNVLVMEFIG 100
>gnl|CDD|238069 cd00122, MBD, MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and
BAZ2A-like proteins constitute a family of proteins that
share the methyl-CpG-binding domain (MBD). The MBD
consists of about 70 residues and is defined as the
minimal region required for binding to methylated DNA by
a methyl-CpG-binding protein which binds specifically to
methylated DNA. The MBD can recognize a single
symmetrically methylated CpG either as naked DNA or
within chromatin. MeCP2, MBD1 and MBD2 (and likely
MBD3) form complexes with histone deacetylase and are
involved in histone deacetylase-dependent repression of
transcription. MBD4 is an endonuclease that forms a
complex with the DNA mismatch-repair protein MLH1. The
MBDs present in putative chromatin remodelling subunit,
BAZ2A, and putative histone methyltransferase, CLLD8,
represent two phylogenetically distinct groups within
the MBD protein family.
Length = 62
Score = 24.6 bits (54), Expect = 7.3
Identities = 7/10 (70%), Positives = 9/10 (90%)
Query: 95 EVYYFGPCGK 104
+VYY+ PCGK
Sbjct: 26 DVYYYSPCGK 35
>gnl|CDD|173736 cd07832, STKc_CCRK, Catalytic domain of the Serine/Threonine
Kinase, Cell Cycle-Related Kinase. Serine/Threonine
Kinases (STKs), Cell Cycle-Related Kinase (CCRK) p42
subfamily, catalytic (c) domain. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
CCRK 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. CCRK was previously called p42. It is a
Cyclin-Dependent Kinase (CDK)-Activating Kinase (CAK)
which is essential for the activation of CDK2. It is
indispensable for cell growth and has been implicated in
the progression of glioblastoma multiforme. In the
heart, a splice variant of CCRK with a different
C-terminal half is expressed, this variant promotes
cardiac cell growth and survival and is significantly
down-regulated during the development of heart failure.
Length = 286
Score = 25.7 bits (57), Expect = 8.8
Identities = 10/40 (25%), Positives = 13/40 (32%)
Query: 101 PCGKYNALVMELLGPSLEDLFDLCNRKFTLKTVLMIAIQL 140
P G LVME + L ++ R V L
Sbjct: 69 PHGSGFVLVMEYMPSDLSEVLRDEERPLPEAQVKSYMRML 108
>gnl|CDD|233249 TIGR01051, topA_bact, DNA topoisomerase I, bacterial. This model
describes DNA topoisomerase I among the members of
bacteria. DNA topoisomerase I transiently cleaves one
DNA strand and thus relaxes negatively supercoiled DNA
during replication, transcription and recombination
events [DNA metabolism, DNA replication, recombination,
and repair].
Length = 610
Score = 26.2 bits (58), Expect = 8.9
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 74 RFSLKTVLMIAQQL 87
FS K +MIAQ+L
Sbjct: 267 GFSAKKTMMIAQRL 280
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 0.142 0.424
Gapped
Lambda K H
0.267 0.0762 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,170,070
Number of extensions: 636748
Number of successful extensions: 439
Number of sequences better than 10.0: 1
Number of HSP's gapped: 439
Number of HSP's successfully gapped: 30
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
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 (21.9 bits)
S2: 54 (24.5 bits)