RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4160
(160 letters)
>gnl|CDD|215109 PLN00410, PLN00410, U5 snRNP protein, DIM1 family; Provisional.
Length = 142
Score = 240 bits (614), Expect = 5e-83
Identities = 104/116 (89%), Positives = 110/116 (94%)
Query: 45 VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITKVPDFNKMYELYDPCTCMFFFR 104
VIRFGHDWD TCM+MDEVL S+AE +KNFAVIYLVDIT+VPDFN MYELYDPCT MFFFR
Sbjct: 27 VIRFGHDWDETCMQMDEVLASVAETIKNFAVIYLVDITEVPDFNTMYELYDPCTVMFFFR 86
Query: 105 NKHIMIDLGTGNNNKINWALEDKQEMIDIVETVYRGARKGRGLVVSPKDYSTKYRY 160
NKHIMIDLGTGNNNKINWAL+DKQE IDIVETVYRGARKGRGLV+SPKDYSTKYRY
Sbjct: 87 NKHIMIDLGTGNNNKINWALKDKQEFIDIVETVYRGARKGRGLVISPKDYSTKYRY 142
>gnl|CDD|190488 pfam02966, DIM1, Mitosis protein DIM1.
Length = 133
Score = 220 bits (563), Expect = 3e-75
Identities = 86/110 (78%), Positives = 96/110 (87%)
Query: 45 VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITKVPDFNKMYELYDPCTCMFFFR 104
VIRFG D DP CM+MDE+L IAEK+ NFAVIYLVDI +VPDFNKMYELYDP T MFFFR
Sbjct: 24 VIRFGRDDDPVCMQMDEILAKIAEKLSNFAVIYLVDIDEVPDFNKMYELYDPVTVMFFFR 83
Query: 105 NKHIMIDLGTGNNNKINWALEDKQEMIDIVETVYRGARKGRGLVVSPKDY 154
NKH+M D GTGNNNK+N+ LEDKQE IDI+ET+YRGA KG+GLVVSPKDY
Sbjct: 84 NKHMMCDFGTGNNNKLNFVLEDKQEFIDIIETIYRGAMKGKGLVVSPKDY 133
>gnl|CDD|239252 cd02954, DIM1, Dim1 family; Dim1 is also referred to as U5 small
nuclear ribonucleoprotein particle (snRNP)-specific 15kD
protein. It is a component of U5 snRNP, which
pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5]
tri-snRNP complex required for pre-mRNA splicing. Dim1
interacts with multiple splicing-associated proteins,
suggesting that it functions at multiple control points
in the splicing of pre-mRNA as part of a large
spliceosomal complex involving many protein-protein
interactions. U5 snRNP contains seven core proteins
(common to all snRNPs) and nine U5-specific proteins,
one of which is Dim1. Dim1 adopts a thioredoxin fold but
does not contain the redox active CXXC motif. It is
essential for G2/M phase transition, as a consequence to
its role in pre-mRNA splicing.
Length = 114
Score = 189 bits (481), Expect = 4e-63
Identities = 79/97 (81%), Positives = 84/97 (86%)
Query: 45 VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITKVPDFNKMYELYDPCTCMFFFR 104
VIRFG DWDP CM+MDEVL IAE V NFAVIYLVDI +VPDFNKMYELYDP T MFFFR
Sbjct: 18 VIRFGRDWDPVCMQMDEVLAKIAEDVSNFAVIYLVDIDEVPDFNKMYELYDPPTVMFFFR 77
Query: 105 NKHIMIDLGTGNNNKINWALEDKQEMIDIVETVYRGA 141
NKH+ IDLGTGNNNKINW EDKQE IDI+ET+YRGA
Sbjct: 78 NKHMKIDLGTGNNNKINWVFEDKQEFIDIIETIYRGA 114
>gnl|CDD|239284 cd02986, DLP, Dim1 family, Dim1-like protein (DLP) subfamily; DLP
is a novel protein which shares 38% sequence identity to
Dim1. Like Dim1, it is also implicated in pre-mRNA
splicing and cell cycle progression. DLP is located in
the nucleus and has been shown to interact with the U5
small nuclear ribonucleoprotein particle
(snRNP)-specific 102kD protein (or Prp6). Dim1 protein,
also known as U5 snRNP-specific 15kD protein is a
component of U5 snRNP, which pre-assembles with U4/U6
snRNPs to form a [U4/U6:U5] tri-snRNP complex required
for pre-mRNA splicing. Dim1 adopts a thioredoxin fold
but does not contain the redox active CXXC motif.
Length = 114
Score = 84.1 bits (208), Expect = 9e-22
Identities = 37/98 (37%), Positives = 64/98 (65%), Gaps = 2/98 (2%)
Query: 45 VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITKVPDFNKMYEL-YDPCTCMFFF 103
V+RFG D D C+++D++L + + A IYLVD+ KVP + + +++ Y P T +FFF
Sbjct: 18 VLRFGRDEDAVCLQLDDILSKTSHDLSKMASIYLVDVDKVPVYTQYFDISYIPST-IFFF 76
Query: 104 RNKHIMIDLGTGNNNKINWALEDKQEMIDIVETVYRGA 141
+H+ +D G+ ++ K + + KQ+ ID++E +YRGA
Sbjct: 77 NGQHMKVDYGSPDHTKFVGSFKTKQDFIDLIEVIYRGA 114
>gnl|CDD|238155 cd00252, SPARC_EC, SPARC_EC; extracellular Ca2+ binding domain
(containing 2 EF-hand motifs) of SPARC and related
proteins (QR1, SC1/hevin, testican and tsc-36/FRP).
SPARC (BM-40) is a multifunctional glycoprotein, a
matricellular protein, that functions to regulate
cell-matrix interactions; binds to such proteins as
collagen and vitronectin and binds to endothelial cells
thus inhibiting cellular proliferation. The EC domain
interacts with a follistatin-like (FS) domain which
appears to stabilize Ca2+ binding. The two EF-hands
interact canonically but their conserved disulfide bonds
confer a tight association between the EF-hand pair and
an acid/amphiphilic N-terminal helix. Proposed active
form involves a Ca2+ dependent symmetric
homodimerization of EC-FS modules.
Length = 116
Score = 60.5 bits (147), Expect = 1e-12
Identities = 18/42 (42%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 1 MALEHCIAPFLNKCDADDDHLITLKEWARCLELNEDEIEDQC 42
EHCI PF CD D D I+L EW C + ED++ + C
Sbjct: 76 DPNEHCIKPFFESCDLDKDGSISLDEWCYCF-IKEDDLCEAC 116
>gnl|CDD|204523 pfam10591, SPARC_Ca_bdg, Secreted protein acidic and rich in
cysteine Ca binding region. The SPARC_Ca_bdg domain of
Secreted Protein Acidic and Rich in Cysteine is
responsible for the anti-spreading activity of human
urothelial cells. It is rich in alpha-helices. This
extracellular calcium-binding domain contains two
EF-hands that each coordinates one Ca2+ ion, forming a
helix-loop-helix structure that not only drives the
conformation of the protein but is also necessary for
biological activity. The anti-spreading activity was
dependent on the coordination of Ca2+ by a Glu residue
at the Z position of EF-hand 2.
Length = 112
Score = 57.4 bits (139), Expect = 2e-11
Identities = 17/30 (56%), Positives = 22/30 (73%)
Query: 1 MALEHCIAPFLNKCDADDDHLITLKEWARC 30
+ +EHCI PF CDAD D LI+L+EW +C
Sbjct: 83 VPMEHCIKPFFKSCDADKDGLISLREWCKC 112
>gnl|CDD|238829 cd01659, TRX_superfamily, Thioredoxin (TRX) superfamily; a large,
diverse group of proteins containing a TRX-fold. Many
members contain a classic TRX domain with a redox active
CXXC motif. They function as protein disulfide
oxidoreductases (PDOs), altering the redox state of
target proteins via the reversible oxidation of their
active site dithiol. The PDO members of this superfamily
include TRX, protein disulfide isomerase (PDI),
tlpA-like, glutaredoxin, NrdH redoxin, and the bacterial
Dsb (DsbA, DsbC, DsbG, DsbE, DsbDgamma) protein
families. Members of the superfamily that do not
function as PDOs but contain a TRX-fold domain include
phosducins, peroxiredoxins and glutathione (GSH)
peroxidases, SCO proteins, GSH transferases (GST,
N-terminal domain), arsenic reductases, TRX-like
ferredoxins and calsequestrin, among others.
Length = 69
Score = 32.3 bits (73), Expect = 0.016
Identities = 14/70 (20%), Positives = 22/70 (31%), Gaps = 2/70 (2%)
Query: 45 VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITKVPDFNK-MYELYDPCTCMFFF 103
++ F W P C + VL +A K VD+ + P K +
Sbjct: 1 LVLFYAPWCPFCQALRPVLAELALLNKGVKFEA-VDVDEDPALEKELKRYGVGGVPTLVV 59
Query: 104 RNKHIMIDLG 113
I + G
Sbjct: 60 FGPGIGVKYG 69
>gnl|CDD|223600 COG0526, TrxA, Thiol-disulfide isomerase and thioredoxins
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 127
Score = 33.3 bits (75), Expect = 0.017
Identities = 10/51 (19%), Positives = 21/51 (41%), Gaps = 1/51 (1%)
Query: 45 VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDIT-KVPDFNKMYELY 94
++ F W P C +L +AE+ + V++ + PD + +
Sbjct: 36 LVDFWAPWCPPCRAEAPLLEELAEEYGGDVEVVAVNVDDENPDLAAEFGVA 86
>gnl|CDD|239282 cd02984, TRX_PICOT, TRX domain, PICOT (for PKC-interacting cousin
of TRX) subfamily; PICOT is a protein that interacts
with protein kinase C (PKC) theta, a calcium independent
PKC isoform selectively expressed in skeletal muscle and
T lymphocytes. PICOT contains an N-terminal TRX-like
domain, which does not contain the catalytic CXXC motif,
followed by one to three glutaredoxin domains. The
TRX-like domain is required for interaction with PKC
theta. PICOT inhibits the activation of c-Jun N-terminal
kinase and the transcription factors, AP-1 and NF-kB,
induced by PKC theta or T-cell activating stimuli.
Length = 97
Score = 29.2 bits (66), Expect = 0.32
Identities = 12/58 (20%), Positives = 30/58 (51%)
Query: 45 VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITKVPDFNKMYELYDPCTCMFF 102
V+ F W C +M++V +A++ + ++ ++P+ ++ +E+ T +FF
Sbjct: 18 VLHFWAPWAEPCKQMNQVFEELAKEAFPSVLFLSIEAEELPEISEKFEITAVPTFVFF 75
>gnl|CDD|132755 cd07070, NR_LBD_SF-1, The ligand binding domain of nuclear
receptor steroidogenic factor 1, a member of nuclear
receptor superfamily. The ligand binding domain of
nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a
member of the nuclear hormone receptor superfamily, is
an essential regulator of endocrine development and
function and is considered a master regulator of
reproduction. Most nuclear receptors function as
homodimer or heterodimers, however SF-1 binds to its
target genes as a monomer, recognizing the variations
of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions
cooperatively with other transcription factors to
modulate gene expression. Phospholipids have been
determined as potential ligands of SF-1. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, SF-1 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 = 237
Score = 29.2 bits (65), Expect = 0.85
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 8 APFLNKCDADDDHLITLKEWAR-CLELNEDEIEDQ 41
APF C D I++ +WAR C+ E E+ DQ
Sbjct: 38 APFGLLCRMADQTFISIVDWARRCMVFKELEVADQ 72
>gnl|CDD|187645 cd08941, 3KS_SDR_c, 3-keto steroid reductase, classical (c) SDRs.
3-keto steroid reductase (in concert with other enzymes)
catalyzes NADP-dependent sterol C-4 demethylation, as
part of steroid biosynthesis. 3-keto reductase is a
classical SDR, with a well conserved canonical active
site tetrad and fairly well conserved characteristic
NAD-binding motif. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 290
Score = 28.9 bits (65), Expect = 0.98
Identities = 15/85 (17%), Positives = 31/85 (36%), Gaps = 19/85 (22%)
Query: 60 DEVLYSIAEKVKNFAVIYLVDITKV-------PDFNKMYELYDPCTCMFFFRNKHIMIDL 112
+L S + F + LVD++ + + K Y D ++ ++
Sbjct: 48 RALLASHPDARVVFDYV-LVDLSNMVSVFAAAKELKKRYPRLD-----------YLYLNA 95
Query: 113 GTGNNNKINWALEDKQEMIDIVETV 137
G N I+W K+ + + + V
Sbjct: 96 GIMPNPGIDWIGAIKEVLTNPLFAV 120
>gnl|CDD|224884 COG1973, HypE, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 449
Score = 28.9 bits (65), Expect = 1.1
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 29 RCLE-LNEDEIEDQCEDVIRFGHDWDP-TCMKMDEVLYSIAEKVKN 72
R LE E+EI ++I DWD ++ + + E+VKN
Sbjct: 16 RMLEKDIEEEIRKLLAELILEIKDWDRERAEEIADA---VLEEVKN 58
>gnl|CDD|233825 TIGR02344, chap_CCT_gamma, T-complex protein 1, gamma subunit.
Members of this family, all eukaryotic, are part of the
group II chaperonin complex called CCT (chaperonin
containing TCP-1) or TRiC. The archaeal equivalent group
II chaperonin is often called the thermosome. Both are
somewhat related to the group I chaperonin of bacterial,
GroEL/GroES. This family consists exclusively of the CCT
gamma chain (part of a paralogous family) from animals,
plants, fungi, and other eukaryotes.
Length = 525
Score = 28.9 bits (65), Expect = 1.2
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 13/56 (23%)
Query: 25 KEWARCLELNEDEIEDQCEDVIRFGHDWDPTCMKMDEVLYSIAEK-VKNFAVIYLV 79
++W R L++ E+ ++ CED+I K D V I EK V + A YL+
Sbjct: 258 EDWNRILQMEEEYVQLMCEDIIAV---------KPDLV---ITEKGVSDLAQHYLL 301
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 28.8 bits (65), Expect = 1.4
Identities = 13/34 (38%), Positives = 15/34 (44%), Gaps = 8/34 (23%)
Query: 7 IAPFLNKCDADDDHLITLKEWARCLELNEDEIED 40
I FLNK D DD LEL E E+ +
Sbjct: 131 IVVFLNKVDMVDD--------EELLELVEMEVRE 156
>gnl|CDD|224193 COG1274, PckA, Phosphoenolpyruvate carboxykinase (GTP) [Energy
production and conversion].
Length = 608
Score = 28.5 bits (64), Expect = 1.7
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 121 NWALEDKQEMIDIVETVYRGARKGRGLVVSP 151
NW D QEM + ++RG +GR + V P
Sbjct: 102 NWM--DPQEMRSEMNELFRGCMRGRTMYVVP 130
>gnl|CDD|239245 cd02947, TRX_family, TRX family; composed of two groups: Group I,
which includes proteins that exclusively encode a TRX
domain; and Group II, which are composed of fusion
proteins of TRX and additional domains. Group I TRX is
a small ancient protein that alter the redox state of
target proteins via the reversible oxidation of an
active site dithiol, present in a CXXC motif, partially
exposed at the protein's surface. TRX reduces protein
disulfide bonds, resulting in a disulfide bond at its
active site. Oxidized TRX is converted to the active
form by TRX reductase, using reducing equivalents
derived from either NADPH or ferredoxins. By altering
their redox state, TRX regulates the functions of at
least 30 target proteins, some of which are enzymes and
transcription factors. It also plays an important role
in the defense against oxidative stress by directly
reducing hydrogen peroxide and certain radicals, and by
serving as a reductant for peroxiredoxins. At least two
major types of functional TRXs have been reported in
most organisms; in eukaryotes, they are located in the
cytoplasm and the mitochondria. Higher plants contain
more types (at least 20 TRX genes have been detected in
the genome of Arabidopsis thaliana), two of which
(types f amd m) are located in the same compartment,
the chloroplast. Also included in the alignment are
TRX-like domains which show sequence homology to TRX
but do not contain the redox active CXXC motif. Group
II proteins, in addition to either a redox active TRX
or a TRX-like domain, also contain additional domains,
which may or may not possess homology to known
proteins.
Length = 93
Score = 27.1 bits (61), Expect = 1.8
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 45 VIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITKVPDF 87
V+ F W C + VL +AE+ VD+ + P+
Sbjct: 14 VVDFWAPWCGPCKAIAPVLEELAEEYPKV-KFVKVDVDENPEL 55
>gnl|CDD|235256 PRK04210, PRK04210, phosphoenolpyruvate carboxykinase; Provisional.
Length = 601
Score = 27.9 bits (63), Expect = 2.6
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 6/41 (14%)
Query: 111 DLGTGNNNKINWALEDKQEMIDIVETVYRGARKGRGLVVSP 151
D G NN W D EM + ++ +++G +GR + V P
Sbjct: 89 DAGPTNN----WM--DPAEMRETLKGLFKGCMRGRTMYVVP 123
>gnl|CDD|185622 PTZ00443, PTZ00443, Thioredoxin domain-containing protein;
Provisional.
Length = 224
Score = 27.3 bits (60), Expect = 3.3
Identities = 13/61 (21%), Positives = 26/61 (42%)
Query: 46 IRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITKVPDFNKMYELYDPCTCMFFFRN 105
++F W C KM +A+ +K + +D T+ + K + + T + F +
Sbjct: 57 VKFYAPWCSHCRKMAPAWERLAKALKGQVNVADLDATRALNLAKRFAIKGYPTLLLFDKG 116
Query: 106 K 106
K
Sbjct: 117 K 117
>gnl|CDD|216136 pfam00821, PEPCK, Phosphoenolpyruvate carboxykinase. catalyzes the
formation of phosphoenolpyruvate by decarboxylation of
oxaloacetate.
Length = 586
Score = 27.5 bits (62), Expect = 3.6
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 120 INWALEDKQEMIDIVETVYRGARKGRGLVVSP 151
NW D +EM + +++G KGR + V P
Sbjct: 80 NNWM--DPEEMKAELRELFKGCMKGRTMYVIP 109
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 27.5 bits (61), Expect = 4.1
Identities = 13/27 (48%), Positives = 16/27 (59%), Gaps = 5/27 (18%)
Query: 10 FLNKCDA-DDDHLITLKEWARCLELNE 35
FLNK D DD+ L+ L E +EL E
Sbjct: 183 FLNKVDVVDDEELLELVE----MELRE 205
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 27.2 bits (61), Expect = 4.2
Identities = 10/18 (55%), Positives = 12/18 (66%), Gaps = 1/18 (5%)
Query: 10 FLNKCDA-DDDHLITLKE 26
FLNK D DD+ L+ L E
Sbjct: 134 FLNKVDLVDDEELLELVE 151
>gnl|CDD|99714 cd06165, Sortase_A_1, Sortase A (SrtA) or subfamily-1 sortases
are cysteine transpeptidases found in gram-positive
bacteria that anchor surface proteins to peptidoglycans
of the bacterial cell wall envelope. They do so by
catalyzing a transpeptidation reaction in which the
surface protein substrate is cleaved at a conserved
cell wall sorting signal (usually a pentapeptide
motif), and covalently linked to peptidoglycan for
display on the bacterial surface. Sortases are grouped
into different classes and subfamilies based on
sequence, membrane topology, genomic positioning, and
cleavage site preference. This group contains a subset
of Class A (subfamily-1) sortases, excluding SrtA from
Staphylococcus aureus. Sortase A cleaves between
threonine and glycine of the LPXTG motif in a wide
range of protein substrates. It affects the ability of
a pathogen to establish successful infection. Sortase A
contains an N-terminal region that functions as both a
signal peptide for secretion and a stop-transfer signal
for membrane anchoring. At the C-terminus, it contains
the catalytic TLXTC signature sequence where X is
usually a valine, isoleucine or a threonine. The gene
encoding SrtA is generally not located in the same gene
cluster as its substrates while the gene encoding SrtB
is usually clustered in the same locus as its
substrate.
Length = 127
Score = 26.4 bits (59), Expect = 5.0
Identities = 14/36 (38%), Positives = 16/36 (44%), Gaps = 5/36 (13%)
Query: 49 GHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITKV 84
GH M+ VL+S KVK IYL D V
Sbjct: 48 GH-----NMRNKGVLFSPLYKVKVGDKIYLTDKDNV 78
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 26.7 bits (60), Expect = 6.1
Identities = 11/18 (61%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 10 FLNKCD-ADDDHLITLKE 26
FLNKCD DD+ L+ L E
Sbjct: 134 FLNKCDMVDDEELLELVE 151
>gnl|CDD|236718 PRK10574, PRK10574, putative major pilin subunit; Provisional.
Length = 146
Score = 26.1 bits (58), Expect = 7.2
Identities = 9/23 (39%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 27 WAR-CLELNEDEIEDQCEDVIRF 48
W R C ++ ++ CEDV RF
Sbjct: 120 WTRNCNIQSDSALQQACEDVFRF 142
>gnl|CDD|206671 cd01884, EF_Tu, Elongation Factor Tu (EF-Tu) GTP-binding proteins.
EF-Tu subfamily. This subfamily includes orthologs of
translation elongation factor EF-Tu in bacteria,
mitochondria, and chloroplasts. It is one of several
GTP-binding translation factors found in the larger
family of GTP-binding elongation factors. The eukaryotic
counterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this family. EF-Tu is
one of the most abundant proteins in bacteria, as well
as, one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation.
Length = 195
Score = 26.4 bits (59), Expect = 7.2
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 8/31 (25%)
Query: 10 FLNKCDADDDHLITLKEWARCLELNEDEIED 40
FLNK D DD +E LEL E E+ +
Sbjct: 124 FLNKADMVDD-----EEL---LELVEMEVRE 146
>gnl|CDD|188642 cd00955, Transaldolase_like, Transaldolase-like proteins from
plants and bacteria. Transaldolase-like proteins from
plants and bacteria. Transaldolase is found in the
non-oxidative branch of the pentose phosphate pathway,
that catalyze the reversible transfer of a
dihydroxyacetone group from fructose-6-phosphate to
erythrose-4-phosphate yielding sedoheptulose-7-phosphate
and glyceraldehyde-3-phosphate. They are members of the
class I aldolases, who are characterized by using a
Schiff-base mechanism for stabilization of the reaction
intermediates.
Length = 338
Score = 26.1 bits (58), Expect = 8.1
Identities = 17/60 (28%), Positives = 22/60 (36%), Gaps = 10/60 (16%)
Query: 15 DADDDHLITLKEWARCLELNEDEIEDQCEDVIRFGHDWDPTCMKMDEVLYSIAEKVKNFA 74
A DH E LE +E E ++ R G D D K+ + E VK F
Sbjct: 284 KAFADH----GEVRPTLEEGLEEAERVLAELERLGIDLDAVTEKL------LKEGVKKFK 333
>gnl|CDD|184084 PRK13490, PRK13490, chemoreceptor glutamine deamidase CheD;
Provisional.
Length = 162
Score = 25.9 bits (57), Expect = 8.2
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 100 MFFFRNKHIMIDLGTGNNNKINWALEDKQEMIDIV-ETVYRGARKGRGLVVSPKDYSTKY 158
MF F +K +++D+G N + L K+ I I+ E + G KGR ++ D
Sbjct: 97 MFNFSDKSMVMDIGNRNGKAVKKKL--KELSIPILAEDI--GGNKGRTMIFDTSDGKVYI 152
Query: 159 R 159
+
Sbjct: 153 K 153
>gnl|CDD|132741 cd06943, NR_LBD_RXR_like, The ligand binding domain of the
retinoid X receptor and Ultraspiracle, members of
nuclear receptor superfamily. The ligand binding
domain of the retinoid X receptor (RXR) and
Ultraspiracle (USP): This family includes two
evolutionary related nuclear receptors: retinoid X
receptor (RXR) and Ultraspiracle (USP). RXR is a
nuclear receptor in mammalian and USP is its
counterpart in invertebrates. The native ligand of
retinoid X receptor is 9-cis retinoic acid (RA). RXR
functions as a DNA binding partner by forming
heterodimers with other nuclear receptors including
CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can
play different roles in these heterodimers. It acts
either as a structural component of the heterodimer
complex, required for DNA binding but not acting as a
receptor or as both a structural and a functional
component of the heterodimer, allowing 9-cis RA to
signal through the corresponding heterodimer. In
addition, RXR can also form homodimers, functioning as
a receptor for 9-cis RA, independently of other nuclear
receptors. Ultraspiracle (USP) plays similar roles as
DNA binding partner of other nuclear rec eptors in
invertebrates. USP has no known high-affinity ligand
and is thought to be a silent component in the
heterodimeric complex with partner receptors. Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors, RXR and USP
have 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 = 207
Score = 26.1 bits (58), Expect = 8.7
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 8 APFLNKCDADDDHLITLKEWARCL-ELNEDEIEDQ 41
P N C A D L L EWA+ + +E ++DQ
Sbjct: 30 DPVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQ 64
>gnl|CDD|176564 cd08627, PI-PLCc_gamma1, Catalytic domain of metazoan
phosphoinositide-specific phospholipase C-gamma1. This
subfamily corresponds to the catalytic domain present
in metazoan phosphoinositide-specific phospholipase C
(PI-PLC, EC 3.1.4.11)-gamma isozyme 1. PI-PLC is a
signaling enzyme that hydrolyzes the membrane
phospholipids phosphatidylinositol-4,5-bisphosphate
(PIP2) to generate two important second messengers in
eukaryotic signal transduction cascades, Inositol
1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG).
InsP3 triggers inflow of calcium from intracellular
stores, while DAG, together with calcium, activates
protein kinase C, which goes on to phosphorylate other
molecules, leading to altered cellular activity.
Calcium is required for the catalysis. PI-PLC-gamma
represents a class of mammalian PI-PLC that has an
N-terminal pleckstrin homology (PH) domain, an array of
EF hands, a PLC catalytic core domain, and a C2 domain.
The PLC catalytic core domain is a TIM barrel with two
highly conserved regions (X and Y) split by a highly
degenerate linker sequence. Unique to PI-PLC-gamma1, a
second PH domain, two SH2 (Src homology 2) regions, and
one SH3 (Src homology 3) region is present within this
linker region. PI-PLC-gamma1 is ubiquitously expressed.
It is activated by receptor and non-receptor tyrosine
kinases due to the presence of two SH2 and a single SH3
domain within the linker region.
Length = 229
Score = 26.1 bits (57), Expect = 8.8
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 7/52 (13%)
Query: 23 TLKEWARCLELNEDEIEDQCED------VIRFGHDWDPTCMKMDEVLYSIAE 68
+L+ +ARCL + IE C D VI GH T +K +VL++I E
Sbjct: 31 SLEAYARCLRMGCRCIELDCWDGPDGMPVIYHGHTLT-TKIKFSDVLHTIKE 81
>gnl|CDD|237564 PRK13930, PRK13930, rod shape-determining protein MreB;
Provisional.
Length = 335
Score = 26.2 bits (59), Expect = 9.3
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 100 MFFFRNKHIMIDLGTGN 116
+F F +K I IDLGT N
Sbjct: 3 LFGFFSKDIGIDLGTAN 19
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 0.140 0.448
Gapped
Lambda K H
0.267 0.0793 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,376,681
Number of extensions: 768112
Number of successful extensions: 715
Number of sequences better than 10.0: 1
Number of HSP's gapped: 715
Number of HSP's successfully gapped: 44
Length of query: 160
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 71
Effective length of database: 6,990,096
Effective search space: 496296816
Effective search space used: 496296816
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (24.8 bits)