RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2752
(99 letters)
>gnl|CDD|215889 pfam00385, Chromo, Chromo (CHRromatin Organisation MOdifier)
domain.
Length = 52
Score = 50.3 bits (121), Expect = 5e-10
Identities = 23/51 (45%), Positives = 33/51 (64%), Gaps = 2/51 (3%)
Query: 11 VIEKIVDKKLTKEGKVKYFLKWKDYPESDNTWEMAEDLDCD--DLIRAFEE 59
+E+I+D +L K G +Y +KWK YP + TWE E+L +LI+AFEE
Sbjct: 1 EVERILDHRLRKGGNKEYLVKWKGYPYDEATWEPEENLKACFPELIQAFEE 51
>gnl|CDD|214605 smart00298, CHROMO, Chromatin organization modifier domain.
Length = 55
Score = 46.8 bits (112), Expect = 1e-08
Identities = 19/52 (36%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
Query: 9 VYVIEKIVDKKLTKEGKVKYFLKWKDYPESDNTWEMAEDLD-CDDLIRAFEE 59
Y +EKI+D + K+G+++Y +KWK Y S++TWE E+L C + +++
Sbjct: 1 EYEVEKILDHRWKKKGELEYLVKWKGYSYSEDTWEPEENLLNCSKKLDNYKK 52
>gnl|CDD|237991 cd00024, CHROMO, Chromatin organization modifier (chromo) domain
is a conserved region of around 50 amino acids found in
a variety of chromosomal proteins, which appear to play
a role in the functional organization of the eukaryotic
nucleus. Experimental evidence implicates the chromo
domain in the binding activity of these proteins to
methylated histone tails and maybe RNA. May occur as
single instance, in a tandem arrangement or followd by
a related "chromo shadow" domain.
Length = 55
Score = 43.8 bits (104), Expect = 2e-07
Identities = 24/54 (44%), Positives = 37/54 (68%), Gaps = 2/54 (3%)
Query: 8 EVYVIEKIVDKKLTKE-GKVKYFLKWKDYPESDNTWEMAEDL-DCDDLIRAFEE 59
E Y +EKI+D + K+ G+ +Y +KWK Y S++TWE E+L DC +LI F++
Sbjct: 1 EEYEVEKILDHRKKKDGGEYEYLVKWKGYSYSEDTWEPEENLEDCKELIDEFKK 54
>gnl|CDD|131469 TIGR02416, CO_dehy_Mo_lg, carbon-monoxide dehydrogenase, large
subunit. This model represents the large subunits of
group of carbon-monoxide dehydrogenases that include
molybdenum as part of the enzymatic cofactor. There are
various forms of carbon-monoxide dehydrogenase;
Salicibacter pomeroyi DSS-3, for example, has two forms.
Note that, at least in some species, the active site Cys
is modified with a selenium attached to (rather than
replacing) the sulfur atom. This is termed
selanylcysteine, and created post-translationally, in
contrast to selenocysteine incorporation during
translation as for many other selenoproteins [Energy
metabolism, Other].
Length = 770
Score = 31.0 bits (70), Expect = 0.069
Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 21/93 (22%)
Query: 7 EEVYVIEKIVD---KKL---TKEGKVKYFLKWKDYPESDNT-WE---------MAEDLDC 50
E VY IE+ VD ++L + + ++K F++ + +P + WE M + +D
Sbjct: 366 EAVYAIERAVDTLAQRLEMDSADLRIKNFIQPEQFPYTAPLGWEYDSGDYPLAMKKAMDT 425
Query: 51 DDLIRAFEENWAVEQEAKKKAGEPTESLETGVS 83
D EQ AK+K GE E + G+S
Sbjct: 426 VDY-----HQLRAEQAAKRKRGETRELMGIGIS 453
>gnl|CDD|240060 cd04709, BAH_MTA, BAH, or Bromo Adjacent Homology domain, as
present in MTA1 and similar proteins. The
Metastasis-associated protein MTA1 is part of the NURD
(nucleosome remodeling and deacetylating) complex and
plays a role in cellular transformation and metastasis.
BAH domains are found in a variety of proteins playing
roles in transcriptional silencing and the remodeling
of chromatin. It is assumed that in most or all of
these instances the BAH domain mediates protein-protein
interactions.
Length = 164
Score = 27.7 bits (62), Expect = 0.80
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 4/41 (9%)
Query: 2 AEEEQEEVYVIEKIVDKKLTKEG----KVKYFLKWKDYPES 38
E Y+I +I + T G KV + + +D P+S
Sbjct: 12 FESSPNNPYLIRRIEELNKTARGHVEAKVVCYYRRRDIPDS 52
>gnl|CDD|173932 cd08173, Gro1PDH, Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH)
catalyzes the reversible conversion between
dihydroxyacetone phosphate and glycerol-1-phosphate
using either NADH or NADPH as a coenzyme.
Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH, EC
1.1.1.261) plays an important role in the formation of
the enantiomeric configuration of the glycerophosphate
backbone (sn-glycerol-1-phosphate) of archaeal ether
lipids. It catalyzes the reversible conversion between
dihydroxyacetone phosphate and glycerol-1-phosphate
using either NADH or NADPH as a coenzyme. The activity
is zinc-dependent. One characteristic feature of archaea
is that their cellular membrane has an ether linkage
between the glycerol backbone and the hydrocarbon
residues. The polar lipids of the members of Archaea
consist of di- and tetraethers of glycerol with
isoprenoid alcohols bound at the sn-2 and sn-3 positions
of the glycerol moiety. The archaeal polar lipids have
the enantiomeric configuration of a glycerophosphate
backbone [sn- glycerol-1-phosphate (G-1-P)] that is the
mirror image structure of the bacterial or eukaryal
counterpart [sn-glycerol- 3-phosphate (G-3-P)]. The
absolute stereochemistry of the glycerol moiety in all
archaeal polar lipids is opposite to that of glycerol
ester lipids in bacteria and eukarya. This protein
family is only found in Archaea.
Length = 339
Score = 27.6 bits (62), Expect = 1.0
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 58 EENWAVEQEAKKKAGEPTESLETGVSDEE 86
NW ++A KK G PT + E G+ DE
Sbjct: 274 GGNWRRIRDALKKVGAPTTAKELGIDDEI 302
>gnl|CDD|213209 cd03242, ABC_RecF, ATP-binding cassette domain of RecF. RecF is a
recombinational DNA repair ATPase that maintains
replication in the presence of DNA damage. When
replication is prematurely disrupted by DNA damage,
several recF pathway gene products play critical roles
processing the arrested replication fork, allowing it to
resume and complete its task. This CD represents the
nucleotide binding domain of RecF. RecF belongs to a
large superfamily of ABC transporters involved in the
transport of a wide variety of different compounds
including sugars, ions, peptides, and more complex
organic molecules. The nucleotide binding domain shows
the highest similarity between all members of the
family. ABC transporters are a subset of nucleotide
hydrolases with a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 270
Score = 26.5 bits (59), Expect = 2.3
Identities = 9/47 (19%), Positives = 17/47 (36%)
Query: 51 DDLIRAFEENWAVEQEAKKKAGEPTESLETGVSDEERRKVGKYKERT 97
+LIR E + +++ GE L + ++ K R
Sbjct: 56 KELIRWGAEEAKISAVLERQGGELALELTIRSGGGRKARLNGIKVRR 102
>gnl|CDD|198442 cd10474, EphR_LBD_B4, Ligand Binding Domain of Ephrin type-B
Receptor 4. Ephrin receptors (EphRs) comprise the
largest subfamily of receptor tyrosine kinases (RTKs).
Class EphB receptors bind to transmembrane ephrin-B
ligands. There are six vertebrate EhpB receptors
(EphB1-6), which display promiscuous interactions with
three ephrin-B ligands. EphB4 plays a role in
osteoblast differentiation and has been linked to
multiple myeloma. EphRs contain a ligand binding domain
and two fibronectin repeats extracellularly, a
transmembrane segment, and a cytoplasmic tyrosine
kinase domain. Binding of the ephrin ligand to EphR
requires cell-cell contact since both are anchored to
the plasma membrane. The resulting downstream signals
occur bidirectionally in both EphR-expressing cells
(forward signaling) and ephrin-expressing cells
(reverse signaling).
Length = 180
Score = 26.1 bits (57), Expect = 3.4
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 30 LKWKDYPESDNTWEMAEDLD 49
LKW YP+ D WE LD
Sbjct: 14 LKWVTYPQVDGQWEELSGLD 33
>gnl|CDD|173672 cd05581, STKc_PDK1, Catalytic domain of the Protein
Serine/Threonine Kinase, Phosphoinositide-dependent
kinase 1. Serine/Threonine Kinases (STKs),
Phosphoinositide-dependent kinase 1 (PDK1) subfamily,
catalytic (c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The PDK1 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 (PI3K). PDK1 carries an
N-terminal catalytic domain and a C-terminal pleckstrin
homology (PH) domain that binds phosphoinositides. It
phosphorylates the activation loop of AGC kinases that
are regulated by PI3K such as PKB, SGK, and PKC, among
others, and is crucial for their activation. Thus, it
contributes in regulating many processes including
metabolism, growth, proliferation, and survival. PDK1
also has the ability to autophosphorylate and is
constitutively active in mammalian cells. PDK1 is
essential for normal embryo development and is
important in regulating cell volume.
Length = 280
Score = 25.6 bits (57), Expect = 4.8
Identities = 13/21 (61%), Positives = 15/21 (71%), Gaps = 2/21 (9%)
Query: 9 VYVIEKIVDKK-LTKEGKVKY 28
Y I KI+DK+ L KE KVKY
Sbjct: 28 EYAI-KILDKRQLIKEKKVKY 47
>gnl|CDD|218498 pfam05206, TRM13, Methyltransferase TRM13. This is a family of
eukaryotic proteins which are responsible for
2'-O-methylation of tRNA at position 4. TRM13 shows no
sequence similarity to other known methyltransferases.
Length = 256
Score = 25.0 bits (55), Expect = 8.0
Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 11/48 (22%)
Query: 61 WAV------EQEAKKKAGEP-----TESLETGVSDEERRKVGKYKERT 97
WAV +++ + E+ +G+SDEER ++G +R
Sbjct: 173 WAVCGTRDSSDREREEEEDDVVEQGVENHISGLSDEEREEIGLKCKRL 220
>gnl|CDD|239429 cd03313, enolase, Enolase: Enolases are homodimeric enzymes that
catalyse the reversible dehydration of
2-phospho-D-glycerate to phosphoenolpyruvate as part of
the glycolytic and gluconeogenesis pathways. The
reaction is facilitated by the presence of metal ions.
Length = 408
Score = 24.8 bits (55), Expect = 9.0
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 7 EEVYVIEKIVDKKLTKEGKVKYFLKW-KDYP 36
E YV + KKLT E + Y+ + K YP
Sbjct: 248 EGKYVYDSDEGKKLTSEELIDYYKELVKKYP 278
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
0.306 0.127 0.363
Gapped
Lambda K H
0.267 0.0780 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,200,390
Number of extensions: 442995
Number of successful extensions: 314
Number of sequences better than 10.0: 1
Number of HSP's gapped: 310
Number of HSP's successfully gapped: 38
Length of query: 99
Length of database: 10,937,602
Length adjustment: 65
Effective length of query: 34
Effective length of database: 8,054,592
Effective search space: 273856128
Effective search space used: 273856128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.9 bits)
S2: 53 (24.1 bits)