RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16237
(133 letters)
>gnl|CDD|204512 pfam10557, Cullin_Nedd8, Cullin protein neddylation domain. This
is the neddylation site of cullin proteins which are a
family of structurally related proteins containing an
evolutionarily conserved cullin domain. With the
exception of APC2, each member of the cullin family is
modified by Nedd8 and several cullins function in
Ubiquitin-dependent proteolysis, a process in which the
26S proteasome recognises and subsequently degrades a
target protein tagged with K48-linked poly-ubiquitin
chains. Cullins are molecular scaffolds responsible for
assembling the ROC1/Rbx1 RING-based E3 ubiquitin
ligases, of which several play a direct role in
tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like
protein, which was originally found to be conjugated to
Cdc53, a cullin component of the SCF
(Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in
Saccharomyces cerevisiae, and Nedd8 modification has now
emerged as a regulatory pathway of fundamental
importance for cell cycle control and for embryogenesis
in metazoans. The only identified Nedd8 substrates are
cullins. Neddylation results in covalent conjugation of
a Nedd8 moiety onto a conserved cullin lysine residue.
Length = 68
Score = 99.2 bits (248), Expect = 1e-28
Identities = 40/68 (58%), Positives = 51/68 (75%), Gaps = 1/68 (1%)
Query: 61 VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYV 119
V+EDRKL +QAAIVRIMKSRK + HN L+ EV+ Q K F PS++ IKK IESLI+K Y+
Sbjct: 1 VEEDRKLEIQAAIVRIMKSRKTLSHNELVAEVIEQLKKRFPPSVADIKKRIESLIEKEYL 60
Query: 120 ERTANSTD 127
ER + +
Sbjct: 61 ERDEDDRN 68
>gnl|CDD|214883 smart00884, Cullin_Nedd8, Cullin protein neddylation domain. This
is the neddylation site of cullin proteins which are a
family of structurally related proteins containing an
evolutionarily conserved cullin domain. With the
exception of APC2, each member of the cullin family is
modified by Nedd8 and several cullins function in
Ubiquitin-dependent proteolysis, a process in which the
26S proteasome recognises and subsequently degrades a
target protein tagged with K48-linked poly-ubiquitin
chains. Cullins are molecular scaffolds responsible for
assembling the ROC1/Rbx1 RING-based E3 ubiquitin
ligases, of which several play a direct role in
tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like
protein, which was originally found to be conjugated to
Cdc53, a cullin component of the SCF
(Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in
Saccharomyces cerevisiae, and Nedd8 modification has now
emerged as a regulatory pathway of fundamental
importance for cell cycle control and for embryogenesis
in metazoans. The only identified Nedd8 substrates are
cullins. Neddylation results in covalent conjugation of
a Nedd8 moiety onto a conserved cullin lysine residue.
Length = 68
Score = 94.9 bits (237), Expect = 5e-27
Identities = 39/68 (57%), Positives = 51/68 (75%), Gaps = 1/68 (1%)
Query: 61 VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYV 119
V+EDRKL +QAAIVRIMKSRK + H+ L+ EV+ Q K F PS+S IKK IESLI++ Y+
Sbjct: 1 VEEDRKLEIQAAIVRIMKSRKTLSHSELVSEVIEQLKKRFKPSVSDIKKRIESLIEREYL 60
Query: 120 ERTANSTD 127
ER + +
Sbjct: 61 ERDEDDPN 68
>gnl|CDD|227934 COG5647, COG5647, Cullin, a subunit of E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 773
Score = 97.2 bits (242), Expect = 1e-24
Identities = 50/135 (37%), Positives = 86/135 (63%), Gaps = 5/135 (3%)
Query: 3 TDNSMDGSCPGYIISV---KELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVS 59
SC ++ + K ++ +T+ +N +++K ++KI+ + E Q+ T
Sbjct: 640 KRVLQSLSCAKLVVLLKDDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHE 699
Query: 60 SVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNY 118
+V+EDR+ LQA IVRIMK+RK+++H L++EV++Q KS F P +SM+K+ IE+LI+K Y
Sbjct: 700 TVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEY 759
Query: 119 VERTANSTDEYSYVA 133
+ER A+ + Y Y+A
Sbjct: 760 LERQADD-EIYVYLA 773
>gnl|CDD|239442 cd03326, MR_like_1, Mandelate racemase (MR)-like subfamily of the
enolase superfamily, subgroup 1. Enzymes of this
subgroup share three conserved carboxylate ligands for
the essential divalent metal ion (usually Mg2+), two
aspartates and a glutamate, and conserved catalytic
residues, a Lys-X-Lys motif and a conserved
histidine-aspartate dyad. This subgroup's function is
unknown.
Length = 385
Score = 28.9 bits (65), Expect = 0.80
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 26 EIR--LNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQA 71
E+R L+ GY K+KI GA E + IE + + + +L + A
Sbjct: 167 EMRRYLDRGYT--VVKIKIGGAPLDEDLRRIEAALDVLGDGARLAVDA 212
>gnl|CDD|233620 TIGR01890, N-Ac-Glu-synth, amino-acid N-acetyltransferase. This
model represents a clade of amino-acid
N-acetyltransferases acting mainly on glutamate in the
first step of the "acetylated" ornithine biosynthesis
pathway. For this reason it is also called
N-acetylglutamate synthase. The enzyme may also act on
aspartate [Amino acid biosynthesis, Glutamate family].
Length = 429
Score = 27.5 bits (61), Expect = 2.7
Identities = 12/57 (21%), Positives = 24/57 (42%), Gaps = 7/57 (12%)
Query: 45 AVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKS---RKQI----RHNALIQEVLS 94
+ +PQE+E + + L +A V+ + R I +L+QE+ +
Sbjct: 213 LAAELSPQEVESLAERLGSETTRRLLSAAVKACRGGVHRSHIVSYAEDGSLLQELFT 269
>gnl|CDD|131258 TIGR02203, MsbA_lipidA, lipid A export permease/ATP-binding protein
MsbA. This family consists of a single polypeptide
chain transporter in the ATP-binding cassette (ABC)
transporter family, MsbA, which exports lipid A. It may
also act in multidrug resistance. Lipid A, a part of
lipopolysaccharide, is found in the outer leaflet of the
outer membrane of most Gram-negative bacteria. Members
of this family are restricted to the Proteobacteria
(although lipid A is more broadly distributed) and often
are clustered with lipid A biosynthesis genes [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides, Transport and
binding proteins, Other].
Length = 571
Score = 26.2 bits (58), Expect = 6.5
Identities = 17/47 (36%), Positives = 30/47 (63%), Gaps = 3/47 (6%)
Query: 36 KRTKLKISGAVQKETPQEI--ERTVSSVDEDRKLYLQAAIVRIMKSR 80
+R +L I+ A+ K+ P I E T S++D + + +QAA+ R+M+ R
Sbjct: 474 QRQRLAIARALLKDAPILILDEAT-SALDNESERLVQAALERLMQGR 519
>gnl|CDD|100039 cd00710, LbH_gamma_CA, Gamma carbonic anhydrases (CA): Carbonic
anhydrases are zinc-containing enzymes that catalyze the
reversible hydration of carbon dioxide in a two-step
mechanism, involving the nucleophilic attack of a
zinc-bound hydroxide ion on carbon dioxide, followed by
the regeneration of the active site by ionization of the
zinc-bound water molecule and removal of a proton from
the active site. They are ubiquitous enzymes involved in
fundamental processes like photosynthesis, respiration,
pH homeostasis and ion transport. There are three
distinct groups of carbonic anhydrases - alpha, beta
and gamma - which show no significant sequence identity
or structural similarity. Gamma CAs are homotrimeric
enzymes, with each subunit containing a left-handed
parallel beta helix (LbH) structural domain.
Length = 167
Score = 25.7 bits (57), Expect = 7.4
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 83 IRHNALIQEVLSQSKSFAPSISMIKK 108
I HNA++ V + P+ ++I
Sbjct: 108 IGHNAVVDGVEIPPGRYVPAGAVITS 133
>gnl|CDD|237103 PRK12447, PRK12447, histidinol dehydrogenase; Reviewed.
Length = 426
Score = 26.0 bits (58), Expect = 7.5
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 7/41 (17%)
Query: 50 TPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQ 90
+ EI+ V+ V E K ++ A Q+R A Q
Sbjct: 59 SAAEIDAAVAKVPEQVKEDIRFAQ-------DQVRRFAEAQ 92
>gnl|CDD|224247 COG1328, NrdD, Oxygen-sensitive ribonucleoside-triphosphate
reductase [Nucleotide transport and metabolism].
Length = 700
Score = 26.2 bits (58), Expect = 7.9
Identities = 18/88 (20%), Positives = 29/88 (32%), Gaps = 12/88 (13%)
Query: 50 TPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRH------NALIQEVLSQSKSFA--P 101
P I+R + DR I + K+ K+I V + A
Sbjct: 2 YPVVIKRDGRVAEFDR----NKIINAVRKAAKEIESFDIAKALIRATGVDEEVARIAREV 57
Query: 102 SISMIKKCIESLIDKNYVERTANSTDEY 129
I I+ +E L+ + A + EY
Sbjct: 58 EIEEIQLLVEYLLMPMINKILARAYIEY 85
>gnl|CDD|221778 pfam12802, MarR_2, MarR family. The Mar proteins are involved in
the multiple antibiotic resistance, a non-specific
resistance system. The expression of the mar operon is
controlled by a repressor, MarR. A large number of
compounds induce transcription of the mar operon. This
is thought to be due to the compound binding to MarR,
and the resulting complex stops MarR binding to the DNA.
With the MarR repression lost, transcription of the
operon proceeds. The structure of MarR is known and
shows MarR as a dimer with each subunit containing a
winged-helix DNA binding motif.
Length = 60
Score = 24.5 bits (54), Expect = 8.2
Identities = 12/58 (20%), Positives = 23/58 (39%), Gaps = 7/58 (12%)
Query: 70 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTD 127
Q ++ + + L L SK ++S + ++ L +K VER + D
Sbjct: 7 QFRVLLALARAGGLTVAELA-RRLGLSKQ---TVSRL---VKRLEEKGLVEREPSPGD 57
>gnl|CDD|233379 TIGR01369, CPSaseII_lrg, carbamoyl-phosphate synthase, large
subunit. Carbamoyl-phosphate synthase (CPSase)
catalyzes the first committed step in pyrimidine,
arginine, and urea biosynthesis. In general, it is a
glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II
in eukaryotes. An exception is the mammalian
mitochondrial urea-cycle form, CPSase I, in which the
glutamine amidotransferase domain active site Cys on the
small subunit has been lost, and the enzyme is
ammonia-dependent. In both CPSase I and the closely
related, glutamine-dependent CPSase III (allosterically
activated by acetyl-glutamate) demonstrated in some
other vertebrates, the small and large chain regions are
fused in a single polypeptide chain. This model
represents the large chain of glutamine-hydrolysing
carbamoyl-phosphate synthases, or the corresponding
regions of larger, multifunctional proteins, as found in
all domains of life, and CPSase I forms are considered
exceptions within the family. In several thermophilic
species (Methanobacterium thermoautotrophicum,
Methanococcus jannaschii, Aquifex aeolicus), the large
subunit appears split, at different points, into two
separate genes [Purines, pyrimidines, nucleosides, and
nucleotides, Pyrimidine ribonucleotide biosynthesis].
Length = 1050
Score = 25.7 bits (57), Expect = 9.0
Identities = 18/97 (18%), Positives = 42/97 (43%), Gaps = 11/97 (11%)
Query: 6 SMDGSCPGYIISVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDR 65
S++ G+ + +E+ D ++ L R I+ A+++ +V + E
Sbjct: 398 SLEIGATGFDLPDREVEPDEDLWRALKKPTDRRIFAIAEALRRGV------SVDEIHELT 451
Query: 66 K-----LYLQAAIVRIMKSRKQIRHNALIQEVLSQSK 97
K L+ IV + + ++++ L E+L ++K
Sbjct: 452 KIDRWFLHKIKNIVDLEEELEEVKLTELDPELLRRAK 488
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
0.312 0.127 0.333
Gapped
Lambda K H
0.267 0.0811 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,256,341
Number of extensions: 533949
Number of successful extensions: 417
Number of sequences better than 10.0: 1
Number of HSP's gapped: 414
Number of HSP's successfully gapped: 33
Length of query: 133
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 47
Effective length of database: 7,123,158
Effective search space: 334788426
Effective search space used: 334788426
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.0 bits)