RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4377
(81 letters)
>gnl|CDD|239729 cd03760, proteasome_beta_type_4, proteasome beta type-4 subunit.
The 20S proteasome, multisubunit proteolytic complex,
is the central enzyme of nonlysosomal protein
degradation in both the cytosol and nucleus. It is
composed of 28 subunits arranged as four homoheptameric
rings that stack on top of one another forming an
elongated alpha-beta-beta-alpha cylinder with a central
cavity. The proteasome alpha and beta subunits are
members of the N-terminal nucleophile (Ntn)-hydrolase
superfamily. Their N-terminal threonine residues are
exposed as a nucleophile in peptide bond
hydrolysis.Mammals have 7 alpha and 7 beta proteasome
subunits while archaea have one of each.
Length = 197
Score = 72.2 bits (178), Expect = 2e-17
Identities = 25/56 (44%), Positives = 38/56 (67%)
Query: 23 ASVFGLQFDRGVLLAADSLVSFEGLALFCNAQRIVKVNESILLGGGNNFADLQYLQ 78
SV +++ GV++AAD+L S+ LA F N +RI KV ++ LLG ++AD QYL+
Sbjct: 3 TSVIAIKYKDGVIIAADTLGSYGSLARFKNVERIFKVGDNTLLGASGDYADFQYLK 58
>gnl|CDD|238893 cd01912, proteasome_beta, proteasome beta subunit. The 20S
proteasome, multisubunit proteolytic complex, is the
central enzyme of nonlysosomal protein degradation in
both the cytosol and nucleus. It is composed of 28
subunits arranged as four homoheptameric rings that
stack on top of one another forming an elongated
alpha-beta-beta-alpha cylinder with a central cavity.
The proteasome alpha and beta subunits are members of
the N-terminal nucleophile (Ntn)-hydrolase superfamily.
Their N-terminal threonine residues are exposed as a
nucleophile in peptide bond hydrolysis. Mammals have 7
alpha and 7 beta proteasome subunits while archaea have
one of each.
Length = 189
Score = 53.6 bits (130), Expect = 2e-10
Identities = 20/56 (35%), Positives = 32/56 (57%)
Query: 24 SVFGLQFDRGVLLAADSLVSFEGLALFCNAQRIVKVNESILLGGGNNFADLQYLQD 79
++ G++ GV+LAAD+ S L N +I K++++ILLG + AD Q L
Sbjct: 2 TIVGIKGKDGVVLAADTRASAGSLVASRNFDKIFKISDNILLGTAGSAADTQALTR 57
>gnl|CDD|238887 cd01906, proteasome_protease_HslV, proteasome_protease_HslV. This
group contains the eukaryotic proteosome alpha and beta
subunits and the prokaryotic protease hslV subunit.
Proteasomes are large multimeric
self-compartmentalizing proteases, involved in the
clearance of misfolded proteins, the breakdown of
regulatory proteins, and the processing of proteins
such as the preparation of peptides for immune
presentation. Two main proteasomal types are
distinguished by their different tertiary structures:
the eukaryotic/archeal 20S proteasome and the
prokaryotic proteasome-like heat shock protein encoded
by heat shock locus V, hslV. The proteasome core
particle is a highly conserved cylindrical structure
made up of non-identical subunits that have their
active sites on the inner walls of a large central
cavity. The proteasome subunits of bacteria, archaea,
and eukaryotes all share a conserved Ntn (N terminal
nucleophile) hydrolase fold and a catalytic mechanism
involving an N-terminal nucleophilic threonine that is
exposed by post-translational processing of an inactive
propeptide.
Length = 182
Score = 46.7 bits (112), Expect = 6e-08
Identities = 16/56 (28%), Positives = 28/56 (50%)
Query: 24 SVFGLQFDRGVLLAADSLVSFEGLALFCNAQRIVKVNESILLGGGNNFADLQYLQD 79
++ G++ GV+LAAD V+ L ++I K+++ I AD Q L +
Sbjct: 2 TIVGIKGKDGVVLAADKRVTSGLLVASSTVEKIFKIDDHIGCAFAGLAADAQTLVE 57
>gnl|CDD|238884 cd01901, Ntn_hydrolase, The Ntn hydrolases (N-terminal
nucleophile) are a diverse superfamily of of enzymes
that are activated autocatalytically via an
N-terminally lcated nucleophilic amino acid.
N-terminal nucleophile (NTN-) hydrolase superfamily,
which contains a four-layered alpha, beta, beta, alpha
core structure. This family of hydrolases includes
penicillin acylase, the 20S proteasome alpha and beta
subunits, and glutamate synthase. The mechanism of
activation of these proteins is conserved, although
they differ in their substrate specificities. All known
members catalyze the hydrolysis of amide bonds in
either proteins or small molecules, and each one of
them is synthesized as a preprotein. For each, an
autocatalytic endoproteolytic process generates a new
N-terminal residue. This mature N-terminal residue is
central to catalysis and acts as both a polarizing base
and a nucleophile during the reaction. The N-terminal
amino group acts as the proton acceptor and activates
either the nucleophilic hydroxyl in a Ser or Thr
residue or the nucleophilic thiol in a Cys residue. The
position of the N-terminal nucleophile in the active
site and the mechanism of catalysis are conserved in
this family, despite considerable variation in the
protein sequences.
Length = 164
Score = 40.5 bits (95), Expect = 1e-05
Identities = 15/54 (27%), Positives = 22/54 (40%)
Query: 24 SVFGLQFDRGVLLAADSLVSFEGLALFCNAQRIVKVNESILLGGGNNFADLQYL 77
+ ++ GV+LAAD +S +I K + I G AD Q L
Sbjct: 2 TSVAIKGKGGVVLAADKRLSSGLPVAGSPVIKIGKNEDGIAWGLAGLAADAQTL 55
>gnl|CDD|223711 COG0638, PRE1, 20S proteasome, alpha and beta subunits
[Posttranslational modification, protein turnover,
chaperones].
Length = 236
Score = 37.7 bits (88), Expect = 2e-04
Identities = 16/54 (29%), Positives = 27/54 (50%)
Query: 24 SVFGLQFDRGVLLAADSLVSFEGLALFCNAQRIVKVNESILLGGGNNFADLQYL 77
+ G++ GV+LAAD + L N ++I K+++ I + AD Q L
Sbjct: 32 TTVGIKGKDGVVLAADKRATSGLLIASSNVEKIFKIDDHIGMAIAGLAADAQVL 85
>gnl|CDD|239733 cd03764, proteasome_beta_archeal, Archeal proteasome, beta
subunit. The 20S proteasome, multisubunit proteolytic
complex, is the central enzyme for non-lysosomal
protein degradation in both the cytosol and the
nucleus. It is composed of 28 subunits arranged as four
homoheptameric rings that stack on top of one another
forming an elongated alpha-beta-beta-alpha cylinder
with a central cavity. The proteasome alpha and beta
subunits are both members of the N-terminal nucleophile
(Ntn)-hydrolase superfamily. Their N-terminal threonine
residues are exposed as a nucleophile in peptide bond
hydrolysis. Mammals have 7 alpha and 7 beta proteasome
subunits while archaea have one of each.
Length = 188
Score = 37.2 bits (87), Expect = 2e-04
Identities = 14/55 (25%), Positives = 25/55 (45%)
Query: 27 GLQFDRGVLLAADSLVSFEGLALFCNAQRIVKVNESILLGGGNNFADLQYLQDSV 81
G+ GV+LAAD S N ++I ++++ I + + D Q L +
Sbjct: 5 GIVCKDGVVLAADKRASMGNFIASKNVKKIFQIDDKIAMTIAGSVGDAQSLVRIL 59
>gnl|CDD|234287 TIGR03634, arc_protsome_B, proteasome endopeptidase complex,
archaeal, beta subunit. This protein family describes
the archaeal proteasome beta subunit, homologous to
both the alpha subunit and to the alpha and beta
subunits of eukaryotic proteasome subunits. This family
is universal in the first 29 complete archaeal genomes
but occasionally is duplicated [Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 185
Score = 36.0 bits (84), Expect = 5e-04
Identities = 14/55 (25%), Positives = 27/55 (49%)
Query: 27 GLQFDRGVLLAADSLVSFEGLALFCNAQRIVKVNESILLGGGNNFADLQYLQDSV 81
G++ GV+LAAD S NA+++ ++++ I + + D Q L +
Sbjct: 6 GIKCKDGVVLAADKRASMGNFVASKNAKKVFQIDDYIAMTIAGSVGDAQSLVRIL 60
>gnl|CDD|215805 pfam00227, Proteasome, Proteasome subunit. The proteasome is a
multisubunit structure that degrades proteins. Protein
degradation is an essential component of regulation
because proteins can become misfolded, damaged, or
unnecessary. Proteasomes and their homologues vary
greatly in complexity: from HslV (heat shock locus v),
which is encoded by 1 gene in bacteria, to the
eukaryotic 20S proteasome, which is encoded by more
than 14 genes. Recently evidence of two novel groups of
bacterial proteasomes was proposed. The first is Anbu,
which is sparsely distributed among cyanobacteria and
proteobacteria. The second is call beta-proteobacteria
proteasome homologue (BPH).
Length = 188
Score = 35.6 bits (83), Expect = 7e-04
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 24 SVFGLQFDRGVLLAADSLVSFEGLALF-CNAQRIVKVNESILLGGGNNFADLQYL 77
++ G++ GV+LAAD + L ++I K+++ I + AD Q L
Sbjct: 6 TIVGIKGKDGVVLAADKRATRGSKLLSKDTVEKIFKIDDHIGMAFAGLAADAQTL 60
>gnl|CDD|239731 cd03762, proteasome_beta_type_6, proteasome beta type-6 subunit.
The 20S proteasome, multisubunit proteolytic complex,
is the central enzyme of nonlysosomal protein
degradation in both the cytosol and nucleus. It is
composed of 28 subunits arranged as four homoheptameric
rings that stack on top of one another forming an
elongated alpha-beta-beta-alpha cylinder with a central
cavity. The proteasome alpha and beta subunits are
members of the N-terminal nucleophile (Ntn)-hydrolase
superfamily. Their N-terminal threonine residues are
exposed as a nucleophile in peptide bond hydrolysis.
Mammals have 7 alpha and 7 beta proteasome subunits
while archaea have one of each.
Length = 188
Score = 28.0 bits (63), Expect = 0.40
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 24 SVFGLQFDRGVLLAADSLVS 43
++ +++D GV+L ADS S
Sbjct: 2 TIIAVEYDGGVVLGADSRTS 21
>gnl|CDD|219237 pfam06951, PLA2G12, Group XII secretory phospholipase A2
precursor (PLA2G12). This family consists of several
group XII secretory phospholipase A2 precursor
(PLA2G12) (EC:3.1.1.4) proteins. Group XII and group V
PLA(2)s are thought to participate in helper T cell
immune response through release of immediate second
signals and generation of downstream eicosanoids.
Length = 186
Score = 27.0 bits (60), Expect = 0.87
Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 11 KPAVQPPQPLSCAS-VFGLQFDRGV 34
+P +PP P C S +FGL+ D G+
Sbjct: 73 RPGYRPPPPNGCGSPLFGLKMDIGI 97
>gnl|CDD|179990 PRK05282, PRK05282, (alpha)-aspartyl dipeptidase; Validated.
Length = 233
Score = 26.4 bits (59), Expect = 1.6
Identities = 10/38 (26%), Positives = 19/38 (50%)
Query: 42 VSFEGLALFCNAQRIVKVNESILLGGGNNFADLQYLQD 79
+ G+ + ++ E+I +GGGN F L+ L +
Sbjct: 62 IEVTGIHRVADPVAAIENAEAIFVGGGNTFQLLKQLYE 99
>gnl|CDD|233144 TIGR00835, agcS, amino acid carrier protein. The Alanine or
Glycine: Cation Symporter (AGCS) Family (TC 2.A.25)
Members of the AGCS family transport alanine and/or
glycine in symport with Na+ and or H+.
Length = 425
Score = 26.1 bits (58), Expect = 1.9
Identities = 11/48 (22%), Positives = 20/48 (41%)
Query: 17 PQPLSCASVFGLQFDRGVLLAADSLVSFEGLALFCNAQRIVKVNESIL 64
Q + AS F+ L+ L L +F +RI K++ ++
Sbjct: 149 VQANAIASALSNAFNVPKLVTGIVLTVLTALIIFGGLKRIAKISSVVV 196
>gnl|CDD|239727 cd03758, proteasome_beta_type_2, proteasome beta type-2 subunit.
The 20S proteasome, multisubunit proteolytic complex,
is the central enzyme of nonlysosomal protein
degradation in both the cytosol and nucleus. It is
composed of 28 subunits arranged as four homoheptameric
rings that stack on top of one another forming an
elongated alpha-beta-beta-alpha cylinder with a central
cavity. The proteasome alpha and beta subunits are
members of the N-terminal nucleophile (Ntn)-hydrolase
superfamily. Their N-terminal threonine residues are
exposed as a nucleophile in peptide bond
hydrolysis.Mammals have 7 alpha and 7 beta proteasome
subunits while archaea have one of each.
Length = 193
Score = 26.0 bits (58), Expect = 2.1
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 8/64 (12%)
Query: 24 SVFGLQFDRGVLLAADSLVSFEGLALFCNAQRIVKVNESILL------GGGNNFADLQYL 77
++ G++ V+LAAD+ + L L + +I K+++ L+ G FA+ Y+
Sbjct: 3 TLIGIKGKDFVILAADTSAARSILVLKDDEDKIYKLSDHKLMACSGEAGDRLQFAE--YI 60
Query: 78 QDSV 81
Q ++
Sbjct: 61 QKNI 64
>gnl|CDD|234807 PRK00648, PRK00648, Maf-like protein; Reviewed.
Length = 191
Score = 25.6 bits (57), Expect = 2.3
Identities = 8/44 (18%), Positives = 19/44 (43%), Gaps = 3/44 (6%)
Query: 9 KAKPAVQPPQPLSC---ASVFGLQFDRGVLLAADSLVSFEGLAL 49
+ + L+ +V F +++ AD++V ++G L
Sbjct: 39 YSLDPEEITLELARLKAEAVRSDLFPDELIITADTIVWYDGKVL 82
>gnl|CDD|239730 cd03761, proteasome_beta_type_5, proteasome beta type-5 subunit.
The 20S proteasome, multisubunit proteolytic complex,
is the central enzyme of nonlysosomal protein
degradation in both the cytosol and nucleus. It is
composed of 28 subunits arranged as four homoheptameric
rings that stack on top of one another forming an
elongated alpha-beta-beta-alpha cylinder with a central
cavity. The proteasome alpha and beta subunits are
members of the N-terminal nucleophile (Ntn)-hydrolase
superfamily. Their N-terminal threonine residues are
exposed as a nucleophile in peptide bond hydrolysis.
Mammals have 7 alpha and 7 beta proteasome subunits
while archaea have one of each.
Length = 188
Score = 25.7 bits (57), Expect = 2.7
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 27 GLQFDRGVLLAADSLVSFEGLALFCNAQRIVKVNESIL--LGGGNNFADLQY 76
F GV++A DS + ++++++N +L + GG AD QY
Sbjct: 5 AFIFQGGVIVAVDSRATAGSYIASQTVKKVIEINPYLLGTMAGGA--ADCQY 54
>gnl|CDD|224604 COG1690, RtcB, Uncharacterized conserved protein [Function
unknown].
Length = 432
Score = 25.0 bits (55), Expect = 4.8
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 65 LGGGNNFADLQYLQD 79
LG GN+F ++Q +
Sbjct: 178 LGSGNHFLEVQAVDR 192
>gnl|CDD|213769 TIGR03073, release_rtcB, release factor H-coupled RctB family
protein. Members of this family are related to RctB.
RctB a protein of known structure but unknown function
that often is encoded near RNA cyclase and therefore is
suggested to be a tRNA or mRNA processing enzyme. This
family of RctB-like proteins in encoded upstream of, and
apparently is translationally coupled to, the putative
peptide chain release factor RF-H (TIGR03072), product
of the prfH gene. Note that a large deletion at the
junction between this gene and the prfH gene in
Escherichia coli K-12 marks both as probable pseudogenes
[Protein synthesis, Other].
Length = 356
Score = 24.7 bits (54), Expect = 7.0
Identities = 8/13 (61%), Positives = 12/13 (92%)
Query: 65 LGGGNNFADLQYL 77
+GGGN+FA+LQ +
Sbjct: 121 IGGGNHFAELQQV 133
>gnl|CDD|216324 pfam01139, UPF0027, Uncharacterized protein family UPF0027.
Length = 419
Score = 24.5 bits (54), Expect = 7.1
Identities = 7/12 (58%), Positives = 10/12 (83%)
Query: 65 LGGGNNFADLQY 76
LGGGN+F ++Q
Sbjct: 157 LGGGNHFIEIQV 168
>gnl|CDD|237690 PRK14365, PRK14365, Maf-like protein; Provisional.
Length = 197
Score = 24.4 bits (53), Expect = 8.7
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 28 LQFDRGVLLAADSLVSFEGLAL 49
FD G++++AD+ V G L
Sbjct: 59 KHFDSGIIISADTSVFCNGEVL 80
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
0.322 0.138 0.411
Gapped
Lambda K H
0.267 0.0533 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,883,851
Number of extensions: 291199
Number of successful extensions: 185
Number of sequences better than 10.0: 1
Number of HSP's gapped: 184
Number of HSP's successfully gapped: 21
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
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 (21.9 bits)
S2: 53 (24.6 bits)