RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780828|ref|YP_003065241.1| ATP-dependent protease
peptidase subunit [Candidatus Liberibacter asiaticus str. psy62]
(190 letters)
>gnl|CDD|48442 cd01913, protease_HslV, Protease HslV and the ATPase/chaperone HslU
are part of an ATP-dependent proteolytic system that is
the prokaryotic homolog of the proteasome. HslV is a
dimer of hexamers (a dodecamer) that forms a central
proteolytic chamber with active sites on the interior
walls of the cavity. HslV shares significant sequence
and structural similarity with the proteasomal
beta-subunit and both are members of the Ntn-family of
hydrolases. HslV has a nucleophilic threonine residue
at its N-terminus that is exposed after processing of
the propeptide and is directly involved in active site
catalysis..
Length = 171
Score = 276 bits (708), Expect = 2e-75
Identities = 124/171 (72%), Positives = 146/171 (85%), Gaps = 1/171 (0%)
Query: 16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
TTIL VRK+G VVIAGDGQV+LG TVMK NARKVRRL G +IAGFAGS+ADAFTL ER
Sbjct: 1 TTILAVRKNGKVVIAGDGQVTLGNTVMKGNARKVRRLYNGKVIAGFAGSTADAFTLFERF 60
Query: 76 EKKLEQYPNQLLRSSVELAKDWRMDKYLRNLEAMILIADKTITLVITGMGDVLEPENGVM 135
E KLEQYP LLR++VELAKDWR D+YLR LEAM+++ADK TL+I+G GDV+EP++G+
Sbjct: 61 EAKLEQYPGNLLRAAVELAKDWRTDRYLRRLEAMLIVADKEHTLLISGNGDVIEPDDGIA 120
Query: 136 AIGSGGSYALSAARALM-STQNSAEEIARKAMSIAADICVYTNHNIVLETL 185
AIGSGG+YAL+AARAL+ T SAEEIARKA+ IAADIC+YTNHNI +E L
Sbjct: 121 AIGSGGNYALAAARALLDHTDLSAEEIARKALKIAADICIYTNHNITVEEL 171
>gnl|CDD|34964 COG5405, HslV, ATP-dependent protease HslVU (ClpYQ), peptidase
subunit [Posttranslational modification, protein
turnover, chaperones].
Length = 178
Score = 263 bits (675), Expect = 1e-71
Identities = 123/175 (70%), Positives = 144/175 (82%), Gaps = 1/175 (0%)
Query: 12 KMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTL 71
H TTI+ VRK+G VVIAGDGQV+LG TVMK NARKVRRL G ++AGFAGS+ADAFTL
Sbjct: 1 TFHMTTIVAVRKNGKVVIAGDGQVTLGNTVMKGNARKVRRLYNGKVLAGFAGSTADAFTL 60
Query: 72 LERLEKKLEQYPNQLLRSSVELAKDWRMDKYLRNLEAMILIADKTITLVITGMGDVLEPE 131
ER E KLEQY L R++VELAKDWR DKYLR LEAM+L+ADKT L+ITG GDV+EPE
Sbjct: 61 FERFEAKLEQYQGDLFRAAVELAKDWRTDKYLRKLEAMLLVADKTHILIITGNGDVIEPE 120
Query: 132 NGVMAIGSGGSYALSAARALMS-TQNSAEEIARKAMSIAADICVYTNHNIVLETL 185
+ ++AIGSGG+YALSAARALM T+ SA EIA K++ IA DIC+YTNHNIV+E L
Sbjct: 121 DDIIAIGSGGNYALSAARALMENTELSAREIAEKSLKIAGDICIYTNHNIVVEEL 175
>gnl|CDD|143982 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 = 108 bits (271), Expect = 1e-24
Identities = 46/189 (24%), Positives = 72/189 (38%), Gaps = 20/189 (10%)
Query: 14 HATTILTVRKDGVVVIAGDGQVSLGQTV-MKANARKVRRLGKGNIIAGFAGSSADAFTLL 72
TTI+ ++ VV+A D + + G + K K+ ++ +I FAG +ADA TL+
Sbjct: 3 TGTTIVGIKGKDGVVLAADKRATRGSKLLSKDTVEKIFKIDD-HIGMAFAGLAADARTLV 61
Query: 73 ERLEKKLEQY--------PNQLLRS-----SVELAKDWRMDKYLRNLEAMILIADKTITL 119
+ + + Y +L + R + L A
Sbjct: 62 DYARAEAQLYRLRYGRPISVELAKRIADKLQAYTQYSGRRPYGVSLLIAGYDEDGGPHLY 121
Query: 120 VITGMGDVLEPENGVMAIGSGGSYALSAARALMS---TQNSAEEIARKAMSIAADICVYT 176
I G V+E + AIGSG YA L T A E+A KA+ A D +
Sbjct: 122 SIDPSGSVIEYK--ATAIGSGSQYAYGFLEKLYKPDMTLEEAVELAVKALKEAIDRDALS 179
Query: 177 NHNIVLETL 185
NI + +
Sbjct: 180 GGNIEVAVI 188
>gnl|CDD|48439 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 = 107 bits (268), Expect = 2e-24
Identities = 54/185 (29%), Positives = 82/185 (44%), Gaps = 18/185 (9%)
Query: 16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
TTI+ ++ VV+A D +V+ G V + K+ ++ +I FAG +ADA TL+ERL
Sbjct: 1 TTIVGIKGKDGVVLAADKRVTSGLLVASSTVEKIFKIDD-HIGCAFAGLAADAQTLVERL 59
Query: 76 EKKLEQY------PNQLLRSSVELAKDWRMDK-YLRNLEAMILIA-----DKTITLVITG 123
K+ + Y P + + LA LR L +L+A +
Sbjct: 60 RKEAQLYRLRYGEPIPVEALAKLLANLLYEYTQSLRPLGVSLLVAGVDEEGGPQLYSVDP 119
Query: 124 MGDVLEPENGVMAIGSGGSYALSAARALM---STQNSAEEIARKAMSIAADICVYTNHNI 180
G +E AIGSG YAL L T A E+A KA+ A + +Y+ NI
Sbjct: 120 SGSYIEY--KATAIGSGSQYALGILEKLYKPDMTLEEAIELALKALKSALERDLYSGGNI 177
Query: 181 VLETL 185
+ +
Sbjct: 178 EVAVI 182
>gnl|CDD|48436 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 = 77.1 bits (189), Expect = 3e-15
Identities = 48/166 (28%), Positives = 73/166 (43%), Gaps = 15/166 (9%)
Query: 16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
+T + ++ G VV+A D ++S G V + K+ + G I G AG +ADA TL+ RL
Sbjct: 1 STSVAIKGKGGVVLAADKRLSSGLPVAGSPVIKIGKNEDG-IAWGLAGLAADAQTLVRRL 59
Query: 76 EKKLEQY------PNQLLRSSVELAKDWRMDKYLRNLEAMILIADKTIT----LVITGMG 125
+ L+ Y P ++ + ELAK ++ R +++A I G
Sbjct: 60 REALQLYRLRYGEPISVVALAKELAKLLQVYTQGRPFGVNLIVAGVDEGGGNLYYIDPSG 119
Query: 126 DVLEPENGVMAIGSGGSYALSAARALMS---TQNSAEEIARKAMSI 168
V+E V A GS A S L T A E+A KA+
Sbjct: 120 PVIENPGAV-ATGSRSQRAKSLLEKLYKPDMTLEEAVELALKALKS 164
>gnl|CDD|48441 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 = 57.8 bits (140), Expect = 2e-09
Identities = 45/183 (24%), Positives = 74/183 (40%), Gaps = 22/183 (12%)
Query: 16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
TTI+ ++ VV+A D + S G V N K+ ++ NI+ G AGS+AD L L
Sbjct: 1 TTIVGIKGKDGVVLAADTRASAGSLVASRNFDKIFKISD-NILLGTAGSAADTQALTRLL 59
Query: 76 EKKLEQYPNQLLRS-SVELAKDWRMDKYLRNLEAMILIADKTITLVITGMGDVLEPENGV 134
++ L Y + R SV+ A L N+ ++L++ G+ P
Sbjct: 60 KRNLRLYELRNGRELSVKAAA-----NLLSNILYSYRGFPYYVSLIVGGVDKGGGPFLYY 114
Query: 135 M------------AIGSGGSYALSAARALMS---TQNSAEEIARKAMSIAADICVYTNHN 179
+ A GSG YA T A E+ +KA+ A + + +
Sbjct: 115 VDPLGSLIEAPFVATGSGSKYAYGILDRGYKPDMTLEEAVELVKKAIDSAIERDLSSGGG 174
Query: 180 IVL 182
+ +
Sbjct: 175 VDV 177
>gnl|CDD|30983 COG0638, PRE1, 20S proteasome, alpha and beta subunits
[Posttranslational modification, protein turnover,
chaperones].
Length = 236
Score = 54.9 bits (132), Expect = 1e-08
Identities = 43/193 (22%), Positives = 72/193 (37%), Gaps = 15/193 (7%)
Query: 10 AVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAF 69
AVK TT + ++ VV+A D + + G + +N K+ ++ +I AG +ADA
Sbjct: 25 AVKRGGTTTVGIKGKDGVVLAADKRATSGLLIASSNVEKIFKIDD-HIGMAIAGLAADAQ 83
Query: 70 TLLERLEKKLEQYPNQLLRS-SVELAKDWRMDK------YLRNLEAMILIA---DKTITL 119
L+ + + Y + SVE + R +L+A D L
Sbjct: 84 VLVRYARAEAQLYRLRYGEPISVEALAKLLSNILQEYTQSGRPYGVSLLVAGVDDGGPRL 143
Query: 120 VITGMGDVLEPENGVMAIGSGGSYALSAARALMS---TQNSAEEIARKAMSIAADICVYT 176
T E AIGSG +A + A E+A KA+ A + +
Sbjct: 144 YSTDPSGSYN-EYKATAIGSGSQFAYGFLEKEYREDLSLEEAIELAVKALRAAIERDAAS 202
Query: 177 NHNIVLETLKVGD 189
I + + +
Sbjct: 203 GGGIEVAVITKDE 215
>gnl|CDD|48460 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 = 49.8 bits (119), Expect = 5e-07
Identities = 43/171 (25%), Positives = 72/171 (42%), Gaps = 25/171 (14%)
Query: 16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
TTI+ V DG VV+ D + S G V K+ +L I +GS+AD + + +
Sbjct: 1 TTIIAVEYDGGVVLGADSRTSTGSYVANRVTDKLTQLHD-RIYCCRSGSAADTQAIADYV 59
Query: 76 EKKLEQYPNQ-----LLRSSVELAKDWRMDKYLRNLEAMILIA--DKTITLVITGMGDVL 128
L+ + + L++++ L K+ Y L A I++A D+ G
Sbjct: 60 RYYLDMHSIELGEPPLVKTAASLFKNL-CYNYKEMLSAGIIVAGWDEQ-----NGGQVYS 113
Query: 129 EPENGVM-----AIGSGGS-----YALSAARALMSTQNSAEEIARKAMSIA 169
P G++ AIG GS Y + + M T + + A+S+A
Sbjct: 114 IPLGGMLIRQPFAIGGSGSTYIYGYVDANYKPGM-TLEECIKFVKNALSLA 163
>gnl|CDD|35406 KOG0185, KOG0185, KOG0185, 20S proteasome, regulatory subunit beta
type PSMB4/PRE4 [Posttranslational modification, protein
turnover, chaperones].
Length = 256
Score = 41.1 bits (96), Expect = 2e-04
Identities = 41/178 (23%), Positives = 73/178 (41%), Gaps = 34/178 (19%)
Query: 16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
T++L ++ VVIA D S G N ++ ++G N + G +G +D F ++R+
Sbjct: 42 TSVLALKYKDGVVIAADTLGSYGSLARYKNVERIFKVGD-NTLLGASGDISD-FQYIQRV 99
Query: 76 EKKLEQYPNQLLRSSVELAKDWRMD-KYLRNLEAMILIADKT------ITLVITGMGDVL 128
++L N+ L + K + + +L A ++ TLV+ G+ +
Sbjct: 100 LEQLVIEDNR-------LDDGQSLGPKAIHSYLTRVLYARRSKMNPLWNTLVVGGVDNTG 152
Query: 129 EP------------ENGVMAIGSGGSYALSAAR------ALMSTQNSAEEIARKAMSI 168
EP E+ V+A G G AL R ++ AE + K M +
Sbjct: 153 EPFLGYVDLLGVAYESPVVATGFGAHLALPLLRDEWEKKGEDLSREEAEALIEKCMRV 210
>gnl|CDD|48455 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 = 40.6 bits (95), Expect = 3e-04
Identities = 18/66 (27%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 17 TILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLE 76
T+L + + VIAGD ++S G +++ ++ K+ +L ++ +G AD L +RL+
Sbjct: 10 TVLAIAGNDFAVIAGDTRLSEGYSILSRDSPKIFKLTDKCVLGS-SGFQADILALTKRLK 68
Query: 77 KKLEQY 82
+++ Y
Sbjct: 69 ARIKMY 74
>gnl|CDD|35395 KOG0174, KOG0174, KOG0174, 20S proteasome, regulatory subunit beta
type PSMB6/PSMB9/PRE3 [Posttranslational modification,
protein turnover, chaperones].
Length = 224
Score = 38.0 bits (88), Expect = 0.002
Identities = 46/180 (25%), Positives = 74/180 (41%), Gaps = 19/180 (10%)
Query: 4 MGDKHYAVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAG 63
+GD TTI+ V DG VV+ D + S G V K+ + NI +G
Sbjct: 8 IGDLPKEEVSTGTTIMAVEYDGGVVLGADSRTSTGAYVANRVTDKLTPI-TDNIYCCRSG 66
Query: 64 SSADAFTLLERLEKKLEQYPNQ-----LLRSSVELAKDWRMDKYLRNLEAMILIA---DK 115
S+AD + + + LE Y Q L+ ++ L ++ Y L A +++A +K
Sbjct: 67 SAADTQAIADIVRYHLELYTIQENKPPLVHTAASLFREI-CYNYREMLSAGLIVAGWDEK 125
Query: 116 TITLVIT-GMGDVLEPENGVMAIGSGGS-----YALSAARALMSTQNSAEEIARKAMSIA 169
V + +G L + AIG GS + + R M T + A+S+A
Sbjct: 126 EGGQVYSIPLGGSLTRQP--FAIGGSGSTFIYGFCDANWRPNM-TLEECVRFVKNAVSLA 182
>gnl|CDD|35400 KOG0179, KOG0179, KOG0179, 20S proteasome, regulatory subunit beta
type PSMB1/PRE7 [Posttranslational modification, protein
turnover, chaperones].
Length = 235
Score = 37.2 bits (86), Expect = 0.003
Identities = 19/77 (24%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 13 MHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLL 72
+ T + + + V+AGD ++S G + + K+ +LG NI+ G +G AD L+
Sbjct: 27 DNGGTTVAIAGEDFAVVAGDTRMSSGYNINSRDQSKIFKLGD-NIVLGSSGFYADTLALV 85
Query: 73 ERLEKKLEQYPNQLLRS 89
+ ++ +++QY + +
Sbjct: 86 KVIKSRIKQYEHDHNKK 102
>gnl|CDD|48457 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 = 35.5 bits (82), Expect = 0.010
Identities = 17/66 (25%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 17 TILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLE 76
++ + V IA D ++ + Q + + +KV R+G + G AG + D TL ++L
Sbjct: 5 AVVAMAGKDCVAIASDLRLGVQQQTVSTDFQKVFRIGD-RLYIGLAGLATDVQTLAQKLR 63
Query: 77 KKLEQY 82
++ Y
Sbjct: 64 FRVNLY 69
>gnl|CDD|48461 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 = 35.1 bits (81), Expect = 0.011
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
TTI+ V VV+ D + + G V N K+ + NI AG++AD + +
Sbjct: 1 TTIVGVVFKDGVVLGADTRATEGPIVADKNCEKIHYIAP-NIYCCGAGTAADTEAVTNMI 59
Query: 76 EKKLEQYPNQLLR 88
LE + R
Sbjct: 60 SSNLELHRLNTGR 72
>gnl|CDD|48458 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 = 34.7 bits (80), Expect = 0.016
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
T+++ ++ V+IA D S G N ++ ++G N + G +G AD L L
Sbjct: 3 TSVIAIKYKDGVIIAADTLGSYGSLARFKNVERIFKVGD-NTLLGASGDYADFQYLKRLL 61
Query: 76 EKK 78
++
Sbjct: 62 DQL 64
>gnl|CDD|35398 KOG0177, KOG0177, KOG0177, 20S proteasome, regulatory subunit
beta type PSMB2/PRE1 [Posttranslational modification,
protein turnover, chaperones].
Length = 200
Score = 34.4 bits (79), Expect = 0.022
Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 17 TILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLE 76
T+L ++ V++A D + V+K + K+ RL ++A G + D E ++
Sbjct: 3 TLLGIKGPDFVILASDTSAARSILVLKDDHDKIHRLSDHILMA-TVGEAGDTVQFTEYIQ 61
Query: 77 KKLEQY 82
K ++ Y
Sbjct: 62 KNIQLY 67
>gnl|CDD|48462 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 = 34.0 bits (78), Expect = 0.026
Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 15 ATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLER 74
TT+ V KDGVV +A D + S+G + N +K+ ++ I AGS DA +L+
Sbjct: 1 TTTVGIVCKDGVV-LAADKRASMGNFIASKNVKKIFQIDD-KIAMTIAGSVGDAQSLVRI 58
Query: 75 LEKKLEQY 82
L+ + Y
Sbjct: 59 LKAEARLY 66
>gnl|CDD|48456 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 = 30.5 bits (69), Expect = 0.27
Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 17 TILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLE 76
T++ ++ V++A D + V+K + K+ +L ++A +G + D E ++
Sbjct: 3 TLIGIKGKDFVILAADTSAARSILVLKDDEDKIYKLSDHKLMA-CSGEAGDRLQFAEYIQ 61
Query: 77 KKLEQYPNQLLRSSVEL 93
K ++ Y +R+ EL
Sbjct: 62 KNIQLYK---MRNGYEL 75
>gnl|CDD|35396 KOG0175, KOG0175, KOG0175, 20S proteasome, regulatory subunit beta
type PSMB5/PSMB8/PRE2 [Posttranslational modification,
protein turnover, chaperones].
Length = 285
Score = 30.7 bits (69), Expect = 0.28
Identities = 45/187 (24%), Positives = 73/187 (39%), Gaps = 30/187 (16%)
Query: 5 GDKHYAVKM---HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGF 61
D+ V + H TT L + G V++A D + S G + +KV + ++
Sbjct: 58 DDETAGVLIKFAHGTTTLAFKFKGGVIVAVDSRASAGSYIASQTVKKVIEINP-YLLGTM 116
Query: 62 AGSSADAFTLLERLEKKLEQYPNQLL---RSSVELAKDWRMDKYLRNLE----------- 107
AG +AD L K+ + +L R SV A K L N+
Sbjct: 117 AGGAADCQFWERVLAKECRLH--ELRNKERISVSAAS-----KLLSNMVYQYKGMGLSMG 169
Query: 108 AMILIADKTITLVITGMGDVLEPENGVMAIGSGGSYAL----SAARALMSTQNSAEEIAR 163
MI DK + + + ++GSG +YA S R +S + A ++AR
Sbjct: 170 TMIAGWDKKGPGLYYVDSEGTRLSGDLFSVGSGSTYAYGVLDSGYRYDLSDEE-AYDLAR 228
Query: 164 KAMSIAA 170
+A+ A
Sbjct: 229 RAIYHAT 235
>gnl|CDD|48450 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 = 30.2 bits (68), Expect = 0.37
Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 10 AVKMHATTILTVRKDGVVVIAGDGQVS--LGQTVMKANARKVRRLGKGNIIAGFAGSSAD 67
A+ T + + KDG+V+ A S L Q+ ++ K+ ++ +I AG ++D
Sbjct: 25 AISHAGTCLGILAKDGIVLAAEKKVTSKLLDQSF---SSEKIYKIDD-HIACAVAGITSD 80
Query: 68 AFTLLERLEKKLEQY 82
A L+ ++Y
Sbjct: 81 ANILINYARLIAQRY 95
>gnl|CDD|48440 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 = 30.0 bits (68), Expect = 0.45
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 10 AVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAF 69
AVK +T + KDGVV+ S + + ++ K+ ++ +I AG +ADA
Sbjct: 23 AVKNGSTAVGIKGKDGVVLAVEKKVTS--KLLDPSSVEKIFKIDD-HIGCAVAGLTADAR 79
Query: 70 TLLERLEKKLEQY 82
L+ R + + Y
Sbjct: 80 VLVNRARVEAQNY 92
>gnl|CDD|48459 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 = 29.8 bits (67), Expect = 0.51
Identities = 43/173 (24%), Positives = 69/173 (39%), Gaps = 27/173 (15%)
Query: 16 TTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERL 75
TT L G V++A D + + G + +KV + ++ AG +AD L
Sbjct: 1 TTTLAFIFQGGVIVAVDSRATAGSYIASQTVKKVIEINP-YLLGTMAGGAADCQYWERVL 59
Query: 76 EKKLEQYPNQLL---RSSVELAKDWRMDKYLRNL-----------EAMILIADKTITLVI 121
++ Y +L R SV A K L N+ MI DKT +
Sbjct: 60 GRECRLY--ELRNKERISVAAAS-----KLLSNMLYQYKGMGLSMGTMICGWDKTGPGLY 112
Query: 122 TGMGDVLEPENGVMAIGSGGSYAL----SAARALMSTQNSAEEIARKAMSIAA 170
D + + ++GSG +YA S R +S + A ++AR+A+ A
Sbjct: 113 YVDSDGTRLKGDLFSVGSGSTYAYGVLDSGYRYDLSVEE-AYDLARRAIYHAT 164
>gnl|CDD|176247 cd08287, FDH_like_ADH3, formaldehyde dehydrogenase (FDH)-like.
This group contains proteins identified as alcohol
dehydrogenases and glutathione-dependant formaldehyde
dehydrogenases (FDH) of the zinc-dependent/medium chain
alcohol dehydrogenase family. The MDR family uses
NAD(H) as a cofactor in the interconversion of alcohols
and aldehydes, or ketones. FDH converts formaldehyde
and NAD to formate and NADH. The initial step in this
process the spontaneous formation of a
S-(hydroxymethyl)glutathione adduct from formaldehyde
and glutathione, followed by FDH-mediated oxidation (and
detoxification) of the adduct to S-formylglutathione.
The medium chain alcohol dehydrogenase family (MDR) has
a NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 345
Score = 29.6 bits (67), Expect = 0.57
Identities = 23/57 (40%), Positives = 26/57 (45%), Gaps = 11/57 (19%)
Query: 3 VMGDKHYAVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIA 59
VMG H HA VR VV+ GDG V L V+ A +RLG IIA
Sbjct: 153 VMGTGH-----HAAVSAGVRPGSTVVVVGDGAVGL-CAVLAA-----KRLGAERIIA 198
>gnl|CDD|35401 KOG0180, KOG0180, KOG0180, 20S proteasome, regulatory subunit
beta type PSMB3/PUP3 [Posttranslational modification,
protein turnover, chaperones].
Length = 204
Score = 28.7 bits (64), Expect = 1.0
Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 17 TILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLE 76
+++ + V IA D ++ + + + +K+ ++G + G G + D TLLERL
Sbjct: 10 SVVAMAGKNCVAIASDLRLGVQSQTISTDFQKIFKIGD-RLYLGLTGLATDVQTLLERLR 68
Query: 77 KKLEQY 82
+ Y
Sbjct: 69 FRKNLY 74
>gnl|CDD|72970 cd04498, hPOT1_OB2, hPOT1_OB2: A subfamily of OB folds similar to
the second OB fold (OB2) of human protection of
telomeres 1 protein (hPOT1). POT1 proteins bind to the
single-stranded (ss) 3-prime ends of the telomere. hPOT1
binds specifically to ss telomeric DNA repeats ending
with the sequence GGTTAG. The hPOT1 monomer consists of
two closely connected OB folds (OB1-OB2) which cooperate
to bind telomeric ssDNA. OB1 makes more extensive
contact with the ssDNA than OB2. OB2 protects the 3' end
of the ssDNA. hPOT1 is implicated in telomere length
regulation..
Length = 123
Score = 28.4 bits (63), Expect = 1.3
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 161 IARKAMSIAADICVYTNHNIVLETLKVGD 189
+ DI VY NH + ++LK GD
Sbjct: 53 REEGGKQLTIDILVYDNHVELAKSLKPGD 81
>gnl|CDD|176218 cd08256, Zn_ADH2, Alcohol dehydrogenases of the MDR family. This
group has the characteristic catalytic and structural
zinc-binding sites of the zinc-dependent alcohol
dehydrogenases of the MDR family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 350
Score = 28.1 bits (63), Expect = 1.6
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 9 YAVKMHATTILTVRKDGVVVIAGDGQVSLG--QTVMKANARKV 49
A +HA ++ D VVV+AG G + LG N +K+
Sbjct: 160 LACALHAVDRANIKFDDVVVLAGAGPLGLGMIGAARLKNPKKL 202
>gnl|CDD|48453 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 = 27.5 bits (61), Expect = 2.1
Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 7/77 (9%)
Query: 8 HYAVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGK--GNIIAGFAGSS 65
AV+ TT + VR VV+ V + R VR++ ++ FAG +
Sbjct: 21 QEAVR-KGTTAVGVRGKDCVVLG----VEKKSVAKLQDPRTVRKICMLDDHVCLAFAGLT 75
Query: 66 ADAFTLLERLEKKLEQY 82
ADA L+ R + + +
Sbjct: 76 ADARVLINRARLECQSH 92
>gnl|CDD|145851 pfam02911, Formyl_trans_C, Formyl transferase, C-terminal domain.
Length = 99
Score = 27.2 bits (61), Expect = 2.7
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 17 TILTVRKDGVVVIAGDGQVSLGQ 39
TI++V K G++V GDG + + +
Sbjct: 58 TIVSVDKGGLLVACGDGALLILE 80
>gnl|CDD|35473 KOG0252, KOG0252, KOG0252, Inorganic phosphate transporter
[Inorganic ion transport and metabolism].
Length = 538
Score = 26.8 bits (59), Expect = 3.5
Identities = 20/66 (30%), Positives = 26/66 (39%), Gaps = 18/66 (27%)
Query: 97 WRMDKYLRN----LEAMILIADKTITLVITGMGDVLEPENGVMA----------IGSGGS 142
W DK+ R E +I+I I ++G+ GVM IG GG
Sbjct: 106 WLGDKFGRKKVYGKELIIMI----ICSALSGLSVGTTSPLGVMMTLCFFRFLLGIGIGGD 161
Query: 143 YALSAA 148
Y LSA
Sbjct: 162 YPLSAT 167
>gnl|CDD|39745 KOG4545, KOG4545, KOG4545, Uncharacterized conserved protein
[Function unknown].
Length = 197
Score = 25.8 bits (56), Expect = 7.5
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 9/49 (18%)
Query: 77 KKLEQYPNQLLRSSVELAKDWRMDKYLRNLEAMILIADKTITLVITGMG 125
K+ QY N L+R E+ D + Y R +A+ + TG+G
Sbjct: 28 KRWGQYWNGLVRDYTEVCVDVVRESYTRPKKAL---------VYGTGLG 67
>gnl|CDD|48454 cd03756, proteasome_alpha_archeal, proteasome_alpha_archeal. 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 = 25.6 bits (56), Expect = 8.0
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 10 AVKMHATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAF 69
AVK T + K+GVV+ S + V + K+ ++ ++ A +G ADA
Sbjct: 24 AVKRGTTALGIKCKEGVVLAVDKRITS--KLVEPESIEKIYKIDD-HVGAATSGLVADAR 80
Query: 70 TLLER 74
L++R
Sbjct: 81 VLIDR 85
>gnl|CDD|145225 pfam01936, DUF88, Protein of unknown function DUF88. This highly
conserved bacterial protein has no known function. The
alignment contains many conserved aspartates, suggesting
an enzymatic function such as an endonuclease or
glycosyl hydrolase (Bateman A pers. obs).
Length = 140
Score = 25.7 bits (57), Expect = 8.4
Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 9/53 (16%)
Query: 18 ILTVRKDGVVVIAGDGQ-VSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAF 69
D V+++GDG L ++R GK + G S++DA
Sbjct: 85 AYDNNPDTFVLVSGDGDFAPL--------LERLRERGKRVEVLGAEPSTSDAL 129
>gnl|CDD|114466 pfam05742, DUF833, Protein of unknown function (DUF833). This
family is found in eukaryotes, prokaryotes and viruses
and has no known function. The Ser/Thr-rich protein T10
has been found to be expressed during early
embryogenesis in mice.
Length = 267
Score = 25.4 bits (56), Expect = 9.0
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 53 GKGNIIAGFAGSSADAFTLLERLEKKLEQYP 83
+G ++A F S+A A LE L+K+ +Y
Sbjct: 82 SRGELVADFLTSNASALEYLENLKKRAHEYN 112
>gnl|CDD|34546 COG4938, COG4938, Uncharacterized conserved protein [Function
unknown].
Length = 374
Score = 25.4 bits (55), Expect = 9.7
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 7/41 (17%)
Query: 17 TILTVRKDGVVVIAG-------DGQVSLGQTVMKANARKVR 50
+L V+K +++I +GQ LG + + AR V+
Sbjct: 254 MLLIVKKKYLIIIENPEAHLHPEGQSKLGDLLAELAARGVQ 294
>gnl|CDD|176985 CHL00044, rpl16, ribosomal protein L16.
Length = 135
Score = 25.6 bits (57), Expect = 9.7
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 159 EEIARKAMSIAA 170
E IAR A+ IAA
Sbjct: 111 ETIARAAIKIAA 122
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.317 0.132 0.358
Gapped
Lambda K H
0.267 0.0694 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,055,805
Number of extensions: 102390
Number of successful extensions: 379
Number of sequences better than 10.0: 1
Number of HSP's gapped: 363
Number of HSP's successfully gapped: 55
Length of query: 190
Length of database: 6,263,737
Length adjustment: 88
Effective length of query: 102
Effective length of database: 4,362,145
Effective search space: 444938790
Effective search space used: 444938790
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (24.7 bits)