RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15275
(205 letters)
>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 = 335 bits (861), Expect = e-119
Identities = 121/196 (61%), Positives = 159/196 (81%), Gaps = 1/196 (0%)
Query: 6 YNGGSIVAMTGKNCVAIACDKRFGIQGTALADNFQKIFQVGSHMYVGLPGLATDTQTVYQ 65
YNGG++VAM GK+CVAIA D R G+Q ++ +FQK+F++G +Y+GL GLATD QT+ Q
Sbjct: 1 YNGGAVVAMAGKDCVAIASDLRLGVQQQTVSTDFQKVFRIGDRLYIGLAGLATDVQTLAQ 60
Query: 66 KIRFRQNLYELKENRKMSPKVLLAMISNMLYERRFGPYFVEPMVVGLDPETAEPIIGNMD 125
K+RFR NLY L+E R++ PK ++IS++LYE+RFGPYFVEP+V GLDP +P I MD
Sbjct: 61 KLRFRVNLYRLREEREIKPKTFSSLISSLLYEKRFGPYFVEPVVAGLDP-DGKPFICTMD 119
Query: 126 LIGCVNQPSDFVVGGPCSDQLYGMCETLWEPNLEPDDLFETIAQALVNACERNAVSGWGA 185
LIGC + PSDFVV G S+QLYGMCE+LW P++EPD+LFETI+QAL++A +R+A+SGWGA
Sbjct: 120 LIGCPSIPSDFVVSGTASEQLYGMCESLWRPDMEPDELFETISQALLSAVDRDALSGWGA 179
Query: 186 VVYIIEQDKVTVRHVK 201
VVYII +DKVT R +K
Sbjct: 180 VVYIITKDKVTTRTLK 195
>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 = 206 bits (526), Expect = 5e-68
Identities = 59/191 (30%), Positives = 103/191 (53%), Gaps = 2/191 (1%)
Query: 9 GSIVAMTGKNCVAIACDKRFGIQGTALADNFQKIFQVGSHMYVGLPGLATDTQTVYQKIR 68
+IV + GK+ V +A D R + NF KIF++ ++ +G G A DTQ + + ++
Sbjct: 1 TTIVGIKGKDGVVLAADTRASAGSLVASRNFDKIFKISDNILLGTAGSAADTQALTRLLK 60
Query: 69 FRQNLYELKENRKMSPKVLLAMISNMLYERRFGPYFVEPMVVGLDPETAEPIIGNMDLIG 128
LYEL+ R++S K ++SN+LY R PY+V +V G+D P + +D +G
Sbjct: 61 RNLRLYELRNGRELSVKAAANLLSNILYSYRGFPYYVSLIVGGVDKGG-GPFLYYVDPLG 119
Query: 129 CVNQPSDFVVGGPCSDQLYGMCETLWEPNLEPDDLFETIAQALVNACERNAVSGWGAVVY 188
+ + + FV G S YG+ + ++P++ ++ E + +A+ +A ER+ SG G V
Sbjct: 120 SLIE-APFVATGSGSKYAYGILDRGYKPDMTLEEAVELVKKAIDSAIERDLSSGGGVDVA 178
Query: 189 IIEQDKVTVRH 199
+I +D V
Sbjct: 179 VITKDGVEELR 189
>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 = 163 bits (415), Expect = 2e-51
Identities = 53/184 (28%), Positives = 90/184 (48%), Gaps = 4/184 (2%)
Query: 9 GSIVAMTGKNCVAIACDKRFGIQGTALADNFQKIFQVGSHMYVGLPGLATDTQTVYQKIR 68
+IV + GK+ V +A DKR + +KIF++ H+ GLA D QT+ +++R
Sbjct: 1 TTIVGIKGKDGVVLAADKRVTSGLLVASSTVEKIFKIDDHIGCAFAGLAADAQTLVERLR 60
Query: 69 FRQNLYELKENRKMSPKVLLAMISNMLYERRF--GPYFVEPMVVGLDPETAEPIIGNMDL 126
LY L+ + + L +++N+LYE P V +V G+D E P + ++D
Sbjct: 61 KEAQLYRLRYGEPIPVEALAKLLANLLYEYTQSLRPLGVSLLVAGVDEEG-GPQLYSVDP 119
Query: 127 IGCVNQPSDFVVGGPCSDQLYGMCETLWEPNLEPDDLFETIAQALVNACERNAVSGWGAV 186
G + G S G+ E L++P++ ++ E +AL +A ER+ SG
Sbjct: 120 SGSYIEY-KATAIGSGSQYALGILEKLYKPDMTLEEAIELALKALKSALERDLYSGGNIE 178
Query: 187 VYII 190
V +I
Sbjct: 179 VAVI 182
>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 = 153 bits (389), Expect = 2e-47
Identities = 55/190 (28%), Positives = 89/190 (46%), Gaps = 6/190 (3%)
Query: 5 TYNGGSIVAMTGKNCVAIACDKRFGIQGTALA-DNFQKIFQVGSHMYVGLPGLATDTQTV 63
G +IV + GK+ V +A DKR L+ D +KIF++ H+ + GLA D QT+
Sbjct: 1 VKTGTTIVGIKGKDGVVLAADKRATRGSKLLSKDTVEKIFKIDDHIGMAFAGLAADAQTL 60
Query: 64 YQKIRFRQNLYELKENRKMSPKV---LLAMISNMLYERRFGPYFVEPMVVGLDPETAEPI 120
R LY L+ R +S ++ + + PY V ++ G D + P
Sbjct: 61 VDYARAEAQLYRLRYGRPISVELAKRIADKLQAYTQYSGRRPYGVSLLIAGYDEDGG-PH 119
Query: 121 IGNMDLIGCVNQPSDFVVGGPCSDQLYGMCETLWEPNLEPDDLFETIAQALVNACERNAV 180
+ ++D G V + G S YG E L++P++ ++ E +AL A ER+A+
Sbjct: 120 LYSIDPSGSVIEY-KATAIGSGSQYAYGFLEKLYKPDMTLEEAVELAVKALKEAIERDAL 178
Query: 181 SGWGAVVYII 190
SG V +I
Sbjct: 179 SGGNIEVAVI 188
>gnl|CDD|223711 COG0638, PRE1, 20S proteasome, alpha and beta subunits
[Posttranslational modification, protein turnover,
chaperones].
Length = 236
Score = 152 bits (386), Expect = 2e-46
Identities = 58/198 (29%), Positives = 92/198 (46%), Gaps = 5/198 (2%)
Query: 3 IMTYNGGSIVAMTGKNCVAIACDKRFGIQGTALADNFQKIFQVGSHMYVGLPGLATDTQT 62
+ G + V + GK+ V +A DKR + N +KIF++ H+ + + GLA D Q
Sbjct: 25 AVKRGGTTTVGIKGKDGVVLAADKRATSGLLIASSNVEKIFKIDDHIGMAIAGLAADAQV 84
Query: 63 VYQKIRFRQNLYELKENRKMSPKVLLAMISNMLYERRFG--PYFVEPMVVGLDPETAEPI 120
+ + R LY L+ +S + L ++SN+L E PY V +V G+D P
Sbjct: 85 LVRYARAEAQLYRLRYGEPISVEALAKLLSNILQEYTQSGRPYGVSLLVAGVDDG--GPR 142
Query: 121 IGNMDLIGCVNQPSDFVVGGPCSDQLYGMCETLWEPNLEPDDLFETIAQALVNACERNAV 180
+ + D G N G S YG E + +L ++ E +AL A ER+A
Sbjct: 143 LYSTDPSGSYN-EYKATAIGSGSQFAYGFLEKEYREDLSLEEAIELAVKALRAAIERDAA 201
Query: 181 SGWGAVVYIIEQDKVTVR 198
SG G V +I +D+ +
Sbjct: 202 SGGGIEVAVITKDEGFRK 219
>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 = 117 bits (295), Expect = 2e-33
Identities = 44/164 (26%), Positives = 73/164 (44%), Gaps = 3/164 (1%)
Query: 9 GSIVAMTGKNCVAIACDKRFGIQGTALADNFQKIFQVGSHMYVGLPGLATDTQTVYQKIR 68
+ VA+ GK V +A DKR KI + + GL GLA D QT+ +++R
Sbjct: 1 STSVAIKGKGGVVLAADKRLSSGLPVAGSPVIKIGKNEDGIAWGLAGLAADAQTLVRRLR 60
Query: 69 FRQNLYELKENRKMSPKVLLAMISNMLYERRFG-PYFVEPMVVGLDPETAEPIIGNMDLI 127
LY L+ +S L ++ +L G P+ V +V G+D + +D
Sbjct: 61 EALQLYRLRYGEPISVVALAKELAKLLQVYTQGRPFGVNLIVAGVDEG--GGNLYYIDPS 118
Query: 128 GCVNQPSDFVVGGPCSDQLYGMCETLWEPNLEPDDLFETIAQAL 171
G V + V G S + + E L++P++ ++ E +AL
Sbjct: 119 GPVIENPGAVATGSRSQRAKSLLEKLYKPDMTLEEAVELALKAL 162
>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 = 103 bits (259), Expect = 6e-28
Identities = 55/188 (29%), Positives = 99/188 (52%), Gaps = 3/188 (1%)
Query: 8 GGSIVAMTGKNCVAIACDKRFGIQGTALADNFQKIFQVGSHMYVGLPGLATDTQTVYQKI 67
G + V + K+ V +A DKR + + N +K+FQ+ ++ + + G D Q++ + +
Sbjct: 1 GTTTVGIKCKDGVVLAADKRASMGNFVASKNAKKVFQIDDYIAMTIAGSVGDAQSLVRIL 60
Query: 68 RFRQNLYELKENRKMSPKVLLAMISNMLYERRFGPYFVEPMVVGLDPETAEPIIGNMDLI 127
+ LYEL+ R MS K L ++SN+L RF P+ V+ +V G+D E P + ++D
Sbjct: 61 KAEAKLYELRRGRPMSVKALATLLSNILNSNRFFPFIVQLLVGGVDEE--GPHLYSLDPA 118
Query: 128 GCVNQPSDFVVGGPCSDQLYGMCETLWEPNLEPDDLFETIAQALVNACERNAVSGWGAVV 187
G + D+ G S YG+ E + ++ ++ + +A+ +A ER+ SG G V
Sbjct: 119 GGII-EDDYTATGSGSPVAYGVLEDEYREDMSVEEAKKLAVRAIKSAIERDVASGNGIDV 177
Query: 188 YIIEQDKV 195
+I +D V
Sbjct: 178 AVITKDGV 185
>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 = 100 bits (250), Expect = 2e-26
Identities = 51/189 (26%), Positives = 97/189 (51%), Gaps = 3/189 (1%)
Query: 11 IVAMTGKNCVAIACDKRFGIQGTALADNFQKIFQVGSHMYVGLPGLATDTQTVYQKIRFR 70
V + K+ V +A DKR + + N +KIFQ+ + + + G D Q++ + ++
Sbjct: 3 TVGIVCKDGVVLAADKRASMGNFIASKNVKKIFQIDDKIAMTIAGSVGDAQSLVRILKAE 62
Query: 71 QNLYELKENRKMSPKVLLAMISNMLYERRFGPYFVEPMVVGLDPETAEPIIGNMDLIGCV 130
LYEL+ R MS K L ++SN+L ++ PY V+ ++ G+D E P + ++D +G +
Sbjct: 63 ARLYELRRGRPMSIKALATLLSNILNSSKYFPYIVQLLIGGVDEE--GPHLYSLDPLGSI 120
Query: 131 NQPSDFVVGGPCSDQLYGMCETLWEPNLEPDDLFETIAQALVNACERNAVSGWGAVVYII 190
+ G S YG+ E ++ ++ ++ + +A+ +A ER++ SG G V +I
Sbjct: 121 I-EDKYTATGSGSPYAYGVLEDEYKEDMTVEEAKKLAIRAIKSAIERDSASGDGIDVVVI 179
Query: 191 EQDKVTVRH 199
+D
Sbjct: 180 TKDGYKELE 188
>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 = 98.9 bits (247), Expect = 7e-26
Identities = 54/210 (25%), Positives = 101/210 (48%), Gaps = 11/210 (5%)
Query: 5 TYNGGSIVAMTGKNCVAIACDKRFGIQGTALADNFQKIFQVGSHMYVGLPGLATDTQTVY 64
T NGG+++A+ G + IA D R + L+ + KIF++ +G G D +
Sbjct: 5 TDNGGTVLAIAGNDFAVIAGDTRLSEGYSILSRDSPKIFKLTDKCVLGSSGFQADILALT 64
Query: 65 QKIRFRQNLYELKENRKMSPKVLLAMISNMLYERRFGPYFVEPMVVGLDPETAEPIIGNM 124
++++ R +Y+ N++MS + + ++S +LY RRF PY+V ++ G+D E + ++ +
Sbjct: 65 KRLKARIKMYKYSHNKEMSTEAIAQLLSTILYSRRFFPYYVFNILAGID-EEGKGVVYSY 123
Query: 125 DLIGCVNQPSDFVVGGPCSDQLYGMCETLWE----PNLEPDDLFETIAQALV-----NAC 175
D +G + + GG S + + + N+E L A +LV +A
Sbjct: 124 DPVGSY-ERETYSAGGSASSLIQPLLDNQVGRKNQNNVERTPLSLEEAVSLVKDAFTSAA 182
Query: 176 ERNAVSGWGAVVYIIEQDKVTVRHVKTRMD 205
ER+ +G + II +D + R D
Sbjct: 183 ERDIYTGDSLEIVIITKDGIEEETFPLRKD 212
>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 = 62.2 bits (152), Expect = 3e-12
Identities = 45/196 (22%), Positives = 86/196 (43%), Gaps = 21/196 (10%)
Query: 10 SIVAMTGKNCVAIACDKRFGIQGTALAD-NFQKIFQVGSHMYVGLPGLATDTQTVYQKIR 68
+I+A+ V + D R G+ +A+ K+ Q+ +Y G A DTQ + +R
Sbjct: 2 TIIAVEYDGGVVLGADSRTST-GSYVANRVTDKLTQLHDRIYCCRSGSAADTQAIADYVR 60
Query: 69 FRQNLYELKENRKMSPKVLLAMISNMLYERRFGPYFVEP-----MVVGLDPETAEPIIGN 123
+ +++ ++ K ++ N+ Y + E +V G D + + +
Sbjct: 61 YYLDMHSIELGEPPLVKTAASLFKNLCYNYK------EMLSAGIIVAGWDEQN-GGQVYS 113
Query: 124 MDLIG-CVNQPSDFVVGGPCSDQLYGMCETLWEPNLEPDDLFETIAQALVNACERNAVSG 182
+ L G + QP F +GG S +YG + ++P + ++ + + AL A R+ S
Sbjct: 114 IPLGGMLIRQP--FAIGGSGSTYIYGYVDANYKPGMTLEECIKFVKNALSLAMSRDGSS- 170
Query: 183 WGAVVY--IIEQDKVT 196
G V+ II +D V
Sbjct: 171 -GGVIRLVIITKDGVE 185
>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 = 59.1 bits (144), Expect = 4e-11
Identities = 38/193 (19%), Positives = 81/193 (41%), Gaps = 14/193 (7%)
Query: 10 SIVAMTGKNCVAIACDKRFGIQGTALADNFQKIFQVGSHMYVGLPGLATDTQTVYQKIRF 69
+++ + GK+ V +A D L D+ KI+++ H + G A D + I+
Sbjct: 3 TLIGIKGKDFVILAADTSAARSILVLKDDEDKIYKLSDHKLMACSGEAGDRLQFAEYIQK 62
Query: 70 RQNLYELKENRKMSPKVLLAMISNMLYE--RRFGPYFVEPMVVGLDPETAEPIIGNMDLI 127
LY+++ ++SPK L E R PY V ++ G D P + +D +
Sbjct: 63 NIQLYKMRNGYELSPKAAANFTRRELAESLRSRTPYQVNLLLAGYDK-VEGPSLYYIDYL 121
Query: 128 GCVNQPSDFVVGGPCSDQLYGMCETLWEPNLEPDDLFETIAQALVNAC-----ERNAVSG 182
G + + G + + + ++P++ ++ A L+ C +R ++
Sbjct: 122 GTL-VKVPYAAHGYGAYFCLSILDRYYKPDMTVEE-----ALELMKKCIKELKKRFIINL 175
Query: 183 WGAVVYIIEQDKV 195
V ++++D +
Sbjct: 176 PNFTVKVVDKDGI 188
>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 = 59.1 bits (144), Expect = 4e-11
Identities = 49/182 (26%), Positives = 81/182 (44%), Gaps = 26/182 (14%)
Query: 8 GGSIVAMTGKNCVAIACDKRFGIQGTALADNFQKIFQVGSHMYVGLPGLATDTQ----TV 63
G S++A+ K+ V IA D A N ++IF+VG + +G G D Q +
Sbjct: 2 GTSVIAIKYKDGVIIAADTLGSYGSLARFKNVERIFKVGDNTLLGASGDYADFQYLKRLL 61
Query: 64 YQKIRFRQNLYELKENRKMSPKVLLAMISNMLYERR--FGPYFVEPMVVGLDPETAEPII 121
Q + + + +SPK + + ++ +LY RR P + +V G+D E EP +
Sbjct: 62 DQLVI-DDECLDDGHS--LSPKEIHSYLTRVLYNRRSKMNPLWNTLVVGGVDNE-GEPFL 117
Query: 122 GNMDLIGCVNQPSDFVVGGPCSDQLYG------MCETLWEPNLEPDDLFETIAQALVNAC 175
G +DL+G + V G +G + WE + DL E A+AL+ C
Sbjct: 118 GYVDLLGTAYE-DPHVATG------FGAYLALPLLREAWE---KKPDLTEEEARALIEEC 167
Query: 176 ER 177
+
Sbjct: 168 MK 169
>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 = 47.2 bits (113), Expect = 7e-07
Identities = 31/105 (29%), Positives = 51/105 (48%), Gaps = 8/105 (7%)
Query: 10 SIVAMTGKNCVAIACDKRFGIQGTALAD-NFQKIFQVGSHMYVGLPGLATDTQTVYQKIR 68
+IV + K+ V + D R +G +AD N +KI + ++Y G A DT+ V I
Sbjct: 2 TIVGVVFKDGVVLGADTR-ATEGPIVADKNCEKIHYIAPNIYCCGAGTAADTEAVTNMIS 60
Query: 69 FRQNLYELKENRKMSPKVLLA--MISNMLYERRFGPYFVEPMVVG 111
L+ L RK P+V+ A M+ L+ R+ + +V+G
Sbjct: 61 SNLELHRLNTGRK--PRVVTALTMLKQHLF--RYQGHIGAALVLG 101
>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 = 39.7 bits (94), Expect = 4e-04
Identities = 30/119 (25%), Positives = 55/119 (46%), Gaps = 15/119 (12%)
Query: 7 NGGSIVAMTGKNCVAIACDKRFGIQGTALAD--NFQKIFQVGSHMYVGLPGLATDTQTVY 64
NG + V + GK+ V +A +K+ + L D + +KIF++ H+ + GL D + +
Sbjct: 26 NGSTAVGIKGKDGVVLAVEKK---VTSKLLDPSSVEKIFKIDDHIGCAVAGLTADARVLV 82
Query: 65 QKIR-FRQNLYELKENRKMSPKVLLAMISNML------YERRFGPYFVEPMVVGLDPET 116
+ R QN Y + +VL+ I+++ R P+ V ++ G D E
Sbjct: 83 NRARVEAQN-YRYTYGEPIPVEVLVKRIADLAQVYTQYGGVR--PFGVSLLIAGYDEEG 138
>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 = 38.5 bits (90), Expect = 8e-04
Identities = 25/113 (22%), Positives = 50/113 (44%), Gaps = 9/113 (7%)
Query: 8 GGSIVAMTGKNCVAIACDKRFGIQGTALAD--NFQKIFQVGSHMYVGLPGLATDTQTVYQ 65
G + V + GK+CV + +K+ L D +KI + H+ + GL D + +
Sbjct: 27 GTTAVGVRGKDCVVLGVEKK---SVAKLQDPRTVRKICMLDDHVCLAFAGLTADARVLIN 83
Query: 66 KIRFRQNLYELKENRKMSPKVLLAMISNML--YERRFG--PYFVEPMVVGLDP 114
+ R + L ++ + + I+ + Y + G P+ + ++VG DP
Sbjct: 84 RARLECQSHRLTVEDPVTVEYITRYIAGLQQRYTQSGGVRPFGISTLIVGFDP 136
>gnl|CDD|185666 PTZ00488, PTZ00488, Proteasome subunit beta type-5; Provisional.
Length = 247
Score = 38.8 bits (90), Expect = 0.001
Identities = 38/189 (20%), Positives = 83/189 (43%), Gaps = 15/189 (7%)
Query: 6 YNGGSIVAMTGKNCVAIACDKRFGIQGTALAD-NFQKIFQVGSHMYVGLPGLATDTQTVY 64
Y GG I+A+ K G +A + +K+ ++ + + G A D
Sbjct: 47 YGGGIIIAVDSK-----------ATAGPYIASQSVKKVIEINPTLLGTMAGGAADCSFWE 95
Query: 65 QKIRFRQNLYELKENRKMSPKVLLAMISNMLYERRFGPYFVEPMVVGLDPETAEPIIGNM 124
+++ + LYEL+ +S +++N+++ + + M+ G D + P + +
Sbjct: 96 RELAMQCRLYELRNGELISVAAASKILANIVWNYKGMGLSMGTMICGWDKKG--PGLFYV 153
Query: 125 DLIGCVNQPSDFVVGGPCSDQLYGMCETLWEPNLEPDDLFETIAQALVNACERNAVSGWG 184
D G + F G S YG+ + ++ +L ++ + +A+ +A R+A SG
Sbjct: 154 DNDGTRLHGNMFSCGSG-STYAYGVLDAGFKWDLNDEEAQDLGRRAIYHATFRDAYSGGA 212
Query: 185 AVVYIIEQD 193
+Y +++D
Sbjct: 213 INLYHMQKD 221
>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 = 38.0 bits (89), Expect = 0.001
Identities = 39/158 (24%), Positives = 79/158 (50%), Gaps = 11/158 (6%)
Query: 40 QKIFQVGSHMYVGLPGLATDTQTVYQKIRFRQ-NLYELKENRKMSPKVLLAMISNMLYER 98
+K+ ++ ++ + G A D Q ++++ R+ LYEL+ ++S ++SNMLY+
Sbjct: 32 KKVIEINPYLLGTMAGGAADCQY-WERVLGRECRLYELRNKERISVAAASKLLSNMLYQY 90
Query: 99 RFGPYFVEPMVVGLDPETAEPIIGNMDLIGCVNQPSDFVVGGPCSDQL--YGMCETLWEP 156
+ + M+ G D P + +D G + F VG S YG+ ++ +
Sbjct: 91 KGMGLSMGTMICGWDKTG--PGLYYVDSDGTRLKGDLFSVG---SGSTYAYGVLDSGYRY 145
Query: 157 NLEPDDLFETIAQALVNACERNAVSGWGAV-VYIIEQD 193
+L ++ ++ +A+ +A R+A SG G V +Y + +D
Sbjct: 146 DLSVEEAYDLARRAIYHATHRDAYSG-GNVNLYHVRED 182
>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 = 36.6 bits (85), Expect = 0.004
Identities = 48/186 (25%), Positives = 81/186 (43%), Gaps = 19/186 (10%)
Query: 8 GGSIVAMTGKNCVAIACDKRFGIQGTALAD-NFQKIFQVGSHMYVGLPG---LATDTQTV 63
G +IVA+T V +A D+R QG +A + +K++ + VG+ G LA + +
Sbjct: 2 GTTIVALTYPGGVLMAGDRR-ATQGNMIASRDVEKVYPTDEYSAVGIAGTAGLAIELVRL 60
Query: 64 YQ-------KIRFRQNLYELKENRKMSPKVLLAMISNMLYERRFGPYFVEPMVVGLDPET 116
+Q KI + K NR L AM+ L G V P++ G D +
Sbjct: 61 FQVELEHYEKIEGVPLTLDGKANR------LAAMVRGNLPAAMQG-LAVVPLLAGYDLDA 113
Query: 117 AEPIIGNMDLIGCVNQPSDFVVGGPCSDQLYGMCETLWEPNLEPDDLFETIAQALVNACE 176
I + D+ G + + G S G + L+ P+L+ DD +AL +A +
Sbjct: 114 GAGRIFSYDVTGGRYEERGYHAVGSGSVFAKGALKKLYSPDLDEDDALRVAVEALYDAAD 173
Query: 177 RNAVSG 182
++ +G
Sbjct: 174 DDSATG 179
>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 = 34.5 bits (80), Expect = 0.021
Identities = 22/109 (20%), Positives = 51/109 (46%), Gaps = 7/109 (6%)
Query: 12 VAMTGKNCVAIACDKRFGIQGTAL-ADNFQKIFQVGSHMYVGLPGLATDTQTVYQKIRFR 70
VA+ GK+C + K+ + + +F++ + + G+ D+++ Q+ R+
Sbjct: 33 VAVRGKDCAVVVTQKK--VPDKLIDPSTVTHLFRITDEIGCVMTGMIADSRSQVQRARYE 90
Query: 71 QNLYELKENRKMSPKVLLAMISNM--LYERRFG--PYFVEPMVVGLDPE 115
++ K +M VL I+++ +Y + P V +++G+D E
Sbjct: 91 AAEFKYKYGYEMPVDVLAKRIADINQVYTQHAYMRPLGVSMILIGIDEE 139
>gnl|CDD|214838 smart00827, PKS_AT, Acyl transferase domain in polyketide synthase
(PKS) enzymes.
Length = 298
Score = 33.1 bits (77), Expect = 0.061
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 108 MVVGLDPETAEPIIGNMDL---IGCVNQPSDFVVGGP 141
+ VGL E EP++ + + VN PS V+ G
Sbjct: 129 LAVGLSEEEVEPLLAGVPDRVSVAAVNSPSSVVLSGD 165
>gnl|CDD|239722 cd03753, proteasome_alpha_type_5, proteasome_alpha_type_5. 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 = 213
Score = 32.7 bits (75), Expect = 0.089
Identities = 26/130 (20%), Positives = 54/130 (41%), Gaps = 18/130 (13%)
Query: 8 GGSIVAMTGKNCVAIACDKRFGIQGTAL-ADNFQKIFQVGSHMYVGLPGLATDTQTVYQK 66
G + + + K V +A +KR I + + +KI ++ H+ + GL D +T+
Sbjct: 27 GSTAIGIKTKEGVVLAVEKR--ITSPLMEPSSVEKIMEIDDHIGCAMSGLIADARTLIDH 84
Query: 67 IRFRQNLYELKENRKMSPKVLLAMISNMLYERRFG-----------PYFVEPMVVGLDPE 115
R + N M+ + + +S++ +FG P+ V ++ G+D
Sbjct: 85 ARVEAQNHRFTYNEPMTVESVTQAVSDLAL--QFGEGDDGKKAMSRPFGVALLIAGVDEN 142
Query: 116 TAEPIIGNMD 125
P + + D
Sbjct: 143 G--PQLFHTD 150
>gnl|CDD|219884 pfam08529, NusA_N, NusA N-terminal domain. This domain represents
the RNA polymerase binding domain of NusA.
Length = 122
Score = 30.6 bits (70), Expect = 0.26
Identities = 9/35 (25%), Positives = 17/35 (48%)
Query: 155 EPNLEPDDLFETIAQALVNACERNAVSGWGAVVYI 189
E ++ + L E I +AL++A ++ V I
Sbjct: 12 EKGIDKEVLIEAIEEALLSAYKKKYGEDENVRVEI 46
>gnl|CDD|237061 PRK12327, nusA, transcription elongation factor NusA; Provisional.
Length = 362
Score = 31.0 bits (71), Expect = 0.41
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 161 DDLFETIAQALVNACERN 178
+DL E I AL++A +RN
Sbjct: 21 EDLIEAIEAALLSAYKRN 38
>gnl|CDD|239718 cd03749, proteasome_alpha_type_1, proteasome_alpha_type_1. 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 = 211
Score = 30.3 bits (69), Expect = 0.54
Identities = 25/116 (21%), Positives = 47/116 (40%), Gaps = 17/116 (14%)
Query: 7 NGGSIVAMTGKNCVAIACDKRFGIQGTALADNFQKIFQVGSHMYVGLPGLATDTQTVYQK 66
G + V + K + KR + L+ +KIF+V H+ + + GL D + +
Sbjct: 26 QGSATVGLKSKTHAVLVALKR---ATSELSSYQKKIFKVDDHIGIAIAGLTADARVL--- 79
Query: 67 IRFRQNL---YELKENRKMSPKVLLAMISNML------YERRFGPYFVEPMVVGLD 113
R+ + Y + + L++ ++ Y RR PY V ++ G D
Sbjct: 80 SRYMRQECLNYRFVYDSPIPVSRLVSKVAEKAQINTQRYGRR--PYGVGLLIAGYD 133
>gnl|CDD|239720 cd03751, proteasome_alpha_type_3, proteasome_alpha_type_3. 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 = 29.6 bits (67), Expect = 0.93
Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 14/75 (18%)
Query: 7 NGGSIVAMTGKNCVAIACDK----RFGIQGTALADNFQKIFQVGSHMYVGLPGLATDTQT 62
N G+ + + K+ V +A +K + G+ ++IF V H+ + + GL D +
Sbjct: 29 NSGTAIGIRCKDGVVLAVEKLVTSKLYEPGSN-----KRIFNVDRHIGIAVAGLLADGRH 83
Query: 63 VYQKIR-----FRQN 72
+ + R +R N
Sbjct: 84 LVSRAREEAENYRDN 98
>gnl|CDD|173491 PTZ00246, PTZ00246, proteasome subunit alpha; Provisional.
Length = 253
Score = 29.1 bits (65), Expect = 1.4
Identities = 13/53 (24%), Positives = 23/53 (43%)
Query: 7 NGGSIVAMTGKNCVAIACDKRFGIQGTALADNFQKIFQVGSHMYVGLPGLATD 59
N V + K V + DK + +KI+++ SH++ + GL D
Sbjct: 30 NASLTVGILCKEGVILGADKPISSKLLDPGKINEKIYKIDSHIFCAVAGLTAD 82
>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of
PolI) [DNA replication, recombination, and repair].
Length = 310
Score = 29.2 bits (66), Expect = 1.5
Identities = 14/39 (35%), Positives = 16/39 (41%), Gaps = 9/39 (23%)
Query: 156 PNLEPDDLFETIAQALVNACERNAVSGWGAVVYIIEQDK 194
+E DD ET+AQ G VV II DK
Sbjct: 116 MGIEADDPIETLAQKAYKK---------GDVVLIISGDK 145
>gnl|CDD|132795 cd06885, PX_SNX17_31, The phosphoinositide binding Phox Homology
domain of Sorting Nexins 17 and 31. The PX domain is a
phosphoinositide (PI) binding module present in many
proteins with diverse functions. Members of this
subfamily include sorting nexin 17 (SNX17), SNX31, and
similar proteins. They contain an N-terminal PX domain
followed by a truncated FERM (4.1, ezrin, radixin, and
moesin) domain and a unique C-terminal region. SNXs
make up the largest group among PX domain containing
proteins. They are involved in regulating membrane
traffic and protein sorting in the endosomal system.
The PX domain of SNXs binds PIs and targets the protein
to PI-enriched membranes. SNXs differ from each other
in PI-binding specificity and affinity, and the
presence of other protein-protein interaction domains,
which help determine subcellular localization and
specific function in the endocytic pathway. SNX17 is
known to regulate the trafficking and processing of a
number of proteins. It binds some members of the
low-density lipoprotein receptor (LDLR) family such as
LDLR, VLDLR, ApoER2, and others, regulating their
endocytosis. It also binds P-selectin and may regulate
its lysosomal degradation. SNX17 is highly expressed in
neurons. It binds amyloid precursor protein (APP) and
may be involved in its intracellular trafficking and
processing to amyloid beta peptide, which plays a
central role in the pathogenesis of Alzheimer's
disease. The biological function of SNX31 is unknown.
Length = 104
Score = 27.3 bits (61), Expect = 2.3
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 11/44 (25%)
Query: 66 KIRFRQNLYELKE-------NRKMS---PKVLLAMISNMLYERR 99
+R+ Q L+ L E NRK+ PK LL + L ERR
Sbjct: 32 SVRYSQ-LHGLNEQLKKEFGNRKLPPFPPKKLLPLTPAQLEERR 74
>gnl|CDD|218151 pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, domain 2. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). Rpb2 is the
second largest subunit of the RNA polymerase. This
domain forms one of the two distinctive lobes of the
Rpb2 structure. This domain is also known as the lobe
domain. DNA has been demonstrated to bind to the concave
surface of the lobe domain, and plays a role in
maintaining the transcription bubble. Many of the
bacterial members contain large insertions within this
domain, as region known as dispensable region 1 (DRI).
Length = 185
Score = 27.7 bits (62), Expect = 3.1
Identities = 13/86 (15%), Positives = 25/86 (29%), Gaps = 14/86 (16%)
Query: 26 KRFGIQGTALADNFQKIFQVGSHMYVGLPGLAT------DTQTVYQKIRFRQ--NLYELK 77
+ I A + +G + + K + L E
Sbjct: 92 EAENIYTQEEA-----LDYIGKGFALRRGEEPRLQRAREILYSRDPKYNLNKHLGLNEPF 146
Query: 78 ENRKMSPKVLLAMISNMLYERRFGPY 103
EN ++ + +L MI + L + G
Sbjct: 147 ENERLKAQDILYMI-DRLLNLKLGRR 171
>gnl|CDD|181084 PRK07688, PRK07688, thiamine/molybdopterin biosynthesis
ThiF/MoeB-like protein; Validated.
Length = 339
Score = 28.0 bits (63), Expect = 3.2
Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 11/62 (17%)
Query: 70 RQNLYELKENRKMSPKVLLAMISNMLYERRF----GPYFVEPMVVGLDPETAEPIIGNMD 125
RQ LY + + PK + A ++R VE +V + E E ++ +D
Sbjct: 66 RQQLYTESDVKNNLPKAVAA-------KKRLEEINSDVRVEAIVQDVTAEELEELVTGVD 118
Query: 126 LI 127
LI
Sbjct: 119 LI 120
>gnl|CDD|240245 PTZ00050, PTZ00050, 3-oxoacyl-acyl carrier protein synthase;
Provisional.
Length = 421
Score = 28.1 bits (63), Expect = 3.3
Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 8/51 (15%)
Query: 44 QVGSHMYVGLPGLATDTQTVYQKIRFRQNLYELKENRKMSPKVLLAMISNM 94
++G ++ G+ LA T + LYE K + ++SP + ++ NM
Sbjct: 104 RIGVNIGSGIGSLADLTDEMK-------TLYE-KGHSRVSPYFIPKILGNM 146
>gnl|CDD|218033 pfam04339, DUF482, Protein of unknown function, DUF482. This
family contains several proteins of uncharacterized
function.
Length = 370
Score = 28.2 bits (64), Expect = 3.4
Identities = 8/31 (25%), Positives = 12/31 (38%)
Query: 153 LWEPNLEPDDLFETIAQALVNACERNAVSGW 183
L P + L + AL E+N +S
Sbjct: 107 LIAPGEDEAALRAALLAALDELAEQNGLSSL 137
>gnl|CDD|239721 cd03752, proteasome_alpha_type_4, proteasome_alpha_type_4. 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 = 213
Score = 27.7 bits (62), Expect = 4.1
Identities = 12/88 (13%), Positives = 39/88 (44%)
Query: 7 NGGSIVAMTGKNCVAIACDKRFGIQGTALADNFQKIFQVGSHMYVGLPGLATDTQTVYQK 66
+ G+ + + K+ + +A +K+ + + + +KI+++ H+ + G+ +D +
Sbjct: 28 HAGTCLGILAKDGIVLAAEKKVTSKLLDQSFSSEKIYKIDDHIACAVAGITSDANILINY 87
Query: 67 IRFRQNLYELKENRKMSPKVLLAMISNM 94
R Y + + L+ + ++
Sbjct: 88 ARLIAQRYLYSYQEPIPVEQLVQRLCDI 115
>gnl|CDD|177123 MTH00048, COX1, cytochrome c oxidase subunit I; Provisional.
Length = 511
Score = 27.7 bits (62), Expect = 5.0
Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 86 VLLAMISNMLYERRFGPYFVEPMVVGLDP 114
VL A I+ +L++R FG F +P+ G DP
Sbjct: 199 VLAAAITMLLFDRNFGSAFFDPLGGG-DP 226
>gnl|CDD|163461 TIGR03749, conj_TIGR03749, integrating conjugative element protein,
PFL_4704 family. Members of this protein family are
found occasionally on plasmids such as the Pseudomonas
putida TOL plasmid pWWO_p085. Usually, however, they are
found on the bacterial main chromosome in a region
flanked by markers of conjugative transfer and/or
transposition [Mobile and extrachromosomal element
functions, Plasmid functions].
Length = 257
Score = 26.9 bits (60), Expect = 8.5
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 7/34 (20%)
Query: 31 QGTALADNFQKIFQVGSHMYVGLPGLATDTQTVY 64
QG +A FQ H ++G G DT T+Y
Sbjct: 220 QGRFVAATFQ-------HPWLGPAGTPEDTTTLY 246
>gnl|CDD|221314 pfam11920, DUF3438, Protein of unknown function (DUF3438). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 276 to 307 amino acids in
length.
Length = 285
Score = 26.9 bits (60), Expect = 8.7
Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 7/40 (17%)
Query: 31 QGTALADNFQKIFQVGSHMYVGLPGLATDTQTVYQKIRFR 70
QG +A FQ H ++G G DT T+Y R R
Sbjct: 230 QGRFVAATFQ-------HPWLGPAGTPEDTTTLYLVTRGR 262
>gnl|CDD|223386 COG0309, HypE, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 339
Score = 26.8 bits (60), Expect = 8.7
Identities = 16/81 (19%), Positives = 25/81 (30%), Gaps = 14/81 (17%)
Query: 108 MVVGLDPETAEPIIGNMDLIGCVNQPSDFVVGGPCSD-------QLYGMCETLWEPNLEP 160
+ DP +P+ IG V G +D Y + L P
Sbjct: 51 LAFTTDPFVIDPLFFPGGDIG------KLAVHGTANDVAVSGAKPRYLSVGLILPEGL-P 103
Query: 161 DDLFETIAQALVNACERNAVS 181
+ E I +++ E VS
Sbjct: 104 IEDLERILKSIDEEAEEAGVS 124
>gnl|CDD|185695 cd01081, Aldose_epim, aldose 1-epimerase superfamily. Aldose
1-epimerases or mutarotases are key enzymes of
carbohydrate metabolism; they catalyze the
interconversion of the alpha- and beta-anomers of hexose
sugars such as glucose and galactose. This
interconversion is an important step that allows anomer
specific metabolic conversion of sugars. Studies of the
catalytic mechanism of the best known member of the
family, galactose mutarotase, have shown a glutamate and
a histidine residue to be critical for catalysis; the
glutamate serves as the active site base to initiate the
reaction by removing the proton from the C-1 hydroxyl
group of the sugar substrate and the histidine as the
active site acid to protonate the C-5 ring oxygen.
Length = 284
Score = 26.7 bits (59), Expect = 8.8
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 43 FQVGSHMYVGLPGLATDTQTVY 64
F +G H Y GLPG+A + +
Sbjct: 142 FGLGWHPYFGLPGVAIEDLRLR 163
>gnl|CDD|163403 TIGR03691, 20S_bact_alpha, proteasome, alpha subunit, bacterial
type. Members of this family are the alpha subunit of
the 20S proteasome as found in Actinobacteria such as
Mycobacterium, Rhodococcus, and Streptomyces. In most
Actinobacteria (an exception is Propionibacterium
acnes), the proteasome is accompanied by a system of
tagging proteins for degradation with Pup [Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 228
Score = 26.6 bits (59), Expect = 9.8
Identities = 15/70 (21%), Positives = 25/70 (35%)
Query: 102 PYFVEPMVVGLDPETAEPIIGNMDLIGCVNQPSDFVVGGPCSDQLYGMCETLWEPNLEPD 161
PY VE V + + + + G + FVV G ++ + + + L
Sbjct: 117 PYEVEICVAEVGETPDQDQLYRITFDGSIVDERGFVVMGGTTEPIATALKESYRDGLSLA 176
Query: 162 DLFETIAQAL 171
D QAL
Sbjct: 177 DALGLAVQAL 186
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 0.420
Gapped
Lambda K H
0.267 0.0893 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,434,139
Number of extensions: 973936
Number of successful extensions: 913
Number of sequences better than 10.0: 1
Number of HSP's gapped: 886
Number of HSP's successfully gapped: 48
Length of query: 205
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 113
Effective length of database: 6,857,034
Effective search space: 774844842
Effective search space used: 774844842
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: 57 (25.4 bits)