RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2644
(119 letters)
>gnl|CDD|213381 cd12196, MARK1-3_C, C-terminal, kinase associated domain 1 (KA1), a
phospholipid binding domain, of microtubule
affinity-regulating kinases 1-3. Microtubule-associated
protein/microtubule affinity regulating kinases (MARKs),
also called partition-defective (Par-1) kinases, are
serine/threonine protein kinases (STKs) that catalyze
the transfer of the gamma-phosphoryl group from ATP to
S/T residues on protein substrates. They phosphorylate
the tau protein and related microtubule-associated
proteins (MAPs) on tubulin binding sites to induce
detachment from microtubules, and are involved in the
regulation of cell shape and polarity, cell cycle
control, transport, and the cytoskeleton. Mammals
contain four proteins, MARK1-4, encoded by distinct
genes belonging to this subfamily, with additional
isoforms arising from alternative splicing. MARK1/2,
through their activation by death-associated protein
kinase (DAPK), modulates polarized neurite outgrowth.
MARK1, also called Par-1c, is also involved in
axon-dendrite specification, and SNPs on the MARK1 gene
is associated with autism spectrum disorders. MARK2,
also called Par-1b, is implicated in many physiological
processes including fertility, immune system
homeostasis, learning and memory, growth, and
metabolism. MARK3, also called Par-1a, is implicated in
gluconeogenesis and adiposity; mice deficient with MARK3
display reduced adiposity, resistance to hepatic
steatosis, and defective gluconeogensis. MARKs contain
an N-terminal catalytic kinase domain, a
ubiquitin-associated domain (UBA), and a C-terminal
kinase associated domain (KA1). The KA1 domain binds
anionic phospholipids and may be involved in membrane
localization as well as in auto-inhibition of the kinase
domain.
Length = 98
Score = 216 bits (551), Expect = 1e-74
Identities = 89/98 (90%), Positives = 92/98 (93%)
Query: 20 KPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQW 79
KPRSLRFTWSMKTTSS DPN++M EIRKVLDANNCDYEQRERFLL CVHGD TDSLVQW
Sbjct: 1 KPRSLRFTWSMKTTSSMDPNDMMREIRKVLDANNCDYEQRERFLLFCVHGDGRTDSLVQW 60
Query: 80 EIEVCKLPRLSLNGVRFKRISGTSIGFKNIASKIANEL 117
E+EVCKLPRLSLNGVRFKRISGTSI FKNIASKIANEL
Sbjct: 61 EMEVCKLPRLSLNGVRFKRISGTSIAFKNIASKIANEL 98
>gnl|CDD|213386 cd12201, MARK2_C, C-terminal, kinase associated domain 1 (KA1), a
phospholipid binding domain, of microtubule
affinity-regulating kinase 2. Microtubule-associated
protein/microtubule affinity regulating kinases (MARKs),
also called partition-defective (Par-1) kinases, are
serine/threonine protein kinases (STKs) that catalyze
the transfer of the gamma-phosphoryl group from ATP to
S/T residues on protein substrates. They phosphorylate
the tau protein and related microtubule-associated
proteins (MAPs) on tubulin binding sites to induce
detachment from microtubules, and are involved in the
regulation of cell shape and polarity, cell cycle
control, transport, and the cytoskeleton. Mammals
contain four proteins, MARK1-4, encoded by distinct
genes belonging to this subfamily, with additional
isoforms arising from alternative splicing. MARK2, also
called Par-1b or ELKL motif kinase 1 (EMK-1), is
implicated in many physiological processes including
fertility, immune system homeostasis, learning and
memory, growth, and metabolism. It also regulates axon
formation and has been implicated in neurodegeneration.
MARKs contain an N-terminal catalytic kinase domain, a
ubiquitin-associated domain (UBA), and a C-terminal
kinase associated domain (KA1). The KA1 domain binds
anionic phospholipids and may be involved in membrane
localization as well as in auto-inhibition of the kinase
domain.
Length = 99
Score = 177 bits (450), Expect = 2e-59
Identities = 81/99 (81%), Positives = 89/99 (89%)
Query: 20 KPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQW 79
KPRSLRFTWSMKTTSS +PNE+M EIRKVLDANNC YE +E+++LLC+HG P D VQW
Sbjct: 1 KPRSLRFTWSMKTTSSMEPNEMMKEIRKVLDANNCQYELQEKYMLLCMHGTPGHDDFVQW 60
Query: 80 EIEVCKLPRLSLNGVRFKRISGTSIGFKNIASKIANELK 118
E+EVCKLPRLSLNGVRFKRISGTSI FKNIASKIANELK
Sbjct: 61 EMEVCKLPRLSLNGVRFKRISGTSIAFKNIASKIANELK 99
>gnl|CDD|213377 cd12121, MARK_C_like, C-terminal kinase associated domain 1 (KA1),
a phospholipid binding domain, of microtubule
affinity-regulating kinases, and similar domains.
Microtubule-associated protein/microtubule affinity
regulating kinases (MARKs), also called
partition-defective (Par-1) kinases, are
serine/threonine protein kinases (STKs) that catalyze
the transfer of the gamma-phosphoryl group from ATP to
S/T residues on protein substrates. They phosphorylate
the tau protein and related microtubule-associated
proteins (MAPs) on tubulin binding sites to induce
detachment from microtubules, and are involved in the
regulation of cell shape and polarity, cell cycle
control, transport, and the cytoskeleton. Mammals
contain four proteins, MARK1-4, encoded by distinct
genes belonging to this subfamily, with additional
isoforms arising from alternative splicing. In yeast,
MARK/Par-1 homologs are called Kin1/2 kinases. Kin1 is a
membrane-associated kinase that is involved in
regulating cytokinesis and the cell surface. MARKs
contain an N-terminal catalytic kinase domain, a
ubiquitin-associated domain (UBA), and a C-terminal
kinase associated domain (KA1). The KA1 domain binds
anionic phospholipids and may be involved in membrane
localization as well as in auto-inhibition of the kinase
domain.
Length = 96
Score = 144 bits (365), Expect = 3e-46
Identities = 53/96 (55%), Positives = 68/96 (70%)
Query: 22 RSLRFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEI 81
RSLR +S+ TTS++ P EIM EI++VL +N DYE+ +LL C HGD + V +EI
Sbjct: 1 RSLRGPFSVATTSTKSPEEIMNEIKRVLRSNGIDYEEVGGYLLECKHGDSSGGEFVIFEI 60
Query: 82 EVCKLPRLSLNGVRFKRISGTSIGFKNIASKIANEL 117
E+CKLPRL LNG+RFKRISG S +K + KI NEL
Sbjct: 61 EICKLPRLGLNGIRFKRISGDSWQYKRLCKKILNEL 96
>gnl|CDD|213382 cd12197, MARK4_C, C-terminal, kinase associated domain 1 (KA1), a
phospholipid binding domain, of microtubule
affinity-regulating kinase 4. Microtubule-associated
protein/microtubule affinity regulating kinases (MARKs),
also called partition-defective (Par-1) kinases, are
serine/threonine protein kinases (STKs) that catalyze
the transfer of the gamma-phosphoryl group from ATP to
S/T residues on protein substrates. They phosphorylate
the tau protein and related microtubule-associated
proteins (MAPs) on tubulin binding sites to induce
detachment from microtubules, and are involved in the
regulation of cell shape and polarity, cell cycle
control, transport, and the cytoskeleton. Mammals
contain four proteins, MARK1-4, encoded by distinct
genes belonging to this subfamily, with additional
isoforms arising from alternative splicing. MARK4 has
two splicing isoforms: MARK4S, predominantly expressed
in the brain; and MARK4L, expressed in all tissues.
Unlike MARK1-3 that show cytoplasmic localization, MARK4
colocalizes with the centrosome and with microtubules.
Decreased MARK4 expression in the brain may be involved
in the pathogenesis of Prion diseases and may be
correlated to PrP(Sc) deposits. MARK4 is also a
component of the ectoplasmic specialization, a
testis-specific adherens junction. MARKs contain an
N-terminal catalytic kinase domain, a
ubiquitin-associated domain (UBA), and a C-terminal
kinase associated domain (KA1). The KA1 domain binds
anionic phospholipids and may be involved in membrane
localization as well as in auto-inhibition of the kinase
domain.
Length = 99
Score = 111 bits (278), Expect = 3e-33
Identities = 46/99 (46%), Positives = 61/99 (61%), Gaps = 1/99 (1%)
Query: 22 RSLRFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDS-LVQWE 80
R LR W ++ SSR P E++ +R+ C Q FLL C+HG + LV +E
Sbjct: 1 RLLRGGWDVRLRSSRPPAEVVLALREATAGCGCRVRQAGPFLLACLHGAAGSPEPLVAFE 60
Query: 81 IEVCKLPRLSLNGVRFKRISGTSIGFKNIASKIANELKL 119
EVC+LPR LNGVRFKR+ GT + F+ IASKI+ EL+L
Sbjct: 61 AEVCQLPRGELNGVRFKRLWGTPLAFRTIASKISKELEL 99
>gnl|CDD|213376 cd12120, AMPKA_C_like, C-terminal regulatory domain of
5'-AMP-activated protein kinase (AMPK) alpha subunit and
similar domains. This family is composed of AMPKs,
microtubule-associated protein/microtubule affinity
regulating kinases (MARKs), yeast Kcc4p-like proteins,
plant calcineurin B-Like (CBL)-interacting protein
kinases (CIPKs), and similar proteins. They are
serine/threonine protein kinases (STKs) that catalyze
the transfer of the gamma-phosphoryl group from ATP to
S/T residues on protein substrates. AMPKs act as sensors
for the energy status of the cell and are activated by
cellular stresses that lead to ATP depletion such as
hypoxia, heat shock, and glucose deprivation, among
others. MARKs phosphorylate the tau protein and related
microtubule-associated proteins (MAPs) on tubulin
binding sites to induce detachment from microtubules,
and are involved in the regulation of cell shape and
polarity, cell cycle control, transport, and the
cytoskeleton. Kcc4p and related proteins are
septin-associated proteins that are involved in septin
organization and in the yeast morphogenesis checkpoint
coordinating the cell cycle with bud formation. CIPKs
interact with the calcineurin B-like (CBL) calcium
sensors to form a signaling network that decode specific
calcium signals triggered by a variety of environmental
stimuli including salinity, drought, cold, light, and
mechanical perturbation, among others. All members of
this family contain an N-terminal catalytic kinase
domain and a C-terminal regulatory domain which is also
called kinase associated domain 1 (KA1) in some cases.
The C-terminal regulatory domain serves as a protein
interaction domain in AMPKs and CIPKs. In MARKs and
Kcc4p-like proteins, this domain binds phospholipids and
may be involved in membrane localization.
Length = 95
Score = 105 bits (264), Expect = 4e-31
Identities = 27/96 (28%), Positives = 46/96 (47%), Gaps = 4/96 (4%)
Query: 25 RFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYEQRER-FLLLCVHGDPN--TDSLVQWEI 81
R W ++ S DP+EI I KVL+ + R F++ + + +EI
Sbjct: 1 RKKWELEIHSRIDPSEIYEGIHKVLEGWGKNLVFRITNFIITGKLVNDHILFLRSTLFEI 60
Query: 82 EVCKLPRLSLNGVRFKRISGTSIGFKNIASKIANEL 117
EV ++ L V FK+ +G++ F +A+KI +L
Sbjct: 61 EVYEVGP-GLFMVDFKKKTGSTKTFTKLATKIQIKL 95
>gnl|CDD|190228 pfam02149, KA1, Kinase associated domain 1.
Length = 46
Score = 70.3 bits (173), Expect = 1e-17
Identities = 27/46 (58%), Positives = 37/46 (80%)
Query: 74 DSLVQWEIEVCKLPRLSLNGVRFKRISGTSIGFKNIASKIANELKL 119
S+V++EIEVCKLPRL L GV FKR+SG +K++A+KI +EL+L
Sbjct: 1 PSVVKFEIEVCKLPRLGLYGVDFKRLSGPQWQYKDLAAKILSELRL 46
>gnl|CDD|213383 cd12198, MELK_C, C-terminal kinase associated domain 1 (KA1) of
Maternal embryonic leucine zipper kinase. MELK, also
called protein kinase 38 (PK38) or pEg3 kinase, is a
cell cycle-regulated serine/threonine protein kinase
(STK) that catalyzes the transfer of the
gamma-phosphoryl group from ATP to S/T residues on
protein substrates. It is phosphorylated and maximally
active during mitosis and is involved in regulating cell
cycle progression, division, proliferation, tumor
growth, and mRNA splicing. MELK shows a broad substrate
specificity, including the zinc finger-like protein
ZPR9, the transcription and splicing factor NIPP1, and
the protein-tyrosine phosphatase Cdc25B, among others.
MELK contains an N-terminal catalytic domain followed by
a ubiquitin-associated (UBA) domain, a TP dipeptide-rich
region, and a C-terminal KA1 domain. The KA1 domain of
MELK, together with its TP dipeptide-rich region,
functions as an autoinhibitory domain. The KA1 domain of
the related microtubule affinity-regulating kinases
(MARKs) has been shown to bind anionic phospholipids and
may be involved in membrane localization.
Length = 96
Score = 56.9 bits (138), Expect = 6e-12
Identities = 28/86 (32%), Positives = 50/86 (58%), Gaps = 2/86 (2%)
Query: 29 SMKTTSSRDPNEIMAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEIEVCKLPR 88
++ TTSS+DP +++ E+++VL D +Q+ + L C D + +E+EVC+LP
Sbjct: 8 NVSTTSSKDPEQVLNELKRVLAKKGIDCKQK-GYTLRCKTKDDFGKVKLTFELEVCRLPG 66
Query: 89 LS-LNGVRFKRISGTSIGFKNIASKI 113
L + G+R KR+ G + +K + I
Sbjct: 67 LDEVVGIRRKRLKGDAWVYKKVCEDI 92
>gnl|CDD|216671 pfam01734, Patatin, Patatin-like phospholipase. This family
consists of various patatin glycoproteins from plants.
The patatin protein accounts for up to 40% of the total
soluble protein in potato tubers. Patatin is a storage
protein but it also has the enzymatic activity of lipid
acyl hydrolase, catalyzing the cleavage of fatty acids
from membrane lipids. Members of this family have been
found also in vertebrates.
Length = 189
Score = 31.0 bits (70), Expect = 0.092
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 79 WEIEVCKLPRLSLNGVRFKRISGTSIG 105
+ + V K L G+RF ISGTS G
Sbjct: 12 YHLGVLK--ALEEAGLRFDVISGTSAG 36
>gnl|CDD|215062 PLN00118, PLN00118, isocitrate dehydrogenase (NAD+).
Length = 372
Score = 28.7 bits (64), Expect = 0.71
Identities = 23/82 (28%), Positives = 34/82 (41%), Gaps = 8/82 (9%)
Query: 40 EIMAEIRKVLDANNCDYEQRERFLLLCVHGDPNTDSLVQWEIEVCKLPRLSLNGVRFKRI 99
EI +++V A E E ++ V DP T S + WE L + N V K
Sbjct: 55 EIAESVKQVFTAAGVPIEWEEHYVGTTV--DPRTGSFLTWE----SLESVRRNKVGLKGP 108
Query: 100 SGTSI--GFKNIASKIANELKL 119
T I G +++ + EL L
Sbjct: 109 MATPIGKGHRSLNLTLRKELGL 130
>gnl|CDD|213378 cd12122, AMPKA_C, C-terminal regulatory domain of
5'-AMP-activated protein kinase (AMPK) alpha catalytic
subunit. AMPK, a serine/threonine protein kinase
(STK), catalyzes the transfer of the gamma-phosphoryl
group from ATP to S/T residues on protein substrates.
It acts as a sensor for the energy status of the cell
and is activated by cellular stresses that lead to ATP
depletion such as hypoxia, heat shock, and glucose
deprivation, among others. AMPK is a heterotrimer of
three subunits: alpha, beta, and gamma. Co-expression
of the three subunits is required for kinase activity;
in the absence of one, the other two subunits get
degraded. The AMPK alpha subunit is the catalytic
subunit and it contains an N-terminal kinase domain and
a C-terminal regulatory domain (RD). Vertebrates
contain two isoforms of the alpha subunit, alpha1 and
alpha2, which are encoded by different genes, PRKAA1
and PRKAA2, respectively. The C-terminal RD of the AMPK
alpha subunit is involved in AMPK heterotrimer
formation. It mainly interacts with the C-terminal
region of the beta subunit to form a tight alpha-beta
complex that is associated with the gamma subunit. The
AMPK alpha subunit RD also contains an auto-inhibitory
region that interacts with the kinase domain; this
inhibition is negated by the interaction with the AMPK
gamma subunit. AMPK is conserved throughout evolution;
the AMPK alpha subunit homologs in yeast and plants are
called Snf1 and SnRK1 (Snf1 related kinase),
respectively.
Length = 132
Score = 27.8 bits (62), Expect = 1.0
Identities = 9/33 (27%), Positives = 14/33 (42%), Gaps = 2/33 (6%)
Query: 25 RFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYE 57
W + S P+EIM E+ + L +E
Sbjct: 1 ERRWHLGIRSQSHPHEIMLEVYRAL--KALGFE 31
>gnl|CDD|193535 cd05659, M18_API, M18 Peptidase Aminopeptidase I. Peptidase M18
family, Aminopeptidase I (Vacuolar aminopeptidase I;
Polypeptidase; Leucine aminopeptidase IV; LAPIV;
Aminopeptidase III; Aminopeptidase yscI; EC 3.4.11.22)
subfamily. Aminopeptidase I is widely distributed in
bacteria and eukaryotes, but only the yeast enzyme has
been characterized to date. It is a vacuolar enzyme,
synthesized as a cytosolic proform, and proteolytically
matured upon arrival in the vacuole. The
pro-aminopeptidase I (proAPI) does not enter the vacuole
via the secretory pathway. In non-starved cells, it uses
the cytoplasm to vacuole targeting (cvt) pathway and in
cells starved for nitrogen, it is targeted to the
vacuole via autophagy. Yeast aminopeptidase I is active
only in its dodecameric form with broad substrate
specificity, acting on all aminoacyl and peptidyl
derivatives that contain a free alpha-amino group; this
is in contrast to the highly selective M18 mammalian
aspartyl aminopeptidase. N-terminal leucine and most
other hydrophobic amino acid residues are the best
substrates while glycine and charged amino acid residues
in P1 position are cleaved much more slowly. This enzyme
is strongly and specifically activated by zinc (Zn2+)
and chloride (Cl-) ions.
Length = 443
Score = 28.3 bits (64), Expect = 1.1
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 7/31 (22%)
Query: 30 MKTTSSR------DPN-EIMAEIRKVLDANN 53
K T SR D N E +AE+RK+ + N
Sbjct: 349 TKYTGSRGKSGSNDANAEFVAEVRKIFNENG 379
>gnl|CDD|132848 cd07209, Pat_hypo_Ecoli_Z1214_like, Hypothetical patatin similar to
Z1214 protein of Escherichia coli. Patatin-like
phospholipase similar to Z1214 protein of Escherichia
coli. This family predominantly consists of bacterial
patatin glycoproteins and some representatives from
eukaryotes and archaea. The patatin protein accounts for
up to 40% of the total soluble protein in potato tubers.
Patatin is a storage protein, but it also has the
enzymatic activity of a lipid acyl hydrolase, catalyzing
the cleavage of fatty acids from membrane lipids.
Members of this family have also been found in
vertebrates.
Length = 215
Score = 27.6 bits (62), Expect = 1.2
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 93 GVRFKRISGTSIG 105
G+ ISGTSIG
Sbjct: 24 GIEPDIISGTSIG 36
>gnl|CDD|224666 COG1752, RssA, Predicted esterase of the alpha-beta hydrolase
superfamily [General function prediction only].
Length = 306
Score = 27.8 bits (62), Expect = 1.5
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 88 RLSLNGVRFKRISGTSIG 105
L G+ I+GTS G
Sbjct: 32 ALEEAGIPIDVIAGTSAG 49
>gnl|CDD|132846 cd07207, Pat_ExoU_VipD_like, ExoU and VipD-like proteins; homologus
to patatin, cPLA2, and iPLA2. ExoU, a 74-kDa enzyme, is
a potent virulence factor of Pseudomonas aeruginosa. One
of the pathogenic mechanisms of P. aeruginosa is to
induce cytotoxicity by the injection of effector
proteins (e.g. ExoU) using the type III secretion (T3S)
system. ExoU is homologus to patatin and also has the
conserved catalytic residues of mammalian
calcium-independent (iPLA2) and cytosolic (cPLA2) PLA2.
In vitro, ExoU cytotoxity is blocked by the inhibitor of
cytosolic and Ca2-independent phospholipase A2 (cPLA2
and iPLA2) enzymes, suggesting that phospholipase A2
inhibitors may represent a novel mode of treatment for
acute P. aeruginosa infections. ExoU requires eukaryotic
superoxide dismutase as a cofactor and cleaves
phosphatidylcholine and phosphatidylethanolamine in
vitro. VipD, a 69-kDa cytosolic protein, belongs to the
members of Legionella pneumophila family and is
homologus to ExoU from Pseudomonas. Even though VipD
shows high sequence similarity with several functional
regions of ExoU (e.g. oxyanion hole, active site serine,
active site aspartate), it has been shown to have no
phospholipase activity. This family includes ExoU from
Pseudomonas aeruginosa and VipD of Legionella
pneumophila.
Length = 194
Score = 26.9 bits (60), Expect = 2.4
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 93 GVRFKRISGTSIG 105
G+ KR++GTS G
Sbjct: 25 GILKKRVAGTSAG 37
>gnl|CDD|173940 cd08181, PPD-like, 1,3-propanediol dehydrogenase-like (PPD).
1,3-propanediol dehydrogenase-like (PPD). This family is
a member of the iron-containing alcohol dehydrogenase
superfamily, and exhibits a dehydroquinate synthase-like
fold. Protein sequence similarity search and other
biochemical evidences suggest that they are close to the
iron-containing 1,3-propanediol dehydrogenase (EC
1.1.1.202). 1,3-propanediol dehydrogenase catalyzes the
oxidation of propane-1,3-diol to 3-hydroxypropanal with
the simultaneous reduction of NADP+ to NADPH. The
protein structure of Thermotoga maritima TM0920 gene
contains one NADP+ and one iron ion.
Length = 357
Score = 26.8 bits (60), Expect = 2.5
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 39 NEIMAEIRKVLDANNCDYEQRERFLL 64
E+ E L N D E RE+ +L
Sbjct: 214 LELFKECLPKLLENELDEEAREKLML 239
>gnl|CDD|235018 PRK02256, PRK02256, putative aminopeptidase 1; Provisional.
Length = 462
Score = 26.7 bits (60), Expect = 2.9
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 7/31 (22%)
Query: 30 MKTTSSR------DPN-EIMAEIRKVLDANN 53
K T SR D N E +AE+R + + NN
Sbjct: 366 TKYTGSRGKYGANDANAEFVAEVRNLFNKNN 396
>gnl|CDD|237265 PRK13009, PRK13009, succinyl-diaminopimelate desuccinylase;
Reviewed.
Length = 375
Score = 27.0 bits (61), Expect = 2.9
Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 20/72 (27%)
Query: 40 EIMAEIRKVLDANNCDYEQRERFLLLCVHGDP-------NTDSLVQWEIEVCKL-PRLSL 91
+ A + +LD + DY L + G+P D++V V + P LS
Sbjct: 266 SLKARVEAILDKHGLDYT-----LEWTLSGEPFLTPPGKLVDAVVAAIEAVTGITPELST 320
Query: 92 NGVRFKRISGTS 103
+G GTS
Sbjct: 321 SG-------GTS 325
>gnl|CDD|219720 pfam08101, DUF1708, Domain of unknown function (DUF1708). This is
a yeast domain of unknown function.
Length = 381
Score = 26.6 bits (59), Expect = 4.0
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 29 SMKTTSSRDPNEIMAEIRKVLDANNCD-YEQRERFLLL 65
++ T SR P E++ + K+LD + D +E RE + +L
Sbjct: 210 TLTTDFSRTPFELLRRVNKLLDFDGKDAFESREDYTIL 247
>gnl|CDD|193511 cd03891, M20_DapE_proteobac, M20 Peptidase proteobacterial DapE
encoded N-succinyl-L,L-diaminopimelic acid
desuccinylase. Peptidase M20 family, proteobacterial
DapE encoded N-succinyl-L,L-diaminopimelic acid
desuccinylase (DapE; aspartyl dipeptidase;
succinyl-diaminopimelate desuccinylase) subfamily. DapE
catalyzes the hydrolysis of
N-succinyl-L,L-diaminopimelate (L,L-SDAP) to
L,L-diaminopimelate and succinate. It has been shown
that DapE is essential for cell growth and
proliferation. DapEs have been purified from Escherichia
coli and Haemophilus influenzae, while the genes that
encode for DapEs have been sequenced from several
bacterial sources such as Corynebacterium glutamicum,
Helicobacter pylori, Neisseria meningitidis and
Mycobacterium tuberculosis. DapE is a small, dimeric
enzyme that requires two zinc atoms per molecule for
full enzymatic activity. All of the amino acids that
function as metal binding ligands are strictly conserved
in DapE.
Length = 366
Score = 26.3 bits (59), Expect = 4.2
Identities = 18/75 (24%), Positives = 28/75 (37%), Gaps = 20/75 (26%)
Query: 37 DPNEIMAEIRKVLDANNCDYEQRERFLLLCVHGDP-------NTDSLVQWEIEVCKL-PR 88
+ A I +LD + DY L + G+P D++ +V + P
Sbjct: 259 TAESLKARIEAILDKHGLDYT-----LEWELSGEPFLTKPGKLVDAVSAAIKKVTGITPE 313
Query: 89 LSLNGVRFKRISGTS 103
LS +G GTS
Sbjct: 314 LSTSG-------GTS 321
>gnl|CDD|233337 TIGR01273, speA, arginine decarboxylase, biosynthetic. Two
alternative pathways can convert arginine to putrescine.
One is decarboxylation by this enzyme followed by
removal of the urea moeity by agmatinase. In the other,
the ureohydrolase (arginase) acts first, followed by
ornithine decarboxylase. This pathway leads to
spermidine biosynthesis, hence the gene symbol speA. A
distinct biodegradative form is also pyridoxal
phosphate-dependent but is not similar in sequence
[Central intermediary metabolism, Polyamine
biosynthesis].
Length = 624
Score = 26.1 bits (58), Expect = 5.4
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 27 TWSMKTTSSRDPNEIMAEIRKVLDANNCDYEQRERFL 63
T M DP E++ R + N D E++++FL
Sbjct: 574 TEDMLRYVQYDPKELLTLYRDKVANNKLDAEEKKQFL 610
>gnl|CDD|224813 COG1901, COG1901, Uncharacterized conserved protein [Function
unknown].
Length = 197
Score = 25.8 bits (57), Expect = 6.0
Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 21 PRSLRFTWSMKTTSSRDPNEIMAEIRKVLDANNCDYEQRE 60
P+++R S + D + I+K LDA EQ
Sbjct: 63 PKTIRVEGSELRYLNPDERSLAILIKKALDA-ELGKEQTR 101
>gnl|CDD|193556 cd05681, M20_dipept_like_4, Uncharacterized M20 Dipeptidases.
Peptidase M20 family, unknown dipeptidase-like subfamily
3 (inferred by homology to be dipeptidases). M20
dipeptidases include a large variety of bacterial
enzymes including cytosolic nonspecific dipeptidase
(CNDP), Xaa-methyl-His dipeptidase (anserinase),and
canosinase. These dipeptidases have been shown to act on
a wide range of dipeptides, but not larger peptides. For
example, anserinase mainly catalyzes the hydrolysis of
N-alpha-acetylhistidine while carnosinase degrades
beta-alanyl-L-histidine.
Length = 430
Score = 25.6 bits (57), Expect = 6.7
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 37 DPNEIMAEIRKVLDANN 53
DP E++ +R LD N
Sbjct: 315 DPEEVLDLLRAHLDKNG 331
>gnl|CDD|239289 cd02991, UAS_ETEA, UAS family, ETEA subfamily; composed of
proteins similar to human ETEA protein, the translation
product of a highly expressed gene in the T-cells and
eosinophils of atopic dermatitis patients compared with
those of normal individuals. ETEA shows homology to
Fas-associated factor 1 (FAF1); both containing UAS and
UBX (ubiquitin-associated) domains. Compared to FAF1,
however, ETEA lacks the ubiquitin-associated UBA domain
and a nuclear targeting domain. The function of ETEA is
still unknown. A yeast two-hybrid assay showed that it
can interact with Fas. Because of its homology to FAF1,
it is postulated that ETEA could be involved in
modulating Fas-mediated apoptosis of T-cells and
eosinophils of atopic dermatitis patients, making them
more resistant to apoptosis.
Length = 116
Score = 25.1 bits (55), Expect = 7.1
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 55 DYEQRERFLLLCVHGDPNTDS 75
D +Q RFLL+ +HGD + D+
Sbjct: 12 DAKQELRFLLVYLHGDDHQDT 32
>gnl|CDD|234832 PRK00772, PRK00772, 3-isopropylmalate dehydrogenase; Provisional.
Length = 358
Score = 25.4 bits (57), Expect = 7.3
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 40 EIMAEIRKVLDA 51
E+MAE KVLDA
Sbjct: 16 EVMAEAVKVLDA 27
>gnl|CDD|201001 pfam00101, RuBisCO_small, Ribulose bisphosphate carboxylase,
small chain.
Length = 99
Score = 24.9 bits (55), Expect = 7.5
Identities = 5/25 (20%), Positives = 11/25 (44%)
Query: 28 WSMKTTSSRDPNEIMAEIRKVLDAN 52
W + D +++AE+ + A
Sbjct: 48 WKLPMFGCTDAAQVLAELEECRKAY 72
>gnl|CDD|238187 cd00307, RuBisCO_small_like, Ribulose bisphosphate
carboxylase/oxygenase (Rubisco), small subunit and
related proteins. Rubisco is a bifunctional enzyme
catalyzes the initial steps of two opposing metabolic
pathways: photosynthetic carbon fixation and the
competing process of photorespiration. Rubisco Form I,
present in plants and green algae, is composed of eight
large and eight small subunits. The nearly identical
small subunits are encoded by a family of nuclear
genes. After translation, the small subunits are
translocated across the chloroplast membrane, where an
N-terminal signal peptide is cleaved off. While the
large subunits contain the catalytic activities, it has
been shown that the small subunits are important for
catalysis by enhancing the catalytic rate through
inducing conformational changes in the large subunits.
This superfamily also contains specific proteins from
cyanobacteria. CcmM plays a role in a CO2 concentrating
mechanism, which cyanobacteria need to to overcome the
low specificity of their Rubisco and fusions to Rubisco
activase, a type of chaperone, which promotes and
maintains the catalytic activity of Rubisco. CcmM
contains an N-terminal carbonic anhydrase fused to four
copies of the Rubisco-small subunit domain.
Length = 84
Score = 24.5 bits (54), Expect = 8.8
Identities = 5/28 (17%), Positives = 11/28 (39%)
Query: 29 SMKTTSSRDPNEIMAEIRKVLDANNCDY 56
S R +++A + L + +Y
Sbjct: 35 SCGPIEGRSEAQVLAALEACLAEHPGEY 62
>gnl|CDD|193514 cd03894, M20_ArgE, M20 Peptidase acetylornithine deacetylase.
Peptidase M20 family, acetylornithine deacetylase (ArgE,
Acetylornithinase, AO, N2-acetyl-L-ornithine
amidohydrolase, EC 3.5.1.16) subfamily. ArgE catalyzes
the conversion of N-acetylornithine to ornithine, which
can then be incorporated into the urea cycle for the
final stage of arginine synthesis. The substrate
specificity of ArgE is quite broad; several
alpha-N-acyl-L-amino acids can be hydrolyzed, including
alpha-N-acetylmethionine and alpha-N-formylmethionine.
ArgE shares significant sequence homology and
biochemical features, and possibly a common origin, with
glutamate carboxypeptidase (CPG2) and
succinyl-diaminopimelate desuccinylase (DapE), and
aminoacylase I (ACY1), having all metal ligand binding
residues conserved.
Length = 372
Score = 25.5 bits (57), Expect = 8.9
Identities = 8/40 (20%), Positives = 15/40 (37%), Gaps = 3/40 (7%)
Query: 12 NAVNDDQVKPRSLRFTWSMKTTSSRDPNEIMAEIRKVLDA 51
A+N + P + + DP E++A +R
Sbjct: 237 TALN---IIPGQCELDFEFRPLPGMDPEELLARLRAYAAE 273
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
0.318 0.133 0.395
Gapped
Lambda K H
0.267 0.0683 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,846,957
Number of extensions: 482815
Number of successful extensions: 574
Number of sequences better than 10.0: 1
Number of HSP's gapped: 568
Number of HSP's successfully gapped: 35
Length of query: 119
Length of database: 10,937,602
Length adjustment: 82
Effective length of query: 37
Effective length of database: 7,300,574
Effective search space: 270121238
Effective search space used: 270121238
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.3 bits)