RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9489
(279 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 = 174 bits (444), Expect = 2e-54
Identities = 60/115 (52%), Positives = 81/115 (70%), Gaps = 1/115 (0%)
Query: 166 TGTSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILGAGNDYADFQYLNDI 225
TGTSV+ + + GVI+AAD+ G YGS+ RF + RI ++ T+LGA DYADFQYL +
Sbjct: 1 TGTSVIAIKYKDGVIIAADTLGSYGSLARFKNVERIFKVGDNTLLGASGDYADFQYLKRL 60
Query: 226 VKQKILDDDLHNDGFVLKPKSLHSWLTRVLYNRRSQFDPLWINAFVAGMQN-GEP 279
+ Q ++DD+ +DG L PK +HS+LTRVLYNRRS+ +PLW V G+ N GEP
Sbjct: 61 LDQLVIDDECLDDGHSLSPKEIHSYLTRVLYNRRSKMNPLWNTLVVGGVDNEGEP 115
Score = 101 bits (254), Expect = 3e-26
Identities = 32/66 (48%), Positives = 45/66 (68%)
Query: 97 TGTSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILGAGNDYADFQYLNDI 156
TGTSV+ + + GVI+AAD+ G YGS+ RF + RI ++ T+LGA DYADFQYL +
Sbjct: 1 TGTSVIAIKYKDGVIIAADTLGSYGSLARFKNVERIFKVGDNTLLGASGDYADFQYLKRL 60
Query: 157 VKQKIT 162
+ Q +
Sbjct: 61 LDQLVI 66
Score = 99.2 bits (248), Expect = 3e-25
Identities = 39/66 (59%), Positives = 50/66 (75%)
Query: 1 FLGTVDKLGTAYEDKILSFGFGTHIAVPLLRQETEKNPQMSKEEAIALIKTCMDLLYVRD 60
FLG VD LGTAYED ++ GFG ++A+PLLR+ EK P +++EEA ALI+ CM +LY RD
Sbjct: 116 FLGYVDLLGTAYEDPHVATGFGAYLALPLLREAWEKKPDLTEEEARALIEECMKVLYYRD 175
Query: 61 ARSGAK 66
ARS K
Sbjct: 176 ARSINK 181
>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 = 102 bits (257), Expect = 1e-26
Identities = 31/111 (27%), Positives = 58/111 (52%), Gaps = 3/111 (2%)
Query: 168 TSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILGAGNDYADFQYLNDIVK 227
T+++G+ GV+LAAD+ GS++ + +I +I+ +LG AD Q L ++K
Sbjct: 1 TTIVGIKGKDGVVLAADTRASAGSLVASRNFDKIFKISDNILLGTAGSAADTQALTRLLK 60
Query: 228 QKILDDDLHNDGFVLKPKSLHSWLTRVLYNRRSQFDPLWINAFVAGMQNGE 278
+ + +L N L K+ + L+ +LY+ R P +++ V G+ G
Sbjct: 61 RNLRLYELRNGRE-LSVKAAANLLSNILYSYR--GFPYYVSLIVGGVDKGG 108
Score = 70.9 bits (175), Expect = 6e-15
Identities = 19/63 (30%), Positives = 36/63 (57%)
Query: 99 TSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILGAGNDYADFQYLNDIVK 158
T+++G+ GV+LAAD+ GS++ + +I +I+ +LG AD Q L ++K
Sbjct: 1 TTIVGIKGKDGVVLAADTRASAGSLVASRNFDKIFKISDNILLGTAGSAADTQALTRLLK 60
Query: 159 QKI 161
+ +
Sbjct: 61 RNL 63
Score = 64.8 bits (159), Expect = 1e-12
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 1 FLGTVDKLGTAYEDKILSFGFGTHIAVPLLRQETEKNPQMSKEEAIALIKTCMDLLYVRD 60
FL VD LG+ E ++ G G+ A +L + + + M+ EEA+ L+K +D RD
Sbjct: 111 FLYYVDPLGSLIEAPFVATGSGSKYAYGILDRGYKPD--MTLEEAVELVKKAIDSAIERD 168
Query: 61 ARSG 64
SG
Sbjct: 169 LSSG 172
>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 = 81.4 bits (202), Expect = 9e-19
Identities = 25/111 (22%), Positives = 48/111 (43%), Gaps = 1/111 (0%)
Query: 168 TSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILGAGNDYADFQYLNDIVK 227
T+++G+ GV+LAAD G ++ + +I +I+ AD Q L + ++
Sbjct: 1 TTIVGIKGKDGVVLAADKRVTSGLLVASSTVEKIFKIDDHIGCAFAGLAADAQTLVERLR 60
Query: 228 QKILDDDLHNDGFVLKPKSLHSWLTRVLYNRRSQFDPLWINAFVAGMQNGE 278
++ G + ++L L +LY PL ++ VAG+
Sbjct: 61 KE-AQLYRLRYGEPIPVEALAKLLANLLYEYTQSLRPLGVSLLVAGVDEEG 110
Score = 57.1 bits (139), Expect = 4e-10
Identities = 15/63 (23%), Positives = 31/63 (49%)
Query: 99 TSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILGAGNDYADFQYLNDIVK 158
T+++G+ GV+LAAD G ++ + +I +I+ AD Q L + ++
Sbjct: 1 TTIVGIKGKDGVVLAADKRVTSGLLVASSTVEKIFKIDDHIGCAFAGLAADAQTLVERLR 60
Query: 159 QKI 161
++
Sbjct: 61 KEA 63
Score = 52.9 bits (128), Expect = 1e-08
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 2/64 (3%)
Query: 1 FLGTVDKLGTAYEDKILSFGFGTHIAVPLLRQETEKNPQMSKEEAIALIKTCMDLLYVRD 60
L +VD G+ E K + G G+ A+ +L + + + M+ EEAI L + RD
Sbjct: 113 QLYSVDPSGSYIEYKATAIGSGSQYALGILEKLYKPD--MTLEEAIELALKALKSALERD 170
Query: 61 ARSG 64
SG
Sbjct: 171 LYSG 174
>gnl|CDD|223711 COG0638, PRE1, 20S proteasome, alpha and beta subunits
[Posttranslational modification, protein turnover,
chaperones].
Length = 236
Score = 61.9 bits (151), Expect = 2e-11
Identities = 26/114 (22%), Positives = 49/114 (42%), Gaps = 1/114 (0%)
Query: 166 TGTSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILGAGNDYADFQYLNDI 225
GT+ +G+ GV+LAAD G ++ ++ +I +I+ + AD Q L
Sbjct: 29 GGTTTVGIKGKDGVVLAADKRATSGLLIASSNVEKIFKIDDHIGMAIAGLAADAQVLVRY 88
Query: 226 VKQKILDDDLHNDGFVLKPKSLHSWLTRVLYNRRSQFDPLWINAFVAGMQNGEP 279
+ + G + ++L L+ +L P ++ VAG+ +G P
Sbjct: 89 ARAEAQ-LYRLRYGEPISVEALAKLLSNILQEYTQSGRPYGVSLLVAGVDDGGP 141
Score = 50.8 bits (122), Expect = 2e-07
Identities = 16/66 (24%), Positives = 30/66 (45%)
Query: 97 TGTSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILGAGNDYADFQYLNDI 156
GT+ +G+ GV+LAAD G ++ ++ +I +I+ + AD Q L
Sbjct: 29 GGTTTVGIKGKDGVVLAADKRATSGLLIASSNVEKIFKIDDHIGMAIAGLAADAQVLVRY 88
Query: 157 VKQKIT 162
+ +
Sbjct: 89 ARAEAQ 94
Score = 43.4 bits (103), Expect = 4e-05
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 5 VDKLGTAYEDKILSFGFGTHIAVPLLRQETEKNPQMSKEEAIALIKTCMDLLYVRDARSG 64
D G+ E K + G G+ A L +E ++ +S EEAI L + RDA SG
Sbjct: 146 TDPSGSYNEYKATAIGSGSQFAYGFLEKEYRED--LSLEEAIELAVKALRAAIERDAASG 203
Query: 65 AKN 67
Sbjct: 204 GGI 206
>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 = 60.5 bits (147), Expect = 2e-11
Identities = 26/112 (23%), Positives = 44/112 (39%), Gaps = 2/112 (1%)
Query: 168 TSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILGAGNDYADFQYLNDIVK 227
++ + + GGV+LAAD G + + +I + G AD Q L ++
Sbjct: 1 STSVAIKGKGGVVLAADKRLSSGLPVAGSPVIKIGKNEDGIAWGLAGLAADAQTLVRRLR 60
Query: 228 QKILDDDLHNDGFVLKPKSLHSWLTRVLYNRRSQFDPLWINAFVAGMQNGEP 279
+ L G + +L L ++L Q P +N VAG+ G
Sbjct: 61 EA-LQLYRLRYGEPISVVALAKELAKLLQVYT-QGRPFGVNLIVAGVDEGGG 110
Score = 43.5 bits (103), Expect = 2e-05
Identities = 14/63 (22%), Positives = 27/63 (42%)
Query: 99 TSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILGAGNDYADFQYLNDIVK 158
++ + + GGV+LAAD G + + +I + G AD Q L ++
Sbjct: 1 STSVAIKGKGGVVLAADKRLSSGLPVAGSPVIKIGKNEDGIAWGLAGLAADAQTLVRRLR 60
Query: 159 QKI 161
+ +
Sbjct: 61 EAL 63
Score = 32.0 bits (73), Expect = 0.16
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 1 FLGTVDKLGTAYED-KILSFGFGTHIAVPLLRQETEKNPQMSKEEAIALIKTCMD 54
L +D G E+ ++ G + A LL E P M+ EEA+ L +
Sbjct: 111 NLYYIDPSGPVIENPGAVATGSRSQRAKSLL--EKLYKPDMTLEEAVELALKALK 163
>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 = 58.4 bits (142), Expect = 2e-10
Identities = 26/117 (22%), Positives = 49/117 (41%), Gaps = 4/117 (3%)
Query: 166 TGTSVLGLVFNGGVILAADSAGYYGSMMRF-NDCPRIMQINKFTILGAGNDYADFQYLND 224
TGT+++G+ GV+LAAD GS + + +I +I+ + AD Q L D
Sbjct: 3 TGTTIVGIKGKDGVVLAADKRATRGSKLLSKDTVEKIFKIDDHIGMAFAGLAADAQTLVD 62
Query: 225 IVKQKILDDDLHNDGFVLKPKSLHSWLTRVLYN-RRSQFDPLWINAFVAGM-QNGEP 279
+ + G + + ++ + S P ++ +AG ++G P
Sbjct: 63 YARAE-AQLYRLRYGRPISVELAKRIADKLQAYTQYSGRRPYGVSLLIAGYDEDGGP 118
Score = 55.7 bits (135), Expect = 2e-09
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 97 TGTSVLGLVFNGGVILAADSAGYYGSMMRF-NDCPRIMQINKFTILGAGNDYADFQYLND 155
TGT+++G+ GV+LAAD GS + + +I +I+ + AD Q L D
Sbjct: 3 TGTTIVGIKGKDGVVLAADKRATRGSKLLSKDTVEKIFKIDDHIGMAFAGLAADAQTLVD 62
Query: 156 IVKQKI 161
+ +
Sbjct: 63 YARAEA 68
Score = 47.6 bits (114), Expect = 1e-06
Identities = 21/64 (32%), Positives = 29/64 (45%), Gaps = 2/64 (3%)
Query: 1 FLGTVDKLGTAYEDKILSFGFGTHIAVPLLRQETEKNPQMSKEEAIALIKTCMDLLYVRD 60
L ++D G+ E K + G G+ A L E P M+ EEA+ L + RD
Sbjct: 119 HLYSIDPSGSVIEYKATAIGSGSQYAYGFL--EKLYKPDMTLEEAVELAVKALKEAIERD 176
Query: 61 ARSG 64
A SG
Sbjct: 177 ALSG 180
>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 = 39.9 bits (94), Expect = 5e-04
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 1 FLGTVDKLGTAYEDKILSFGFGTHIAVPLLRQETEKNPQMSKEEAIALIKTCMDLLYVR 59
L +D LGT + + G+G + + +L + P M+ EEA+ L+K C+ L R
Sbjct: 114 SLYYIDYLGTLVKVPYAAHGYGAYFCLSIL--DRYYKPDMTVEEALELMKKCIKELKKR 170
Score = 33.3 bits (77), Expect = 0.067
Identities = 24/106 (22%), Positives = 53/106 (50%), Gaps = 3/106 (2%)
Query: 169 SVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILGAGNDYADFQYLNDIVKQ 228
+++G+ VILAAD++ ++ +D +I +++ ++ + D + +++
Sbjct: 3 TLIGIKGKDFVILAADTSAARSILVLKDDEDKIYKLSDHKLMACSGEAGDRLQFAEYIQK 62
Query: 229 KILDDDLHNDGFVLKPKSLHSWLTRVL-YNRRSQFDPLWINAFVAG 273
I + N G+ L PK+ ++ R L + RS+ P +N +AG
Sbjct: 63 NIQLYKMRN-GYELSPKAAANFTRRELAESLRSR-TPYQVNLLLAG 106
>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 = 38.7 bits (91), Expect = 0.001
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 98 GTSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQIN-KFTILGAGNDYADFQYLNDI 156
GT+ +G+ GV+LAAD G+ + + ++ QI+ + AG D Q L I
Sbjct: 1 GTTTVGIKCKDGVVLAADKRASMGNFVASKNAKKVFQIDDYIAMTIAG-SVGDAQSLVRI 59
Query: 157 VK 158
+K
Sbjct: 60 LK 61
Score = 38.7 bits (91), Expect = 0.001
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 167 GTSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQIN-KFTILGAGNDYADFQYLNDI 225
GT+ +G+ GV+LAAD G+ + + ++ QI+ + AG D Q L I
Sbjct: 1 GTTTVGIKCKDGVVLAADKRASMGNFVASKNAKKVFQIDDYIAMTIAG-SVGDAQSLVRI 59
Query: 226 VK 227
+K
Sbjct: 60 LK 61
Score = 34.1 bits (79), Expect = 0.037
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 10/65 (15%)
Query: 4 TVDKLGTAYEDKILSFGFGTHIAVPLLRQETEKNPQMSKEEAIAL----IKTCMDLLYVR 59
++D G ED + G G+ +A +L E E MS EEA L IK+ ++ R
Sbjct: 114 SLDPAGGIIEDDYTATGSGSPVAYGVL--EDEYREDMSVEEAKKLAVRAIKSAIE----R 167
Query: 60 DARSG 64
D SG
Sbjct: 168 DVASG 172
>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 = 0.004
Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 10/67 (14%)
Query: 2 LGTVDKLGTAYEDKILSFGFGTHIAVPLLRQETEKNPQMSKEEAIAL----IKTCMDLLY 57
L ++D LG+ EDK + G G+ A +L E E M+ EEA L IK+ ++
Sbjct: 111 LYSLDPLGSIIEDKYTATGSGSPYAYGVL--EDEYKEDMTVEEAKKLAIRAIKSAIE--- 165
Query: 58 VRDARSG 64
RD+ SG
Sbjct: 166 -RDSASG 171
Score = 36.8 bits (86), Expect = 0.005
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 99 TSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQIN-KFTILGAGNDYADFQYLNDIV 157
T+ +G+V GV+LAAD G+ + + +I QI+ K + AG D Q L I+
Sbjct: 1 TTTVGIVCKDGVVLAADKRASMGNFIASKNVKKIFQIDDKIAMTIAG-SVGDAQSLVRIL 59
Query: 158 K 158
K
Sbjct: 60 K 60
Score = 36.8 bits (86), Expect = 0.005
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 168 TSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQIN-KFTILGAGNDYADFQYLNDIV 226
T+ +G+V GV+LAAD G+ + + +I QI+ K + AG D Q L I+
Sbjct: 1 TTTVGIVCKDGVVLAADKRASMGNFIASKNVKKIFQIDDKIAMTIAG-SVGDAQSLVRIL 59
Query: 227 K 227
K
Sbjct: 60 K 60
>gnl|CDD|185666 PTZ00488, PTZ00488, Proteasome subunit beta type-5; Provisional.
Length = 247
Score = 37.7 bits (87), Expect = 0.004
Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 8/72 (11%)
Query: 78 PNVLPHYFRRSGSFSTP-------LTTGTSVLGLVFNGGVILAADSAGYYGSMMRFNDCP 130
P P F +F GT+ L + GG+I+A DS G +
Sbjct: 12 PGAHPGDFLAEYTFDHGDANKAIEFAHGTTTLAFKYGGGIIIAVDSKATAGPYIASQSVK 71
Query: 131 RIMQINKFTILG 142
++++IN T+LG
Sbjct: 72 KVIEINP-TLLG 82
Score = 33.8 bits (77), Expect = 0.074
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 167 GTSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILG 211
GT+ L + GG+I+A DS G + ++++IN T+LG
Sbjct: 39 GTTTLAFKYGGGIIIAVDSKATAGPYIASQSVKKVIEINP-TLLG 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 = 36.8 bits (86), Expect = 0.005
Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 4/56 (7%)
Query: 99 TSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILG--AGNDYADFQY 152
T+ L +F GGVI+A DS GS + ++++IN + +LG AG AD QY
Sbjct: 1 TTTLAFIFQGGVIVAVDSRATAGSYIASQTVKKVIEINPY-LLGTMAGGA-ADCQY 54
Score = 36.8 bits (86), Expect = 0.005
Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 4/56 (7%)
Query: 168 TSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILG--AGNDYADFQY 221
T+ L +F GGVI+A DS GS + ++++IN + +LG AG AD QY
Sbjct: 1 TTTLAFIFQGGVIVAVDSRATAGSYIASQTVKKVIEINPY-LLGTMAGGA-ADCQY 54
>gnl|CDD|239726 cd03757, proteasome_beta_type_1, proteasome beta type-1 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 = 212
Score = 35.7 bits (83), Expect = 0.015
Identities = 28/110 (25%), Positives = 52/110 (47%), Gaps = 9/110 (8%)
Query: 167 GTSVLGLVFNGGVILAAD---SAGYYGSMMRFNDCPRIMQINKFTILGAGNDYADFQYLN 223
G +VL + N ++A D S GY + D P+I ++ +LG+ AD L
Sbjct: 8 GGTVLAIAGNDFAVIAGDTRLSEGY---SILSRDSPKIFKLTDKCVLGSSGFQADILALT 64
Query: 224 DIVKQKILDDDLHNDGFVLKPKSLHSWLTRVLYNRRSQFDPLWINAFVAG 273
+K +I ++ + +++ L+ +LY+RR F P ++ +AG
Sbjct: 65 KRLKARIKMYK-YSHNKEMSTEAIAQLLSTILYSRR--FFPYYVFNILAG 111
Score = 30.7 bits (70), Expect = 0.68
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 6/68 (8%)
Query: 98 GTSVLGLVFNGGVILAAD---SAGYYGSMMRFNDCPRIMQINKFTILGAGNDYADFQYLN 154
G +VL + N ++A D S GY + D P+I ++ +LG+ AD L
Sbjct: 8 GGTVLAIAGNDFAVIAGDTRLSEGY---SILSRDSPKIFKLTDKCVLGSSGFQADILALT 64
Query: 155 DIVKQKIT 162
+K +I
Sbjct: 65 KRLKARIK 72
>gnl|CDD|239732 cd03763, proteasome_beta_type_7, proteasome beta type-7 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 = 33.7 bits (78), Expect = 0.057
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 99 TSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQI-NKFTILGAG 144
T+++G+VF GV+L AD+ G ++ +C +I I GAG
Sbjct: 1 TTIVGVVFKDGVVLGADTRATEGPIVADKNCEKIHYIAPNIYCCGAG 47
Score = 33.7 bits (78), Expect = 0.057
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 168 TSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQI-NKFTILGAG 213
T+++G+VF GV+L AD+ G ++ +C +I I GAG
Sbjct: 1 TTIVGVVFKDGVVLGADTRATEGPIVADKNCEKIHYIAPNIYCCGAG 47
>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 = 33.4 bits (77), Expect = 0.068
Identities = 16/60 (26%), Positives = 30/60 (50%)
Query: 99 TSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILGAGNDYADFQYLNDIVK 158
T+++ + ++GGV+L ADS GS + ++ Q++ AD Q + D V+
Sbjct: 1 TTIIAVEYDGGVVLGADSRTSTGSYVANRVTDKLTQLHDRIYCCRSGSAADTQAIADYVR 60
Score = 33.4 bits (77), Expect = 0.068
Identities = 16/60 (26%), Positives = 30/60 (50%)
Query: 168 TSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILGAGNDYADFQYLNDIVK 227
T+++ + ++GGV+L ADS GS + ++ Q++ AD Q + D V+
Sbjct: 1 TTIIAVEYDGGVVLGADSRTSTGSYVANRVTDKLTQLHDRIYCCRSGSAADTQAIADYVR 60
Score = 31.4 bits (72), Expect = 0.30
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 37 NPQMSKEEAIALIKTCMDLLYVRDARSG 64
P M+ EE I +K + L RD SG
Sbjct: 144 KPGMTLEECIKFVKNALSLAMSRDGSSG 171
>gnl|CDD|239403 cd03150, alpha_CA_IX, Carbonic anhydrase alpha, isozyme IX.
Carbonic anhydrases (CAs) are zinc-containing enzymes
that catalyze the reversible hydration of carbon dioxide
in a two-step mechanism: a 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
evolutionary distinct groups - alpha, beta and gamma
carbonic anhydrases - which show no significant sequence
identity or structural similarity. Alpha CAs are
strictly monomeric enzymes. The zinc ion is complexed by
three histidine residues. This sub-family comprises the
membrane protein CA IX. CA IX is functionally implicated
in tumor growth and survival. CA IX is mainly present in
solid tumors and its expression in normal tissues is
limited to the mucosa of alimentary tract. CA IX is a
transmembrane protein with two extracellular domains:
carbonic anhydrase and, a proteoglycan-like segment
mediating cell-cell adhesion. There is evidence for an
involvement of the MAPK pathway in the regulation of CA9
expression.
Length = 247
Score = 32.2 bits (73), Expect = 0.19
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 69 PSLGKYHDFPNVLPHYFRRSGSFSTPLTTGTSVLGLVFNGGVILAA 114
P L P+ L YFR GS +TP V+ VFN V L+A
Sbjct: 165 PGLDVSALLPSDLSRYFRYEGSLTTPPCAQG-VIWTVFNQTVRLSA 209
>gnl|CDD|226227 COG3704, VirB6, Type IV secretory pathway, VirB6 components
[Intracellular trafficking and secretion].
Length = 406
Score = 32.4 bits (74), Expect = 0.25
Identities = 25/110 (22%), Positives = 36/110 (32%), Gaps = 11/110 (10%)
Query: 84 YFRRSGSFSTPLTTGTSVLGLVFNGGVILAADSAGYYG--SMMRFNDCPRIMQINKFTIL 141
YF G S + GT L + G L A++AGY + I K +
Sbjct: 89 YFVIRGPSSQLILDGTPFLRIKIAGVAALVANAAGYVQTYVFSFLWGALDLR-IAKILGV 147
Query: 142 GAGNDYADFQYLNDIVK--------QKITPLTTGTSVLGLVFNGGVILAA 183
A F I + P + L V NGG+++A
Sbjct: 148 SGLPSAAFFNTYLFIGQILNFDILATSARPFISLLIPLLGVGNGGILVAI 197
>gnl|CDD|239397 cd03123, alpha_CA_VI_IX_XII_XIV, Carbonic anhydrase alpha, isozymes
VI, IX, XII and XIV. Carbonic anhydrases (CAs) are
zinc-containing enzymes that catalyze the reversible
hydration of carbon dioxide in a two-step mechanism: a
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
evolutionary distinct groups - alpha, beta and gamma
carbonic anhydrases - which show no significant sequence
identity or structural similarity. Alpha CAs are mostly
monomeric enzymes. The zinc ion is complexed by three
histidine residues. This sub-family comprises the
secreted CA VI, which is found in saliva, for example,
and the membrane proteins CA IX, XII, and XIV.
Length = 248
Score = 31.1 bits (71), Expect = 0.48
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 77 FPNVLPHYFRRSGSFSTPLTTGTSVLGLVFNGGVILAA 114
P L HY+R GS +TP SVL VF V L+
Sbjct: 175 LPEDLSHYYRYEGSLTTPPCY-ESVLWTVFRDPVTLSK 211
>gnl|CDD|163402 TIGR03690, 20S_bact_beta, proteasome, beta subunit, bacterial type.
Members of this family are the beta subunit of the 20S
proteasome as found in Actinobacteria such as
Mycobacterium, Rhodococcus, and Streptomyces. In
Streptomyces, maturation during proteasome assembly was
shown to remove a 53-amino acid propeptide. Most of the
length of the propeptide is not included in this model
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 219
Score = 30.8 bits (70), Expect = 0.49
Identities = 14/48 (29%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 98 GTSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILG-AG 144
GT+++ L + GGV++A D G+M+ D ++ ++++ +G AG
Sbjct: 2 GTTIVALTYPGGVLMAGDRRATQGNMIASRDVEKVYPTDEYSAVGIAG 49
Score = 30.8 bits (70), Expect = 0.49
Identities = 14/48 (29%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 167 GTSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINKFTILG-AG 213
GT+++ L + GGV++A D G+M+ D ++ ++++ +G AG
Sbjct: 2 GTTIVALTYPGGVLMAGDRRATQGNMIASRDVEKVYPTDEYSAVGIAG 49
>gnl|CDD|176363 cd01768, RA, RA (Ras-associating) ubiquitin domain. The RA
(Ras-associating) domain is structurally similar to
ubiquitin and is present in one or two copies in a
number of signalling molecules that bind and regulate a
small GTPase called Ras or the Ras-related GTPases, Ral
and Rap. RA-containing proteins include RalGDS, AF6,
RIN1, RASSF1, SNX27, CYR1, STE50, and phospholipase C
epsilon.
Length = 87
Score = 28.8 bits (65), Expect = 0.73
Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 198 CPRIMQ--INKFTILGAGNDYADFQYLNDIVKQKILDDD 234
++Q + KF + DYA + L D +++L D
Sbjct: 25 AQDVIQQLLKKFGLDDDPEDYALVEVLGDGGLERLLLPD 63
>gnl|CDD|219952 pfam08645, PNK3P, Polynucleotide kinase 3 phosphatase.
Polynucleotide kinase 3 phosphatases play a role in the
repair of single breaks in DNA induced by DNA-damaging
agents such as gamma radiation and camptothecin.
Length = 158
Score = 28.4 bits (64), Expect = 2.7
Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 14/52 (26%)
Query: 215 DYADFQYLNDIVKQKILDDDLHNDGFVL------------KPKSLHSWLTRV 254
D D+++L V +K+ LH DG+ + KS S+ ++
Sbjct: 23 DADDWKWLYPSVPEKLK--KLHEDGYKIVIFTNQGGISTKGKKSAESFKNKI 72
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 28.9 bits (64), Expect = 3.4
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 3/47 (6%)
Query: 227 KQKILDD---DLHNDGFVLKPKSLHSWLTRVLYNRRSQFDPLWINAF 270
+Q+++D D F+L K+ L + FDP W A
Sbjct: 750 RQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNPAV 796
>gnl|CDD|225198 COG2316, COG2316, Predicted hydrolase (HD superfamily) [General
function prediction only].
Length = 212
Score = 28.3 bits (63), Expect = 4.0
Identities = 7/30 (23%), Positives = 14/30 (46%), Gaps = 5/30 (16%)
Query: 31 RQETEKNPQMSKEEAIALIKTCMDLLYVRD 60
R+ T ++++EA L+K +V
Sbjct: 21 RRRTTIMAAINRDEAYELLKE-----HVPS 45
>gnl|CDD|181465 PRK08557, PRK08557, hypothetical protein; Provisional.
Length = 417
Score = 28.6 bits (64), Expect = 4.5
Identities = 22/63 (34%), Positives = 28/63 (44%), Gaps = 7/63 (11%)
Query: 203 QINKFTILG-AGNDYADFQYLNDIVKQKILDDDLHNDGFVLKPKSLHSWLTRV------L 255
Q N F IL D + YLNDI+ + D G L P +L+S RV L
Sbjct: 313 QTNVFPILDWNSLDIWSYIYLNDILYNPLYDKGFERIGCYLCPSALNSEFLRVKELYPEL 372
Query: 256 YNR 258
+NR
Sbjct: 373 FNR 375
>gnl|CDD|185210 PRK15310, PRK15310, fimbrial outer membrane usher protein TcfC;
Provisional.
Length = 895
Score = 28.0 bits (62), Expect = 7.7
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 57 YVRDARSGAKNGPSLGKYHDFPNVLPHYFRRSGSFSTPLTTG-TSVLGLVFNG 108
Y D+ SG+ G G+ + + + +R+ ++ LT G +S L L NG
Sbjct: 631 YNDDSWSGSLGGRMSGRMGELSATISNSHQRNAGSASSLTAGYSSSLALSRNG 683
>gnl|CDD|234069 TIGR02950, SigM_subfam, RNA polymerase sigma factor, SigM family.
This family of RNA polymerase sigma factors is a member
of the Sigma-70 subfamily (TIGR02937) and is restricted
to certain lineages of the order Bacillales. This family
encompasses at least two distinct sigma factors as two
proteins are found in each of B. anthracis, B. subtilis
subsp. subtilis str. 168, and B. lichiniformis (although
these are not apparently the same two in each). One of
these is designated as SigM in B. subtilis (Swiss_Prot:
SIGM_BACSU) and is activated by various stressors.
Length = 154
Score = 27.0 bits (60), Expect = 8.2
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 8/47 (17%)
Query: 219 FQYLNDIVKQKILDDDLHNDGFV--------LKPKSLHSWLTRVLYN 257
F+YL + K K L +DL + F+ K S+ WL R+ N
Sbjct: 9 FRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKDSSIKPWLFRIARN 55
>gnl|CDD|239399 cd03125, alpha_CA_VI, Carbonic anhydrase alpha, isozyme VI.
Carbonic anhydrases (CAs) are zinc-containing enzymes
that catalyze the reversible hydration of carbon dioxide
in a two-step mechanism: a 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
evolutionary distinct groups - alpha, beta and gamma
carbonic anhydrases - which show no significant sequence
identity or structural similarity. Most alpha CAs are
monomeric enzymes. The zinc ion is complexed by three
histidine residues. This sub-family comprises the
secreted CA VI, which is found in saliva.
Length = 249
Score = 27.4 bits (61), Expect = 8.3
Identities = 25/80 (31%), Positives = 33/80 (41%), Gaps = 12/80 (15%)
Query: 78 PNVLPHYFRRSGSFSTPLTTGTSVLGLVFNGGVILAADSAGYYGSMMRFNDCPRIMQINK 137
P L HY+ GS +TP T +VL VF+ V L+ + +M +
Sbjct: 176 PENLHHYYTYQGSLTTPPCT-ENVLWFVFDDPVTLSKTQIVKLENT--------LMDHHN 226
Query: 138 FTILGAGNDYADFQYLNDIV 157
TI NDY Q LN V
Sbjct: 227 KTIR---NDYRRTQPLNHRV 243
>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional.
Length = 813
Score = 27.8 bits (62), Expect = 8.9
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 35 EKNPQMSKEEAIALIKTCMDLLYVRDARSGAKNG-PSLGKYHDFP 78
E+ Q + +A LI+ CM L + AR K P+L + HD P
Sbjct: 445 ERIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKP 489
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 0.140 0.424
Gapped
Lambda K H
0.267 0.0768 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,751,403
Number of extensions: 1429532
Number of successful extensions: 1288
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1275
Number of HSP's successfully gapped: 59
Length of query: 279
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 183
Effective length of database: 6,679,618
Effective search space: 1222370094
Effective search space used: 1222370094
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: 58 (26.0 bits)