RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12804
(182 letters)
>gnl|CDD|238365 cd00713, GltS, Glutamine amidotransferases class-II (Gn-AT),
glutamate synthase (GltS)-type. GltS is a homodimer that
synthesizes L-glutamate from 2-oxoglutarate and
L-glutamine, an important step in ammonia assimilation
in bacteria, cyanobacteria and plants. The N-terminal
glutaminase domain catalyzes the hydrolysis of glutamine
to glutamic acid and ammonia, and has a fold similar to
that of other glutamine amidotransferases such as
glucosamine-fructose 6-phosphate synthase (GLMS or
GFAT), glutamine phosphoribosylpyrophosphate (Prpp)
amidotransferase (GPATase), asparagine synthetase B
(AsnB), and beta lactam synthetase (beta-LS), as well as
the Ntn hydrolase folds of the proteasomal alpha and
beta subunits.
Length = 413
Score = 107 bits (269), Expect = 7e-28
Identities = 37/102 (36%), Positives = 55/102 (53%), Gaps = 2/102 (1%)
Query: 39 EREACGVGFIVAIDRKRSHKSAGIGEVARNSEPFMRQVFLTGKQ--DEEEFKRQIYVLRK 96
E E G V R ++ +G AR +EP + QVF+ D E F+R++Y+LRK
Sbjct: 94 EEELEAEGLRVLGWRDVPVDNSVLGPTARATEPLIEQVFVGAPSGDDGEAFERKLYLLRK 153
Query: 97 VSTHKIPKPGQRFYICSLSNRIVVYKGQFTADQLWKYFTDLN 138
I + FY+CSLS+R +VYKG +QL +++ DL
Sbjct: 154 RIEKAIRAADEDFYVCSLSSRTIVYKGMLLPEQLGQFYPDLQ 195
Score = 72.2 bits (178), Expect = 3e-15
Identities = 20/44 (45%), Positives = 29/44 (65%)
Query: 139 IIEDAEKLSMRMNHRGACACDNDSGDGAGVLVAIPHAFYIQKLR 182
I++DA + RM HRG D +GDGAG+L+ IPH F+ ++L
Sbjct: 17 IVQDALEALERMEHRGGVGADGKTGDGAGILIQIPHEFFREELA 60
Score = 31.7 bits (73), Expect = 0.15
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 43 CGVGFIVAIDRKRSHK 58
CGVGF+ ID K SH
Sbjct: 1 CGVGFVANIDGKPSHD 16
>gnl|CDD|223145 COG0067, GltB, Glutamate synthase domain 1 [Amino acid transport
and metabolism].
Length = 371
Score = 77.4 bits (191), Expect = 3e-17
Identities = 34/103 (33%), Positives = 55/103 (53%), Gaps = 5/103 (4%)
Query: 39 EREACGVGFIVAIDRKRSHKSAGIGEVARNSEPFMRQVFLTGKQDEEEFKRQIYVLRKVS 98
E EA G V R S+ +GEVA + P + QVF+ ++F+R +++ RK
Sbjct: 102 EEEAVAEGLSVLGWRDVPVNSSVLGEVALATMPRIEQVFIG--ASGDDFERVLFIARKRI 159
Query: 99 THKIPKPGQRFYICSLSNRIVVYKGQFTADQLWKYFTDLNIIE 141
+I G FY+CSLS+R +VYKG + + +++ DL+
Sbjct: 160 EKRI---GADFYVCSLSSRTIVYKGVGLPEDVAEFYLDLDDER 199
Score = 51.6 bits (124), Expect = 3e-08
Identities = 18/41 (43%), Positives = 27/41 (65%)
Query: 139 IIEDAEKLSMRMNHRGACACDNDSGDGAGVLVAIPHAFYIQ 179
I+EDA + + + HRGA D +GDGAG+L+ IP F+ +
Sbjct: 29 IVEDALEALVNLTHRGAPGADGYAGDGAGILLQIPDYFFRE 69
Score = 47.3 bits (113), Expect = 9e-07
Identities = 16/32 (50%), Positives = 19/32 (59%)
Query: 32 GLYDPANEREACGVGFIVAIDRKRSHKSAGIG 63
GLYDPA E +ACG+G I D + SHK
Sbjct: 2 GLYDPAFEHDACGIGGIAHKDGRPSHKIVEDA 33
>gnl|CDD|236968 PRK11750, gltB, glutamate synthase subunit alpha; Provisional.
Length = 1485
Score = 59.5 bits (145), Expect = 1e-10
Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 3/77 (3%)
Query: 63 GEVARNSEPFMRQVFLTG--KQDEEEFKRQIYVLRKVSTHKIPKPGQRFYICSLSNRIVV 120
GE+A +S P + QVF+ E +F+R++++ R+ ++ + FY+CSLSN +++
Sbjct: 130 GEIALSSLPRIEQVFVNAPAGWRERDFERRLFIARRRIEKRLAD-DKDFYVCSLSNLVII 188
Query: 121 YKGQFTADQLWKYFTDL 137
YKG L +++ DL
Sbjct: 189 YKGLMMPADLPRFYLDL 205
Score = 39.1 bits (92), Expect = 8e-04
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 149 RMNHRGACACDNDSGDGAGVLVAIPHAFY 177
RM HRG A D +GDG G+L+ P F+
Sbjct: 41 RMTHRGGIAADGKTGDGCGLLLQKPDRFF 69
Score = 38.7 bits (91), Expect = 0.001
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 30 ASGLYDPANEREACGVGFIVAIDRKRSHK 58
GLYDP+ ER+ CG G I ++ + SHK
Sbjct: 2 HMGLYDPSLERDNCGFGLIAHMEGEPSHK 30
>gnl|CDD|215851 pfam00310, GATase_2, Glutamine amidotransferases class-II.
Length = 223
Score = 52.0 bits (125), Expect = 2e-08
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 138 NIIEDAEKLSMRMNHRGACACDNDSGDGAGVLVAIPHAFYIQKLR 182
+++EDA + R+ HRG D + DGAG+L IP F R
Sbjct: 17 DVVEDALEALERLEHRGGVGADGN--DGAGILTQIPDGFGAPSER 59
>gnl|CDD|223265 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), B subunit [DNA replication,
recombination, and repair].
Length = 635
Score = 30.2 bits (69), Expect = 0.54
Identities = 20/78 (25%), Positives = 31/78 (39%), Gaps = 25/78 (32%)
Query: 83 DEEEFKRQIYVLRKVSTHKIPKPGQRFYICSLSNRIVVYKG--QFTADQLWKYFTDLNI- 139
D+EE ++ + L K ++I QR YKG + DQLW+ D
Sbjct: 548 DDEELEKLLERLGKKKGYEI----QR------------YKGLGEMNPDQLWETTMDPETR 591
Query: 140 ------IEDAEKLSMRMN 151
IEDA++ +
Sbjct: 592 RLLQVTIEDADEADEIFS 609
>gnl|CDD|198347 cd07769, FGGY_GK, Glycerol kinases; a subfamily of the FGGY family
of carbohydrate kinases. This subfamily includes
glycerol kinases (GK; EC 2.7.1.30) and glycerol
kinase-like proteins from all three kingdoms of living
organisms. Glycerol is an important intermediate of
energy metabolism and it plays fundamental roles in
several vital physiological processes. GKs are involved
in the entry of external glycerol into cellular
metabolism. They catalyze the rate-limiting step in
glycerol metabolism by transferring a phosphate from ATP
to glycerol thus producing glycerol 3-phosphate (G3P) in
the cytoplasm. Human GK deficiency, called
hyperglycerolemia, is an X-linked recessive trait
associated with psychomotor retardation, osteoporosis,
spasticity, esotropia, and bone fractures. Under
different conditions, GKs from different species may
exist in different oligomeric states. The monomer of GKs
is composed of two large domains separated by a deep
cleft that forms the active site. This model includes
both the N-terminal domain, which adopts a ribonuclease
H-like fold, and the structurally related C-terminal
domain. The high affinity ATP binding site of GKs is
created only by a substrate-induced conformational
change. Based on sequence similarity, some GK-like
proteins from metazoa, which have lost their GK
enzymatic activity, are also included in this CD.
Members in this subfamily belong to the FGGY family of
carbohydrate kinases.
Length = 484
Score = 30.3 bits (69), Expect = 0.62
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 7/49 (14%)
Query: 14 VESVVEEVRDE---YLGPAASGLYDPANEREACGVGFIVAIDR--KRSH 57
VE + V D Y PA SGL+ P + +A G I+ + R R+H
Sbjct: 326 VEELAASVEDTGGVYFVPAFSGLFAPYWDPDARGT--ILGLTRGTTRAH 372
>gnl|CDD|221765 pfam12772, GHBP, Growth hormone receptor binding. Growth hormone
receptor binding protein is produced either by
proteolysis of the GHR (growth hormone receptor) at the
cell surface thereby releasing its extracellular domain,
the GHBP (growth hormone-binding protein), or, in
rodents, by alternative processing of the GHR
transcript. The sheddase proteolytic enzyme responsible
for the cleavage is TACE (tumour necrosis
factor-alpha-converting enzyme). Growth hormone (GH)
binding to GH receptor (GHR) is the initial step that
leads to the physiological functions of the hormone. The
biological effects of GHBP are determined by the serum
levels of growth hormone (GH), which can vary. Low
levels of GH can result in a dwarf phenotype and have
been positively correlated with an increased life
expectancy. High levels of GH can lead to gigantism or a
clinical syndrome termed acromegaly and have been
implicated in diabetic eye and kidney damage.
Length = 289
Score = 28.6 bits (64), Expect = 1.7
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 13/57 (22%)
Query: 120 VYKGQFTADQLWKYFTDLNIIEDAEK---------LSMRMNHRGACAC----DNDSG 163
YK D W F +L+I + EK LS M+ + + C D+DSG
Sbjct: 16 SYKPDLYNDDPWVEFIELDIDDPDEKNEGSDTQRLLSHDMHSKSSGNCLGFKDDDSG 72
>gnl|CDD|238212 cd00352, Gn_AT_II, Glutamine amidotransferases class-II (GATase).
The glutaminase domain catalyzes an amide nitrogen
transfer from glutamine to the appropriate substrate. In
this process, glutamine is hydrolyzed to glutamic acid
and ammonia. This domain is related to members of the
Ntn (N-terminal nucleophile) hydrolase superfamily and
is found at the N-terminus of enzymes such as
glucosamine-fructose 6-phosphate synthase (GLMS or
GFAT), glutamine phosphoribosylpyrophosphate (Prpp)
amidotransferase (GPATase), asparagine synthetase B
(AsnB), beta lactam synthetase (beta-LS) and glutamate
synthase (GltS). GLMS catalyzes the formation of
glucosamine 6-phosphate from fructose 6-phosphate and
glutamine in amino sugar synthesis. GPATase catalyzes
the first step in purine biosynthesis, an amide transfer
from glutamine to PRPP, resulting in
phosphoribosylamine, pyrophosphate and glutamate.
Asparagine synthetase B synthesizes asparagine from
aspartate and glutamine. Beta-LS catalyzes the formation
of the beta-lactam ring in the beta-lactamase inhibitor
clavulanic acid. GltS synthesizes L-glutamate from
2-oxoglutarate and L-glutamine. These enzymes are
generally dimers, but GPATase also exists as a
homotetramer.
Length = 220
Score = 27.8 bits (62), Expect = 2.6
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 152 HRGACACDNDSGDGAGVLVAIPHAFYIQK 180
RG A ++ DGAG+ V +++K
Sbjct: 21 LRGLAALEHRGPDGAGIAVYDGDGLFVEK 49
>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 = 28.0 bits (63), Expect = 2.8
Identities = 13/70 (18%), Positives = 28/70 (40%), Gaps = 13/70 (18%)
Query: 81 KQDEEEFKRQIYVLRKVSTHKIPKP------GQRFYI-------CSLSNRIVVYKGQFTA 127
EE R+I +L+K++ I K Y+ SL + + +G+ +
Sbjct: 32 SSLLEELLREIEILKKLNHPNIVKLYGVFEDENHLYLVMEYCEGGSLKDLLKENEGKLSE 91
Query: 128 DQLWKYFTDL 137
D++ + +
Sbjct: 92 DEILRILLQI 101
>gnl|CDD|233353 TIGR01311, glycerol_kin, glycerol kinase. This model describes
glycerol kinase, a member of the FGGY family of
carbohydrate kinases [Energy metabolism, Other].
Length = 493
Score = 27.2 bits (61), Expect = 5.4
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 7 TAEQSTAVESVVEEVRDEYLGPAASGLYDPANEREACGVGFIVAIDRK--RSH 57
A +S A+ VE+ Y PA +GL P + +A G I + R ++H
Sbjct: 322 HAAESEALARSVEDNGGVYFVPAFTGLGAPYWDPDARGA--IFGLTRGTTKAH 372
>gnl|CDD|200562 cd10936, CE4_DAC2, Putative catalytic domain of family 2
polysaccharide deacetylases (DACs) from bacteria. This
family contains an uncharacterized protein BH1492 from
Bacillus halodurans, an uncharacterized protein ATU2773
from Agrobacterium tumefaciens C58, and other bacterial
hypothetical proteins. Although their functions are
still unknown, structural superposition and sequence
comparison suggest that BH1492 and ATU2773 might be
divergently related to the 7-stranded barrel catalytic
domain of polysaccharide deacetylases (DACs) from the
carbohydrate esterase 4 (CE4) superfamily, which remove
N-linked acetyl groups from cell wall polysaccharides.
This family is designated as DAC family 2, a divergent
DAC family.
Length = 215
Score = 26.4 bits (59), Expect = 7.7
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 44 GVGFIVAIDRKRSHKSAGIGEVARNSE-PFM-RQVFLTGKQDEEEFKRQIY 92
G+ F+ D + + KS VA+ P R VFL +QDE +RQ+
Sbjct: 123 GLFFV---DSRTTPKSVA-YRVAKELGVPTARRDVFLDNEQDEAAIRRQLD 169
>gnl|CDD|173725 cd06608, STKc_myosinIII_like, Catalytic domain of Class III
myosin-like Protein Serine/Threonine Kinases.
Serine/threonine kinases (STKs), Class III myosin-like
subfamily, catalytic (c) domain. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
class III myosin-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. Class III myosins are motor
proteins with an N-terminal kinase catalytic domain and
a C-terminal actin-binding motor domain. Class III
myosins are present in the photoreceptors of
invertebrates and vertebrates and in the auditory hair
cells of mammals. The kinase domain of myosin III can
phosphorylate several cytoskeletal proteins,
conventional myosin regulatory light chains, and can
autophosphorylate the C-terminal motor domain. Myosin
III may play an important role in maintaining the
structural integrity of photoreceptor cell microvilli.
It may also function as a cargo carrier during
light-dependent translocation, in photoreceptor cells,
of proteins such as transducin and arrestin. The
Drosophila class III myosin, called NinaC (Neither
inactivation nor afterpotential protein C), is critical
in normal adaptation and termination of photoresponse.
Vertebrates contain two isoforms of class III myosin,
IIIA and IIIB. This subfamily also includes mammalian
NIK-like embryo-specific kinase (NESK), Traf2- and
Nck-interacting kinase (TNIK), mitogen-activated protein
kinase (MAPK) kinase kinase kinase 4 (MAPKKKK4 or
MAP4K4) and MAPKKKK6 (or MAP4K6). MAP4Ks are involved in
some MAPK signaling pathways by activating a MAPK kinase
kinase (MAPKKK or MAP3K or MKKK). Each MAPK cascade is
activated either by a small GTP-binding protein or by an
adaptor protein, which transmits the signal either
directly to a MAP3K to start the triple kinase core
cascade or indirectly through a mediator kinase, a
MAP4K. MAPK signaling cascades are important in
mediating cellular responses to extracellular signals.
Length = 275
Score = 26.5 bits (59), Expect = 8.2
Identities = 16/49 (32%), Positives = 19/49 (38%), Gaps = 10/49 (20%)
Query: 84 EEEFKRQIYVLRKVSTHK-IPKPGQRFYICSLSNRIVVYKGQFTADQLW 131
EEE K + +LRK S H I FY + DQLW
Sbjct: 46 EEEIKEEYNILRKYSNHPNIA----TFYGAFIKKNPPG-----NDDQLW 85
>gnl|CDD|214659 smart00433, TOP2c, TopoisomeraseII. Eukaryotic DNA topoisomerase
II, GyrB, ParE.
Length = 594
Score = 26.4 bits (59), Expect = 9.4
Identities = 9/19 (47%), Positives = 11/19 (57%), Gaps = 2/19 (10%)
Query: 121 YK--GQFTADQLWKYFTDL 137
YK G+ ADQLW+ D
Sbjct: 536 YKGLGEMNADQLWETTMDP 554
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 0.135 0.393
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,239,187
Number of extensions: 843140
Number of successful extensions: 714
Number of sequences better than 10.0: 1
Number of HSP's gapped: 709
Number of HSP's successfully gapped: 25
Length of query: 182
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 91
Effective length of database: 6,901,388
Effective search space: 628026308
Effective search space used: 628026308
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: 56 (25.2 bits)