RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10322
(261 letters)
>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 = 266 bits (683), Expect = 1e-90
Identities = 116/256 (45%), Positives = 155/256 (60%), Gaps = 55/256 (21%)
Query: 17 FSPYSDNGGTTVAVAGPDYAIIASDTRLSAGYNIYTREQSKLFDHYYYRPTYNFL----- 71
FSPY+DNGGT +A+AG D+A+IA DTRLS GY+I +R+ K+F + T +
Sbjct: 1 FSPYTDNGGTVLAIAGNDFAVIAGDTRLSEGYSILSRDSPKIF-----KLTDKCVLGSSG 55
Query: 72 MIFTITILP------FQMYLHEHNKVMSTTSLAKMISIMMYGKRFFPYYTSTIIAGLDPE 125
I L +MY + HNK MST ++A+++S ++Y +RFFPYY I+AG+D E
Sbjct: 56 FQADILALTKRLKARIKMYKYSHNKEMSTEAIAQLLSTILYSRRFFPYYVFNILAGIDEE 115
Query: 126 GKGCVYSYDPIGHTERANFRAGGSSGALLQALLDNQVGIIQHSSKQMKSVLGGIRTHDLA 185
GKG VYSYDP+G ER + AGGS+ +L+Q LLDNQV
Sbjct: 116 GKGVVYSYDPVGSYERETYSAGGSASSLIQPLLDNQV----------------------- 152
Query: 186 LTREINALSSKLTILLGFRNQENVDKTPVPLEKAISVVKDAFTAAAERDIYTGDGVHLCA 245
G +NQ NV++TP+ LE+A+S+VKDAFT+AAERDIYTGD + +
Sbjct: 153 ----------------GRKNQNNVERTPLSLEEAVSLVKDAFTSAAERDIYTGDSLEIVI 196
Query: 246 ITKDGIKEYNFPLRKD 261
ITKDGI+E FPLRKD
Sbjct: 197 ITKDGIEEETFPLRKD 212
>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 = 140 bits (355), Expect = 2e-41
Identities = 64/243 (26%), Positives = 98/243 (40%), Gaps = 68/243 (27%)
Query: 25 GTTVAVAGPDYAIIASDTRLSAGYNIYTREQSKLF---DHYYYRPTYNFLMI-------- 73
T V + G D ++A+DTR SAG + +R K+F D+ L
Sbjct: 1 TTIVGIKGKDGVVLAADTRASAGSLVASRNFDKIFKISDN-------ILLGTAGSAADTQ 53
Query: 74 FTITILPFQMYLHE--HNKVMSTTSLAKMISIMMYGKRFFPYYTSTIIAGLDPEGKGCVY 131
+L + L+E + + +S + A ++S ++Y R FPYY S I+ G+D G +Y
Sbjct: 54 ALTRLLKRNLRLYELRNGRELSVKAAANLLSNILYSYRGFPYYVSLIVGGVDKGGGPFLY 113
Query: 132 SYDPIGHTERANFRAGGSSGALLQALLDNQVGIIQHSSKQMKSVLGGIRTHDLALTREIN 191
DP+G A F A GS +LD
Sbjct: 114 YVDPLGSLIEAPFVATGSGSKYAYGILDRGY----------------------------- 144
Query: 192 ALSSKLTILLGFRNQENVDKTPVPLEKAISVVKDAFTAAAERDIYTGDGVHLCAITKDGI 251
+T LE+A+ +VK A +A ERD+ +G GV + ITKDG+
Sbjct: 145 --KPDMT-----------------LEEAVELVKKAIDSAIERDLSSGGGVDVAVITKDGV 185
Query: 252 KEY 254
+E
Sbjct: 186 EEL 188
>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 = 97.6 bits (244), Expect = 4e-25
Identities = 46/236 (19%), Positives = 83/236 (35%), Gaps = 68/236 (28%)
Query: 25 GTTVAVAGPDYAIIASDTRLSAGYNIYTREQSKLFDHYYYRPTYNFLMI----------F 74
T V + G D ++A+D R+++G + + K+F + +
Sbjct: 1 TTIVGIKGKDGVVLAADKRVTSGLLVASSTVEKIF------KIDDHIGCAFAGLAADAQT 54
Query: 75 TITILPF--QMYLHEHNKVMSTTSLAKMISIMMYGKRF--FPYYTSTIIAGLDPEGKGCV 130
+ L Q+Y + + + +LAK+++ ++Y P S ++AG+D EG +
Sbjct: 55 LVERLRKEAQLYRLRYGEPIPVEALAKLLANLLYEYTQSLRPLGVSLLVAGVDEEGGPQL 114
Query: 131 YSYDPIGHTERANFRAGGSSGALLQALLDNQVGIIQHSSKQMKSVLGGIRTHDLALTREI 190
YS DP G A GS +L+
Sbjct: 115 YSVDPSGSYIEYKATAIGSGSQYALGILEKLY---------------------------- 146
Query: 191 NALSSKLTILLGFRNQENVDKTPVPLEKAISVVKDAFTAAAERDIYTGDGVHLCAI 246
+T LE+AI + A +A ERD+Y+G + + I
Sbjct: 147 ---KPDMT-----------------LEEAIELALKALKSALERDLYSGGNIEVAVI 182
>gnl|CDD|223711 COG0638, PRE1, 20S proteasome, alpha and beta subunits
[Posttranslational modification, protein turnover,
chaperones].
Length = 236
Score = 93.1 bits (232), Expect = 6e-23
Identities = 55/252 (21%), Positives = 89/252 (35%), Gaps = 61/252 (24%)
Query: 13 IQHHFSPYSDNGGTTVAVAGPDYAIIASDTRLSAGYNIYTREQSKLF---DHYYYRPTYN 69
+++ G TTV + G D ++A+D R ++G I + K+F DH
Sbjct: 19 VEYALEAVKRGGTTTVGIKGKDGVVLAADKRATSGLLIASSNVEKIFKIDDHIGM--AIA 76
Query: 70 -----FLMIFTITILPFQMYLHEHNKVMSTTSLAKMISIMMYGKRF--FPYYTSTIIAGL 122
++ Q+Y + + +S +LAK++S ++ PY S ++AG+
Sbjct: 77 GLAADAQVLVRYARAEAQLYRLRYGEPISVEALAKLLSNILQEYTQSGRPYGVSLLVAGV 136
Query: 123 DPEGKGCVYSYDPIGHTERANFRAGGSSGALLQALLDNQVGIIQHSSKQMKSVLGGIRTH 182
D G +YS DP G A GS L+ +
Sbjct: 137 DDGG-PRLYSTDPSGSYNEYKATAIGSGSQFAYGFLEKEY-------------------- 175
Query: 183 DLALTREINALSSKLTILLGFRNQENVDKTPVPLEKAISVVKDAFTAAAERDIYTGDGVH 242
L+ LE+AI + A AA ERD +G G+
Sbjct: 176 -----------REDLS-----------------LEEAIELAVKALRAAIERDAASGGGIE 207
Query: 243 LCAITKDGIKEY 254
+ ITKD
Sbjct: 208 VAVITKDEGFRK 219
>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 = 88.0 bits (219), Expect = 2e-21
Identities = 54/239 (22%), Positives = 96/239 (40%), Gaps = 65/239 (27%)
Query: 24 GGTTVAVAGPDYAIIASDTRLSAGYNIYTREQSKLFDHYYYRPTYNFLMIFT-------- 75
G TTV + D ++A+D R S G + ++ K+F + M
Sbjct: 1 GTTTVGIKCKDGVVLAADKRASMGNFVASKNAKKVF-----QIDDYIAMTIAGSVGDAQS 55
Query: 76 -ITILPFQMYLHE--HNKVMSTTSLAKMISIMMYGKRFFPYYTSTIIAGLDPEGKGCVYS 132
+ IL + L+E + MS +LA ++S ++ RFFP+ ++ G+D EG +YS
Sbjct: 56 LVRILKAEAKLYELRRGRPMSVKALATLLSNILNSNRFFPFIVQLLVGGVDEEGPH-LYS 114
Query: 133 YDPIGHTERANFRAGGSSGALLQALLDNQVGIIQHSSKQMKSVLGGIRTHDLALTREINA 192
DP G ++ A GS + +L+++ D++
Sbjct: 115 LDPAGGIIEDDYTATGSGSPVAYGVLEDEY------------------REDMS------- 149
Query: 193 LSSKLTILLGFRNQENVDKTPVPLEKAISVVKDAFTAAAERDIYTGDGVHLCAITKDGI 251
+E+A + A +A ERD+ +G+G+ + ITKDG+
Sbjct: 150 -----------------------VEEAKKLAVRAIKSAIERDVASGNGIDVAVITKDGV 185
>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 = 86.5 bits (215), Expect = 8e-21
Identities = 46/241 (19%), Positives = 76/241 (31%), Gaps = 70/241 (29%)
Query: 22 DNGGTTVAVAGPDYAIIASDTRLSAGYNIYTREQ-SKLF---DHYY---------YRPTY 68
G T V + G D ++A+D R + G + +++ K+F DH +
Sbjct: 2 KTGTTIVGIKGKDGVVLAADKRATRGSKLLSKDTVEKIFKIDDHIGMAFAGLAADAQTLV 61
Query: 69 NFLMIFTITILPFQMYLHEHNKVMS---TTSLAKMISIMMYGKRFFPYYTSTIIAGLDPE 125
++ Q+Y + + +S +A + PY S +IAG D +
Sbjct: 62 DYARAEA------QLYRLRYGRPISVELAKRIADKLQAYTQYSGRRPYGVSLLIAGYDED 115
Query: 126 GKGCVYSYDPIGHTERANFRAGGSSGALLQALLDNQVGIIQHSSKQMKSVLGGIRTHDLA 185
G +YS DP G A GS L+ K K +
Sbjct: 116 GGPHLYSIDPSGSVIEYKATAIGSGSQYAYGFLE----------KLYKPDMT-------- 157
Query: 186 LTREINALSSKLTILLGFRNQENVDKTPVPLEKAISVVKDAFTAAAERDIYTGDGVHLCA 245
LE+A+ + A A ERD +G + +
Sbjct: 158 ------------------------------LEEAVELAVKALKEAIERDALSGGNIEVAV 187
Query: 246 I 246
I
Sbjct: 188 I 188
>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 = 83.8 bits (208), Expect = 8e-20
Identities = 55/235 (23%), Positives = 91/235 (38%), Gaps = 55/235 (23%)
Query: 26 TTVAVAGPDYAIIASDTRLSAGYNIYTREQSKLFD-HYYYRPTY-----NFLMIFTITIL 79
TTV + D ++A+D R S G I ++ K+F T + + I
Sbjct: 2 TTVGIVCKDGVVLAADKRASMGNFIASKNVKKIFQIDDKIAMTIAGSVGDAQSLVRILKA 61
Query: 80 PFQMYLHEHNKVMSTTSLAKMISIMMYGKRFFPYYTSTIIAGLDPEGKGCVYSYDPIGHT 139
++Y + MS +LA ++S ++ ++FPY +I G+D EG +YS DP+G
Sbjct: 62 EARLYELRRGRPMSIKALATLLSNILNSSKYFPYIVQLLIGGVDEEGPH-LYSLDPLGSI 120
Query: 140 ERANFRAGGSSGALLQALLDNQVGIIQHSSKQMKSVLGGIRTHDLALTREINALSSKLTI 199
+ A GS +L+++ +T+
Sbjct: 121 IEDKYTATGSGSPYAYGVLEDE-------------------------------YKEDMTV 149
Query: 200 LLGFRNQENVDKTPVPLEKAISVVKDAFTAAAERDIYTGDGVHLCAITKDGIKEY 254
E+A + A +A ERD +GDG+ + ITKDG KE
Sbjct: 150 -----------------EEAKKLAIRAIKSAIERDSASGDGIDVVVITKDGYKEL 187
>gnl|CDD|239728 cd03759, proteasome_beta_type_3, proteasome beta type-3 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 = 195
Score = 72.7 bits (179), Expect = 1e-15
Identities = 59/245 (24%), Positives = 94/245 (38%), Gaps = 65/245 (26%)
Query: 23 NGGTTVAVAGPDYAIIASDTRLSAGYNIYTREQSKLFDHYYYRPTYNFLM--------IF 74
NGG VA+AG D IASD RL + + K+F R + +
Sbjct: 2 NGGAVVAMAGKDCVAIASDLRLGVQQQTVSTDFQKVF-----RIGDRLYIGLAGLATDVQ 56
Query: 75 TIT-ILPFQ--MYLHEHNKVMSTTSLAKMISIMMYGKRFFPYYTSTIIAGLDPEGKGCVY 131
T+ L F+ +Y + + + + +IS ++Y KRF PY+ ++AGLDP+GK +
Sbjct: 57 TLAQKLRFRVNLYRLREEREIKPKTFSSLISSLLYEKRFGPYFVEPVVAGLDPDGKPFIC 116
Query: 132 SYDPIGHTERA-NFRAGGSSGALLQALLDNQVGIIQHSSKQMKSVLGGIRTHDLALTREI 190
+ D IG +F G++ + G+ + +L R
Sbjct: 117 TMDLIGCPSIPSDFVVSGTAS-------EQLYGMCE------------------SLWRP- 150
Query: 191 NALSSKLTILLGFRNQENVDKTPVPLEKAISVVKDAFTAAAERDIYTGDGVHLCAITKDG 250
D P L + IS A +A +RD +G G + ITKD
Sbjct: 151 -------------------DMEPDELFETIS---QALLSAVDRDALSGWGAVVYIITKDK 188
Query: 251 IKEYN 255
+
Sbjct: 189 VTTRT 193
>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 = 64.0 bits (156), Expect = 9e-13
Identities = 35/148 (23%), Positives = 62/148 (41%), Gaps = 15/148 (10%)
Query: 25 GTTVAVAGPDYAIIASDTRLSAGYNIYTREQSKLF---DH------YYYRPTYNFLMIFT 75
T+VA+ G ++A+D RLS+G + K+ D +
Sbjct: 1 STSVAIKGKGGVVLAADKRLSSGLPVAGSPVIKIGKNEDGIAWGLAGLAADAQTLVRRLR 60
Query: 76 ITILPFQMYLHEHNKVMSTTSLAKMISIMMYGKRF-FPYYTSTIIAGLDPEGKGCVYSYD 134
+ Q+Y + + +S +LAK ++ ++ P+ + I+AG+D G G +Y D
Sbjct: 61 EAL---QLYRLRYGEPISVVALAKELAKLLQVYTQGRPFGVNLIVAGVDEGG-GNLYYID 116
Query: 135 PIGH-TERANFRAGGSSGALLQALLDNQ 161
P G E A GS ++LL+
Sbjct: 117 PSGPVIENPGAVATGSRSQRAKSLLEKL 144
>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 = 42.6 bits (101), Expect = 5e-05
Identities = 45/240 (18%), Positives = 72/240 (30%), Gaps = 65/240 (27%)
Query: 26 TTVAVAGPDYAIIASDTRLSAGYNIYTREQSKLFDHYYYRPTYNFLM-----------IF 74
T +AV ++ +D+R S G + R KL + I
Sbjct: 2 TIIAVEYDGGVVLGADSRTSTGSYVANRVTDKLT-----QLHDRIYCCRSGSAADTQAIA 56
Query: 75 TITILPFQMYLHEHNKVMSTTSLAKMISIMMYGKRFFPYYTSTIIAGLDPEGKGCVYSYD 134
M+ E + + A + + Y + I+AG D + G VYS
Sbjct: 57 DYVRYYLDMHSIELGEPPLVKTAASLFKNLCYNYKEM-LSAGIIVAGWDEQNGGQVYSIP 115
Query: 135 PIGHTERANFRAGGSSGALLQALLDNQVGIIQHSSKQMKSVLGGIRTHDLALTREINALS 194
G R F GGS + +D
Sbjct: 116 LGGMLIRQPFAIGGSGSTYIYGYVDAN--------------------------------- 142
Query: 195 SKLTILLGFRNQENVDKTPVPLEKAISVVKDAFTAAAERDIYTGDGVHLCAITKDGIKEY 254
++ + E+ I VK+A + A RD +G + L ITKDG++
Sbjct: 143 --------YK--PGMTL-----EECIKFVKNALSLAMSRDGSSGGVIRLVIITKDGVERK 187
>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 = 38.7 bits (91), Expect = 0.001
Identities = 35/157 (22%), Positives = 58/157 (36%), Gaps = 35/157 (22%)
Query: 24 GGTTVAVAGPDYAIIASDTRLSAG----YNIYTREQSKLFDHYYYRPTYNFLMIFTITIL 79
G + +A+ D IIA+DT S G + R K+ D+ L+ +
Sbjct: 2 GTSVIAIKYKDGVIIAADTLGSYGSLARFKNVER-IFKVGDNT--------LLGASGDYA 52
Query: 80 PFQMYLHEH-------------NKVMSTTSLAKMISIMMYGKR--FFPYYTSTIIAGLDP 124
FQ YL +S + ++ ++Y +R P + + ++ G+D
Sbjct: 53 DFQ-YLKRLLDQLVIDDECLDDGHSLSPKEIHSYLTRVLYNRRSKMNPLWNTLVVGGVDN 111
Query: 125 EGK---GCVYSYDPIGHTERANFRAGGSSGALLQALL 158
EG+ G V D +G A G L LL
Sbjct: 112 EGEPFLGYV---DLLGTAYEDPHVATGFGAYLALPLL 145
>gnl|CDD|238892 cd01911, proteasome_alpha, proteasome alpha 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
different alpha and 10 different beta proteasome subunit
genes while archaea have one of each.
Length = 209
Score = 38.6 bits (91), Expect = 0.001
Identities = 34/143 (23%), Positives = 52/143 (36%), Gaps = 45/143 (31%)
Query: 22 DNGGTTVAVAGPDYAIIASDTRLSAGYNIYTREQSKLFDHYYYRPTYNFLMIFTIT---- 77
NG T V + G D ++A + ++ SKL D P+ IF I
Sbjct: 25 KNGSTAVGIKGKDGVVLAVEKKV----------TSKLLD-----PSSVEK-IFKIDDHIG 68
Query: 78 -----------ILPFQM------YLHEHNKVMSTTSLAKMISIMM------YGKRFFPYY 114
+L + Y + + + + L K I+ + G R P+
Sbjct: 69 CAVAGLTADARVLVNRARVEAQNYRYTYGEPIPVEVLVKRIADLAQVYTQYGGVR--PFG 126
Query: 115 TSTIIAGLDPEGKGCVYSYDPIG 137
S +IAG D EG +Y DP G
Sbjct: 127 VSLLIAGYDEEGGPQLYQTDPSG 149
>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 = 37.6 bits (88), Expect = 0.003
Identities = 29/147 (19%), Positives = 57/147 (38%), Gaps = 18/147 (12%)
Query: 26 TTVAVAGPDYAIIASDTRLSAGYNIYTREQSKLFDHYYYRPTYNFLMI----------FT 75
T + + G D+ I+A+DT + + ++ K+ Y+ + + LM F
Sbjct: 3 TLIGIKGKDFVILAADTSAARSILVLKDDEDKI-----YKLSDHKLMACSGEAGDRLQFA 57
Query: 76 ITILP-FQMYLHEHNKVMSTTSLAKMI--SIMMYGKRFFPYYTSTIIAGLDPEGKGCVYS 132
I Q+Y + +S + A + + PY + ++AG D +Y
Sbjct: 58 EYIQKNIQLYKMRNGYELSPKAAANFTRRELAESLRSRTPYQVNLLLAGYDKVEGPSLYY 117
Query: 133 YDPIGHTERANFRAGGSSGALLQALLD 159
D +G + + A G ++LD
Sbjct: 118 IDYLGTLVKVPYAAHGYGAYFCLSILD 144
>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 = 35.6 bits (83), Expect = 0.012
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 216 LEKAISVVKDAFTAAAERDIYTGDGVHLCAITKDGIKEY 254
E+A +V +A A D+ +G V LC ITKDG++
Sbjct: 148 EEEAKKLVCEAIEAGIFNDLGSGSNVDLCVITKDGVEYL 186
>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 = 33.0 bits (76), Expect = 0.093
Identities = 27/121 (22%), Positives = 50/121 (41%), Gaps = 18/121 (14%)
Query: 26 TTVAVAGPDYAIIASDTRLSAGYNIYTREQSKLFDHYYYRPTYNFLM----------IFT 75
TT+A I+A D+R +AG I ++ K+ +L+ +
Sbjct: 2 TTLAFIFQGGVIVAVDSRATAGSYIASQTVKKVI------EINPYLLGTMAGGAADCQYW 55
Query: 76 ITILPFQMYLHE--HNKVMSTTSLAKMISIMMYGKRFFPYYTSTIIAGLDPEGKGCVYSY 133
+L + L+E + + +S + +K++S M+Y + T+I G D G G Y
Sbjct: 56 ERVLGRECRLYELRNKERISVAAASKLLSNMLYQYKGMGLSMGTMICGWDKTGPGLYYVD 115
Query: 134 D 134
Sbjct: 116 S 116
Score = 28.4 bits (64), Expect = 2.6
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 215 PLEKAISVVKDAFTAAAERDIYTGDGVHLCAITKDG 250
+E+A + + A A RD Y+G V+L + +DG
Sbjct: 148 SVEEAYDLARRAIYHATHRDAYSGGNVNLYHVREDG 183
>gnl|CDD|239724 cd03755, proteasome_alpha_type_7, proteasome_alpha_type_7. 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 = 207
Score = 32.7 bits (75), Expect = 0.13
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 107 GKRFFPYYTSTIIAGLDPEGKGCVYSYDPIG 137
G R P+ ST+I G DP+G +Y DP G
Sbjct: 121 GVR--PFGISTLIVGFDPDGTPRLYQTDPSG 149
>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 = 32.0 bits (73), Expect = 0.22
Identities = 40/148 (27%), Positives = 59/148 (39%), Gaps = 33/148 (22%)
Query: 24 GGTTVAVAGPDYAIIASDTRLSAGYNIYTREQSKLFDHYYYRPT--YNFLMIFTITILP- 80
G T VA+ P ++A D R + G I +R+ K++ PT Y+ + I L
Sbjct: 2 GTTIVALTYPGGVLMAGDRRATQGNMIASRDVEKVY------PTDEYSAVGIAGTAGLAI 55
Query: 81 -----FQMYLHEHNKVMSTT--------SLAKMI----SIMMYGKRFFPYYTSTIIAGLD 123
FQ+ L + K+ LA M+ M G P ++AG D
Sbjct: 56 ELVRLFQVELEHYEKIEGVPLTLDGKANRLAAMVRGNLPAAMQGLAVVP-----LLAGYD 110
Query: 124 -PEGKGCVYSYDPI-GHTERANFRAGGS 149
G G ++SYD G E + A GS
Sbjct: 111 LDAGAGRIFSYDVTGGRYEERGYHAVGS 138
>gnl|CDD|239723 cd03754, proteasome_alpha_type_6, proteasome_alpha_type_6. 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 = 215
Score = 29.5 bits (67), Expect = 1.5
Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 10/88 (11%)
Query: 112 PYYTSTIIAGLDPEGKGCVYSYDPIGHTERANFRAGGSSGALLQALLDNQVGIIQHSSKQ 171
P S I+ G+D E +Y DP G+ A ++A ++G + K+
Sbjct: 126 PLGVSMILIGIDEELGPQLYKCDPAGYF--AGYKA-TAAGV-------KEQEATNFLEKK 175
Query: 172 MKSVLGGIRTHDLALTREINALSSKLTI 199
+K I +++ + I+ L + L+
Sbjct: 176 LKKKPDLIESYEETVELAISCLQTVLST 203
>gnl|CDD|233707 TIGR02071, PBP_1b, penicillin-binding protein 1B. Bacterial that
synthesize a cell wall of peptidoglycan (murein)
generally have several transglycosylases and
transpeptidases for the task. This family consists of a
particular bifunctional transglycosylase/transpeptidase
in E. coli and other Proteobacteria, designated
penicillin-binding protein 1B [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan].
Length = 730
Score = 27.8 bits (62), Expect = 7.3
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 6/65 (9%)
Query: 182 HDLALTREINALSSKLTILLGFRNQENVDKTPVPLEKAISVVKDAFTAAAERDIYTGDGV 241
+ R L KL +L N E + VP ++ ++ D A +RD Y DG+
Sbjct: 124 KEFGFFR----LDPKLIAMLYSPNGE--QRLFVPRDQFPELLVDTLLATEDRDFYEHDGI 177
Query: 242 HLCAI 246
L +I
Sbjct: 178 SLYSI 182
>gnl|CDD|235682 PRK06041, PRK06041, flagellar assembly protein J; Reviewed.
Length = 553
Score = 27.2 bits (61), Expect = 9.7
Identities = 9/29 (31%), Positives = 13/29 (44%), Gaps = 1/29 (3%)
Query: 172 MKSVLGGIRTHDL-ALTREINALSSKLTI 199
L + D LT +INAL +L +
Sbjct: 348 TTEALKYLDKKDFGPLTPDINALYKRLNL 376
>gnl|CDD|173866 cd08501, PBP2_Lpqw, The substrate-binding domain of mycobacterial
lipoprotein Lpqw contains type 2 periplasmic binding
fold. LpqW is one of key players in synthesis and
transport of the unique components of the mycobacterial
cell wall which is a complex structure rich in two
related lipoglycans, the phosphatidylinositol mannosides
(PIMs) and lipoarabinomannans (LAMs). Lpqw is a highly
conserved lipoprotein that transport intermediates from
a pathway for mature PIMs production into a pathway for
LAMs biosynthesis, thus controlling the relative
abundance of these two essential components of cell
wall. LpqW is thought to have been adapted by the
cell-wall biosynthesis machinery of mycobacteria and
other closely related pathogens, evolving to play an
important role in PIMs/LAMs biosynthesis. Most of
periplasmic binding proteins are comprised of only two
globular subdomains corresponding to domains I and III
of the LpqW protein. The structural topology of these
domains is most similar to that of the type 2
periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 486
Score = 27.3 bits (61), Expect = 9.9
Identities = 14/69 (20%), Positives = 24/69 (34%), Gaps = 8/69 (11%)
Query: 138 HTERANFRAGGSSGALLQALLDNQVGIIQ-HSSKQMKSVLGG-----IRTHDLALTREI- 190
++ FRA A + AL + ++ ++ LG +RT D +
Sbjct: 196 KLDKITFRAMEDPDAQINALRNGEIDAADVGPTEDTLEALGLLPGVEVRTGDGPRYLHLT 255
Query: 191 -NALSSKLT 198
N S L
Sbjct: 256 LNTKSPALA 264
>gnl|CDD|129926 TIGR00846, caca2, calcium/proton exchanger. The Ca2+:Cation
Antiporter (CaCA) Family (TC 2.A.19)Proteins of the CaCA
family are found ubiquitously, having been identified in
animals, plants, yeast, archaea and widely divergent
bacteria.All of the characterized animal proteins
catalyze Ca2+:Na+ exchange although some also transport
K+. The NCX1 plasma membrane protein exchanges 3 Na+ for
1 Ca2+. The E. coli ChaA protein catalyzes Ca2+:H+
antiport but may also catalyze Na+:H+ antiport. All
remaining well-characterized members of the family
catalyze Ca2+:H+ exchange.This model is generated from
the calcium ion/proton exchangers of the CacA family
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 365
Score = 27.0 bits (60), Expect = 10.0
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 138 HTERANFRAGGSSGALLQALLDNQVGII 165
TE+ R G + G LL A N V +I
Sbjct: 57 ATEQLAHRLGPTLGGLLNATFGNAVELI 84
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
0.320 0.136 0.396
Gapped
Lambda K H
0.267 0.0786 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,295,116
Number of extensions: 1257200
Number of successful extensions: 1162
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1148
Number of HSP's successfully gapped: 50
Length of query: 261
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 166
Effective length of database: 6,723,972
Effective search space: 1116179352
Effective search space used: 1116179352
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: 58 (26.0 bits)