RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy351
(146 letters)
>gnl|CDD|212672 cd10230, HYOU1-like_NBD, Nucleotide-binding domain of human HYOU1
and similar proteins. This subgroup includes human
HYOU1 (also known as human hypoxia up-regulated 1,
GRP170; HSP12A; ORP150; GRP-170; ORP-150; the human
HYOU1 gene maps to11q23.1-q23.3) and Saccharomyces
cerevisiae Lhs1p (also known as Cer1p, SsI1). Mammalian
HYOU1 functions as a nucleotide exchange factor (NEF)
for HSPA5 (alos known as BiP, Grp78 or HspA5) and may
also function as a HSPA5-independent chaperone. S.
cerevisiae Lhs1p, does not have a detectable endogenous
ATPase activity like canonical HSP70s, but functions as
a NEF for Kar2p; it's interaction with Kar2p is
stimulated by nucleotide-binding. In addition, Lhs1p has
a nucleotide-independent holdase activity that prevents
heat-induced aggregation of proteins in vitro. This
subgroup belongs to the 105/110 kDa heat shock protein
(HSP105/110) subfamily of the HSP70-like family.
HSP105/110s are believed to function generally as
co-chaperones of HSP70 chaperones, acting as NEFs, to
remove ADP from their HSP70 chaperone partners during
the ATP hydrolysis cycle. HSP70 chaperones assist in
protein folding and assembly, and can direct incompetent
"client" proteins towards degradation. Like HSP70
chaperones, HSP105/110s have an N-terminal
nucleotide-binding domain (NBD) and a C-terminal
substrate-binding domain (SBD). For HSP70 chaperones,
the nucleotide sits in a deep cleft formed between the
two lobes of the NBD. The two subdomains of each lobe
change conformation between ATP-bound, ADP-bound, and
nucleotide-free states. ATP binding opens up the
substrate-binding site; substrate-binding increases the
rate of ATP hydrolysis. Hsp70 chaperone activity is also
regulated by J-domain proteins.
Length = 388
Score = 178 bits (454), Expect = 9e-56
Identities = 67/115 (58%), Positives = 80/115 (69%)
Query: 32 MSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHKGERTFGEDAQIIGTRFPSN 91
+ +DLGSEW+KVA+V PGVP EI LN+ESKRKTP+ VAF GER FG DA + RFP
Sbjct: 1 LGIDLGSEWIKVALVKPGVPFEIVLNEESKRKTPSAVAFKGGERLFGSDASSLAARFPQQ 60
Query: 92 SYGYFLDLLGKSIDSPVVQLFKSRFPYYDIVADEERGTIVFKTNDNELYHVEELV 146
Y + DLLGK D P V L++SR P +V DE RGT+ FK +D E Y VEELV
Sbjct: 61 VYLHLKDLLGKPADDPSVSLYQSRHPLPYLVVDESRGTVAFKISDGEEYSVEELV 115
>gnl|CDD|212682 cd11732, HSP105-110_like_NBD, Nucleotide-binding domain of 105/110
kDa heat shock proteins including HSPA4, HYOU1, and
similar proteins. This subfamily include the human
proteins, HSPA4 (also known as 70-kDa heat shock protein
4, APG-2, HS24/P52, hsp70 RY, and HSPH2; the human HSPA4
gene maps to 5q31.1), HSPA4L (also known as 70-kDa heat
shock protein 4-like, APG-1, HSPH3, and OSP94; the human
HSPA4L gene maps to 4q28), and HSPH1 (also known as heat
shock 105kDa/110kDa protein 1, HSP105; HSP105A; HSP105B;
NY-CO-25; the human HSPH1 gene maps to 13q12.3), HYOU1
(also known as human hypoxia up-regulated 1, GRP170;
HSP12A; ORP150; GRP-170; ORP-150; the human HYOU1 gene
maps to11q23.1-q23.3), Saccharomyces cerevisiae Sse1p,
Sse2p, and Lhs1p, and a sea urchin sperm receptor. It
belongs to the 105/110 kDa heat shock protein
(HSP105/110) subfamily of the HSP70-like family, and
includes proteins believed to function generally as
co-chaperones of HSP70 chaperones, acting as nucleotide
exchange factors (NEFs), to remove ADP from their HSP70
chaperone partners during the ATP hydrolysis cycle.
HSP70 chaperones assist in protein folding and assembly,
and can direct incompetent "client" proteins towards
degradation. Like HSP70 chaperones, HSP105/110s have an
N-terminal nucleotide-binding domain (NBD) and a
C-terminal substrate-binding domain (SBD). For HSP70
chaperones, the nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. HSP70 chaperone
activity is also regulated by J-domain proteins.
Length = 377
Score = 95.9 bits (238), Expect = 2e-24
Identities = 24/116 (20%), Positives = 46/116 (39%), Gaps = 2/116 (1%)
Query: 32 MSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHKGERTFGEDAQIIGTRFPSN 91
+DLG+ +A+ ++I +N+ S R TP++V F R GE + T N
Sbjct: 1 FGLDLGNNNSVLAVARN-RGIDIVVNEVSNRSTPSVVGFGPKNRYLGETGKNKQTSNIKN 59
Query: 92 SYGYFLDLLGKSIDSPVVQLF-KSRFPYYDIVADEERGTIVFKTNDNELYHVEELV 146
+ ++G P + K + D++ G V + ++ +L
Sbjct: 60 TVANLKRIIGLDYHHPDFEQESKHFTSKLVELDDKKTGAEVRFAGEKHVFSATQLA 115
>gnl|CDD|212670 cd10228, HSPA4_like_NDB, Nucleotide-binding domain of 105/110 kDa
heat shock proteins including HSPA4 and similar
proteins. This subgroup includes the human proteins,
HSPA4 (also known as 70-kDa heat shock protein 4, APG-2,
HS24/P52, hsp70 RY, and HSPH2; the human HSPA4 gene maps
to 5q31.1), HSPA4L (also known as 70-kDa heat shock
protein 4-like, APG-1, HSPH3, and OSP94; the human
HSPA4L gene maps to 4q28), and HSPH1 (also known as heat
shock 105kDa/110kDa protein 1, HSP105; HSP105A; HSP105B;
NY-CO-25; the human HSPH1 gene maps to 13q12.3),
Saccharomyces cerevisiae Sse1p and Sse2p, and a sea
urchin sperm receptor. It belongs to the 105/110 kDa
heat shock protein (HSP105/110) subfamily of the
HSP70-like family, and includes proteins believed to
function generally as co-chaperones of HSP70 chaperones,
acting as nucleotide exchange factors (NEFs), to remove
ADP from their HSP70 chaperone partners during the ATP
hydrolysis cycle. HSP70 chaperones assist in protein
folding and assembly, and can direct incompetent
"client" proteins towards degradation. Like HSP70
chaperones, HSP105/110s have an N-terminal
nucleotide-binding domain (NBD) and a C-terminal
substrate-binding domain (SBD). For HSP70 chaperones,
the nucleotide sits in a deep cleft formed between the
two lobes of the NBD. The two subdomains of each lobe
change conformation between ATP-bound, ADP-bound, and
nucleotide-free states. ATP binding opens up the
substrate-binding site; substrate-binding increases the
rate of ATP hydrolysis. Hsp70 chaperone activity is also
regulated by J-domain proteins.
Length = 381
Score = 64.1 bits (157), Expect = 6e-13
Identities = 31/106 (29%), Positives = 53/106 (50%), Gaps = 3/106 (2%)
Query: 30 AVMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHKGERTFGEDAQIIGTRFP 89
+V+ +D G+ VA+ G +++ N+ S R+TP+LV+F + +R GE A+
Sbjct: 1 SVVGIDFGNLNSVVAVARKGG-IDVVANEYSNRETPSLVSFGEKQRLIGEAAKNQAISNF 59
Query: 90 SNSYGYFLDLLGKSIDSPVVQLFKSRFPYYDIVADEERGTIVFKTN 135
N+ F L+G+ D P VQ P + +V + G + K N
Sbjct: 60 KNTVRNFKRLIGRKFDDPEVQKELKFLP-FKVVELPD-GKVGIKVN 103
>gnl|CDD|215656 pfam00012, HSP70, Hsp70 protein. Hsp70 chaperones help to fold
many proteins. Hsp70 assisted folding involves repeated
cycles of substrate binding and release. Hsp70 activity
is ATP dependent. Hsp70 proteins are made up of two
regions: the amino terminus is the ATPase domain and the
carboxyl terminus is the substrate binding region.
Length = 598
Score = 57.6 bits (140), Expect = 1e-10
Identities = 35/115 (30%), Positives = 52/115 (45%), Gaps = 2/115 (1%)
Query: 31 VMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHKGERTFGEDAQIIGTRFPS 90
V+ +DLG+ VA++ G P E+ N E R TP++VAF ER G+ A+ P
Sbjct: 1 VIGIDLGTTNSCVAVMEGGGP-EVIANDEGNRTTPSVVAFTPKERLVGQAAKRQAVTNPK 59
Query: 91 NSYGYFLDLLGKSIDSPVVQLFKSRFPYYDIVADEERGTIVFKTNDNELYHVEEL 145
N+ L+G+ PVVQ P Y +V V E + E++
Sbjct: 60 NTVFSVKRLIGRKFSDPVVQRDIKHVP-YKVVKLPNGDAGVEVRYLGETFTPEQI 113
>gnl|CDD|223520 COG0443, DnaK, Molecular chaperone [Posttranslational modification,
protein turnover, chaperones].
Length = 579
Score = 49.3 bits (118), Expect = 1e-07
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 34 VDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHK-GERTFGEDAQIIGTRFPSNS 92
+DLG+ VA++ G ++ N E +R TP++VAF K GE G+ A+ P N+
Sbjct: 10 IDLGTTNSVVAVMRGGGLPKVIENAEGERLTPSVVAFSKNGEVLVGQAAKRQAVDNPENT 69
Query: 93 YGYFLDLLGKS 103
+G+
Sbjct: 70 IFSIKRKIGRG 80
>gnl|CDD|212681 cd10241, HSPA5-like_NBD, Nucleotide-binding domain of human HSPA5
and similar proteins. This subfamily includes human
HSPA5 (also known as 70-kDa heat shock protein 5,
glucose-regulated protein 78/GRP78, and immunoglobulin
heavy chain-binding protein/BIP, MIF2; the gene encoding
HSPA5 maps to 9q33.3.), Sacchaormyces cerevisiae Kar2p
(also known as Grp78p), and related proteins. This
subfamily belongs to the heat shock protein 70 (HSP70)
family of chaperones that assist in protein folding and
assembly and can direct incompetent "client" proteins
towards degradation. HSPA5 and Kar2p are chaperones of
the endoplasmic reticulum (ER). Typically, HSP70s have a
nucleotide-binding domain (NBD) and a substrate-binding
domain (SBD). The nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. HSP70 chaperone
activity is regulated by various co-chaperones: J-domain
proteins and nucleotide exchange factors (NEFs).
Multiple ER DNAJ domain proteins have been identified
and may exist in distinct complexes with HSPA5 in
various locations in the ER, for example DNAJC3-p58IPK
in the lumen. HSPA5-NEFs include SIL1 and an atypical
HSP70 family protein HYOU1/ORP150. The ATPase activity
of Kar2p is stimulated by the NEFs: Sil1p and Lhs1p.
Length = 374
Score = 46.9 bits (112), Expect = 7e-07
Identities = 32/108 (29%), Positives = 49/108 (45%), Gaps = 2/108 (1%)
Query: 31 VMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHKGERTFGEDAQIIGTRFPS 90
V+ +DLG+ + V + G +EI N + R TP+ VAF GER G+ A+ T P
Sbjct: 3 VIGIDLGTTYSCVGVFKNG-RVEIIANDQGNRITPSYVAFTDGERLIGDAAKNQATSNPE 61
Query: 91 NSYGYFLDLLGKSIDSPVVQLFKSRFPYYDIVADEERGTIVFKTNDNE 138
N+ L+G+ D VQ P Y +V + + I +
Sbjct: 62 NTIFDVKRLIGRKFDDKEVQKDIKLLP-YKVVNKDGKPYIEVDVKGEK 108
>gnl|CDD|212689 cd11739, HSPH1_NBD, Nucleotide-binding domain of HSPH1. Human
HSPH1 (also known as heat shock 105kDa/110kDa protein 1,
HSP105; HSP105A; HSP105B; NY-CO-25; the human HSPH1 gene
maps to 13q12.3) suppresses the aggregation of denatured
proteins caused by heat shock in vitro, and may
substitute for HSP70 family proteins to suppress the
aggregation of denatured proteins in cells under severe
stress. It reduces the protein aggregation and
cytotoxicity associated with Polyglutamine (PolyQ)
diseases, including Huntington's disease, which are a
group of inherited neurodegenerative disorders sharing
the characteristic feature of having insoluble protein
aggregates in neurons. The expression of HSPH1 is
elevated in various malignant tumors, including
malignant melanoma, and there is a direct correlation
between HSPH1 expression and B-cell non-Hodgkin
lymphomas (B-NHLs) aggressiveness and proliferation.
HSPH1 belongs to the 105/110 kDa heat shock protein
(HSP105/110) subfamily of the HSP70-like family.
HSP105/110s are believed to function generally as
co-chaperones of HSP70 chaperones, acting as nucleotide
exchange factors (NEFs), to remove ADP from their HSP70
chaperone partners during the ATP hydrolysis cycle.
HSP70 chaperones assist in protein folding and assembly,
and can direct incompetent "client" proteins towards
degradation. Like HSP70 chaperones, HSP105/110s have an
N-terminal nucleotide-binding domain (NBD) and a
C-terminal substrate-binding domain (SBD). For HSP70
chaperones, the nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. Hsp70 chaperone
activity is also regulated by J-domain proteins.
Length = 383
Score = 46.5 bits (110), Expect = 1e-06
Identities = 31/118 (26%), Positives = 55/118 (46%), Gaps = 4/118 (3%)
Query: 30 AVMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHKGERTFGEDAQIIGTRFP 89
+V+ D+G + +A+ G +E N+ S R TP++++F RT G A+
Sbjct: 1 SVVGFDVGFQSCYIAVARAG-GIETVANEFSDRCTPSVISFGSKNRTIGVAAKNQQITHA 59
Query: 90 SNSYGYFLDLLGKSIDSPVVQLFKSRFPYYDIVA--DEERGTIVFKTNDNELYHVEEL 145
+N+ F G++ + P VQ K YD+V + G V + L+ VE++
Sbjct: 60 NNTVSNFKRFHGRAFNDPFVQKEKENLS-YDLVPLKNGGVGVKVMYMGEEHLFSVEQI 116
>gnl|CDD|212684 cd11734, Ssq1_like_NBD, Nucleotide-binding domain of Saccharomyces
cerevisiae Ssq1 and similar proteins. Ssq1p (also
called Stress-seventy subfamily Q protein 1, Ssc2p,
Ssh1p, mtHSP70 homolog) belongs to the heat shock
protein 70 (HSP70) family of chaperones that assist in
protein folding and assembly, and can direct incompetent
"client" proteins towards degradation. Typically, HSP70s
have a nucleotide-binding domain (NBD) and a
substrate-binding domain (SBD). The nucleotide sits in a
deep cleft formed between the two lobes of the NBD. The
two subdomains of each lobe change conformation between
ATP-bound, ADP-bound, and nucleotide-free states. ATP
binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
Hsp70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs). S. cerevisiae Ssq1p is a mitochondrial
chaperone that is involved in iron-sulfur (Fe/S) center
biogenesis. Ssq1p plays a role in the maturation of
Yfh1p, a nucleus-encoded mitochondrial protein involved
in iron homeostasis (and a homolog of human frataxin,
implicated in the neurodegenerative disease,
Friedreich's ataxia).
Length = 373
Score = 46.3 bits (110), Expect = 1e-06
Identities = 31/92 (33%), Positives = 47/92 (51%), Gaps = 2/92 (2%)
Query: 31 VMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHKGERTFGEDAQIIGTRFPS 90
++ +DLG+ VA++ P+ I N E KR TP++V+F K GE A+ P
Sbjct: 4 IIGIDLGTTNSCVAVIDKTTPVIIE-NAEGKRTTPSIVSFTKTGILVGEAAKRQEALHPE 62
Query: 91 NSYGYFLDLLGKSIDSPVVQLFKSRFPYYDIV 122
N++ L+G+ VQ K + PYY IV
Sbjct: 63 NTFFATKRLIGRQFKDVEVQR-KMKVPYYKIV 93
>gnl|CDD|240227 PTZ00009, PTZ00009, heat shock 70 kDa protein; Provisional.
Length = 653
Score = 43.6 bits (103), Expect = 9e-06
Identities = 35/121 (28%), Positives = 57/121 (47%), Gaps = 3/121 (2%)
Query: 26 SYGIAVMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHKGERTFGEDAQIIG 85
+ G A+ +DLG+ + V V +EI N + R TP+ VAF ER G+ A+
Sbjct: 2 TKGPAI-GIDLGTTYSCVG-VWKNENVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQV 59
Query: 86 TRFPSNSYGYFLDLLGKSIDSPVVQLFKSRFPYYDIVADEERGTI-VFKTNDNELYHVEE 144
R P N+ L+G+ D VVQ +P+ +++ I V + + +H EE
Sbjct: 60 ARNPENTVFDAKRLIGRKFDDSVVQSDMKHWPFKVTTGGDDKPMIEVTYQGEKKTFHPEE 119
Query: 145 L 145
+
Sbjct: 120 I 120
>gnl|CDD|212667 cd10170, HSP70_NBD, Nucleotide-binding domain of the HSP70 family.
HSP70 (70-kDa heat shock protein) family chaperones
assist in protein folding and assembly and can direct
incompetent "client" proteins towards degradation.
Typically, HSP70s have a nucleotide-binding domain (NBD)
and a substrate-binding domain (SBD). The nucleotide
sits in a deep cleft formed between the two lobes of the
NBD. The two subdomains of each lobe change conformation
between ATP-bound, ADP-bound, and nucleotide-free
states. ATP binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
HSP70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs). Some HSP70 family members are not
chaperones but instead, function as NEFs to remove ADP
from their HSP70 chaperone partners during the ATP
hydrolysis cycle, some may function as both chaperones
and NEFs.
Length = 369
Score = 41.4 bits (98), Expect = 5e-05
Identities = 39/123 (31%), Positives = 48/123 (39%), Gaps = 16/123 (13%)
Query: 27 YGIAVMSVDLG---SEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHK-GERTFGEDAQ 82
GI DLG S VA V G EI N E R TP++V F GE GE A+
Sbjct: 1 IGI-----DLGTTNSA---VAYVDNGGKPEIIPNGEGSRTTPSVVYFDGDGEVLVGEAAK 52
Query: 83 IIGTRFPSNSYGYFLDLLGKSIDSPVVQLFKSRFPYYDIVADEERGTIVFKTNDNELYHV 142
P N+ G F L+G+ D P+VQ K V + Y
Sbjct: 53 RQALDNPENTVGDFKRLIGRKFDDPLVQSAKKVIGVDRGAPIIP----VPVELGGKKYSP 108
Query: 143 EEL 145
EE+
Sbjct: 109 EEV 111
>gnl|CDD|240403 PTZ00400, PTZ00400, DnaK-type molecular chaperone; Provisional.
Length = 663
Score = 41.0 bits (96), Expect = 8e-05
Identities = 27/89 (30%), Positives = 42/89 (47%), Gaps = 2/89 (2%)
Query: 31 VMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHK-GERTFGEDAQIIGTRFP 89
++ +DLG+ VAI+ P I N E R TP++VAF + G+R G A+ P
Sbjct: 43 IVGIDLGTTNSCVAIMEGSQPKVIE-NSEGMRTTPSVVAFTEDGQRLVGIVAKRQAVTNP 101
Query: 90 SNSYGYFLDLLGKSIDSPVVQLFKSRFPY 118
N+ L+G+ D + + PY
Sbjct: 102 ENTVFATKRLIGRRYDEDATKKEQKILPY 130
>gnl|CDD|212683 cd11733, HSPA9-like_NBD, Nucleotide-binding domain of human HSPA9,
Escherichia coli DnaK, and similar proteins. This
subgroup includes human mitochondrial HSPA9 (also known
as 70-kDa heat shock protein 9, CSA; MOT; MOT2; GRP75;
PBP74; GRP-75; HSPA9B; MTHSP75; the gene encoding HSPA9
maps to 5q31.1), Escherichia coli DnaK, and
Saccharomyces cerevisiae Stress-Seventy subfamily
C/Ssc1p (also called mtHSP70, Endonuclease SceI 75 kDa
subunit). It belongs to the heat shock protein 70
(HSP70) family of chaperones that assist in protein
folding and assembly, and can direct incompetent
"client" proteins towards degradation. Typically, HSP70s
have a nucleotide-binding domain (NBD) and a
substrate-binding domain (SBD). The nucleotide sits in a
deep cleft formed between the two lobes of the NBD. The
two subdomains of each lobe change conformation between
ATP-bound, ADP-bound, and nucleotide-free states. ATP
binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
Hsp70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs); for Escherichia coli DnaK, these are the
DnaJ and GrpE, respectively. HSPA9 is involved in
multiple processses including mitochondrial import,
antigen processing, control of cellular proliferation
and differentiation, and regulation of glucose
responses. During glucose deprivation-induced cellular
stress, HSPA9 plays an important role in the suppression
of apoptosis by inhibiting a conformational change in
Bax that allow the release of cytochrome c. DnaK
modulates the heat shock response in Escherichia coli.
It protects E. coli from protein carbonylation, an
irreversible oxidative modification that increases
during organism aging and bacterial growth arrest. Under
severe thermal stress, it functions as part of a
bi-chaperone system: the DnaK system and the
ring-forming AAA+ chaperone ClpB (Hsp104) system, to
promote cell survival. DnaK has also been shown to
cooperate with GroEL and the ribosome-associated
Escherichia coli Trigger Factor in the proper folding of
cytosolic proteins. S. cerevisiae Ssc1p is the major
HSP70 chaperone of the mitochondrial matrix, promoting
translocation of proteins from the cytosol, across the
inner membrane, to the matrix, and their subsequent
folding. Ssc1p interacts with Tim44, a peripheral inner
membrane protein associated with the TIM23 protein
translocase. It is also a subunit of the endoSceI
site-specific endoDNase and is required for full
endoSceI activity. Ssc1p plays roles in the import of
Yfh1p, a nucleus-encoded mitochondrial protein involved
in iron homeostasis (and a homolog of human frataxin,
implicated in the neurodegenerative disease,
Friedreich's ataxia). Ssc1 also participates in
translational regulation of cytochrome c oxidase (COX)
biogenesis by interacting with Mss51 and
Mss51-containing complexes.
Length = 377
Score = 40.1 bits (94), Expect = 2e-04
Identities = 35/94 (37%), Positives = 46/94 (48%), Gaps = 3/94 (3%)
Query: 30 AVMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHK-GERTFGEDAQIIGTRF 88
AV+ +DLG+ VA++ P I N E R TP++VAF K GER G A+
Sbjct: 3 AVIGIDLGTTNSCVAVMEGKTPKVIE-NAEGARTTPSVVAFTKDGERLVGMPAKRQAVTN 61
Query: 89 PSNSYGYFLDLLGKSIDSPVVQLFKSRFPYYDIV 122
P N+ L+G+ D P VQ P Y IV
Sbjct: 62 PENTLYATKRLIGRRFDDPEVQKDIKNVP-YKIV 94
>gnl|CDD|215618 PLN03184, PLN03184, chloroplast Hsp70; Provisional.
Length = 673
Score = 39.1 bits (91), Expect = 4e-04
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 31 VMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHK-GERTFGEDAQIIGTRFP 89
V+ +DLG+ VA + G P I N E +R TP++VA+ K G+R G+ A+ P
Sbjct: 41 VVGIDLGTTNSAVAAMEGGKPT-IVTNAEGQRTTPSVVAYTKNGDRLVGQIAKRQAVVNP 99
Query: 90 SNSY 93
N++
Sbjct: 100 ENTF 103
>gnl|CDD|212675 cd10233, HSPA1-2_6-8-like_NBD, Nucleotide-binding domain of
HSPA1-A, -B, -L, HSPA-2, -6, -7, -8, and similar
proteins. This subfamily includes human HSPA1A (70-kDa
heat shock protein 1A, also known as HSP72; HSPA1;
HSP70I; HSPA1B; HSP70-1; HSP70-1A), HSPA1B (70-kDa heat
shock protein 1B, also known as HSPA1A; HSP70-2;
HSP70-1B), and HSPA1L (70-kDa heat shock protein 1-like,
also known as HSP70T; hum70t; HSP70-1L; HSP70-HOM). The
genes for these three HSPA1 proteins map in close
proximity on the major histocompatibility complex (MHC)
class III region on chromosome 6, 6p21.3. This subfamily
also includes human HSPA8 (heat shock 70kDa protein 8,
also known as LAP1; HSC54; HSC70; HSC71; HSP71; HSP73;
NIP71; HSPA10; the HSPA8 gene maps to 11q24.1), human
HSPA2 (70-kDa heat shock protein 2, also known as
HSP70-2; HSP70-3, the HSPA2 gene maps to 14q24.1), human
HSPA6 (also known as heat shock 70kDa protein 6
(HSP70B') gi 94717614, the HSPA6 gene maps to 1q23.3),
human HSPA7 (heat shock 70kDa protein 7 , also known as
HSP70B; the HSPA7 gene maps to 1q23.3) and Saccharmoyces
cerevisiae Stress-Seventy subfamily B/Ssb1p. This
subfamily belongs to the heat shock protein 70 (HSP70)
family of chaperones that assist in protein folding and
assembly and can direct incompetent "client" proteins
towards degradation. Typically, HSP70s have a
nucleotide-binding domain (NBD) and a substrate-binding
domain (SBD). The nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. HSP70 chaperone
activity is regulated by various co-chaperones: J-domain
proteins and nucleotide exchange factors (NEFs).
Associations of polymorphisms within the MHC-III HSP70
gene locus with longevity, systemic lupus erythematosus,
Meniere's disease, noise-induced hearing loss,
high-altitude pulmonary edema, and coronary heart
disease, have been found. HSPA2 is involved in cancer
cell survival, is required for maturation of male
gametophytes, and is linked to male infertility. The
induction of HSPA6 is a biomarker of cellular stress.
HSPA8 participates in the folding and trafficking of
client proteins to different subcellular compartments,
and in the signal transduction and apoptosis process; it
has been shown to protect cardiomyocytes against
oxidative stress partly through an interaction with
alpha-enolase. S. cerevisiae Ssb1p, is part of the
ribosome-associated complex (RAC), it acts as a
chaperone for nascent polypeptides, and is important for
translation fidelity; Ssb1p is also a [PSI+]
prion-curing factor.
Length = 376
Score = 38.9 bits (91), Expect = 4e-04
Identities = 31/112 (27%), Positives = 53/112 (47%), Gaps = 1/112 (0%)
Query: 34 VDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHKGERTFGEDAQIIGTRFPSNSY 93
+DLG+ + V + G +EI N + R TP+ VAF ER G+ A+ P+N+
Sbjct: 4 IDLGTTYSCVGVFQHG-KVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTV 62
Query: 94 GYFLDLLGKSIDSPVVQLFKSRFPYYDIVADEERGTIVFKTNDNELYHVEEL 145
L+G+ PVVQ +P+ + + IV + + ++ EE+
Sbjct: 63 FDAKRLIGRKFSDPVVQSDMKHWPFKVVNGGGKPPIIVEYKGETKTFYPEEI 114
>gnl|CDD|184038 PRK13410, PRK13410, molecular chaperone DnaK; Provisional.
Length = 668
Score = 38.8 bits (91), Expect = 5e-04
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 31 VMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHK-GERTFGEDAQIIGTRFP 89
++ +DLG+ VA++ G P+ IA N E R TP++V F K GE G+ A+ P
Sbjct: 4 IVGIDLGTTNSVVAVMEGGKPVVIA-NAEGMRTTPSVVGFTKDGELLVGQLARRQLVLNP 62
Query: 90 SNSY 93
N++
Sbjct: 63 QNTF 66
>gnl|CDD|212674 cd10232, ScSsz1p_like_NBD, Nucleotide-binding domain of
Saccharmomyces cerevisiae Ssz1pp and similar proteins.
Saccharomyces cerevisiae Ssz1p (also known as
/Pdr13p/YHR064C) belongs to the heat shock protein 70
(HSP70) family of chaperones that assist in protein
folding and assembly and can direct incompetent "client"
proteins towards degradation. Typically, HSP70s have a
nucleotide-binding domain (NBD) and a substrate-binding
domain (SBD). The nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. HSP70 chaperone
activity is regulated by various co-chaperones: J-domain
proteins and nucleotide exchange factors (NEFs). Some
family members are not chaperones but rather, function
as NEFs for their Hsp70 partners, while other family
members function as both chaperones and NEFs. Ssz1 does
not function as a chaperone; it facilitates the
interaction between the HSP70 Ssb protein and its
partner J-domain protein Zuo1 (also known as zuotin) on
the ribosome. Ssz1 is found in a stable heterodimer
(called RAC, ribosome associated complex) with Zuo1.
Zuo1 can only stimulate the ATPase activity of Ssb, when
it is in complex with Ssz1. Ssz1 binds ATP but neither
nucleotide-binding, hydrolysis, or its SBD, is needed
for its in vivo function.
Length = 386
Score = 37.4 bits (87), Expect = 0.001
Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 5/80 (6%)
Query: 30 AVMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHKGERTFGEDA--QIIGTR 87
V+ ++ G+ + +A ++ G IA N++ +R+ P+ +++H + G A Q+I R
Sbjct: 1 TVIGINFGNTYSSIACINQGKADVIA-NEDGERQIPSAISYHGEQEYHGNQAKAQLI--R 57
Query: 88 FPSNSYGYFLDLLGKSIDSP 107
N+ F DLLGK
Sbjct: 58 NAKNTITNFRDLLGKPFSEI 77
>gnl|CDD|212676 cd10234, HSPA9-Ssq1-like_NBD, Nucleotide-binding domain of human
HSPA9 and similar proteins. This subfamily includes
human mitochondrial HSPA9 (also known as 70-kDa heat
shock protein 9, CSA; MOT; MOT2; GRP75; PBP74; GRP-75;
HSPA9B; MTHSP75; the gene encoding HSPA9 maps to
5q31.1), Escherichia coli DnaK, Saccharomyces
cerevisiae Stress-seventy subfamily Q protein 1/Ssq1p
(also called Ssc2p, Ssh1p, mtHSP70 homolog), and S.
cerevisiae Stress-Seventy subfamily C/Ssc1p (also
called mtHSP70, Endonuclease SceI 75 kDa subunit). It
belongs to the heat shock protein 70 (HSP70) family of
chaperones that assist in protein folding and assembly,
and can direct incompetent "client" proteins towards
degradation. Typically, HSP70s have a
nucleotide-binding domain (NBD) and a substrate-binding
domain (SBD). The nucleotide sits in a deep cleft
formed between the two lobes of the NBD. The two
subdomains of each lobe change conformation between
ATP-bound, ADP-bound, and nucleotide-free states. ATP
binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
Hsp70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide
exchange factors (NEFs); for Escherichia coli DnaK,
these are the DnaJ and GrpE, respectively.
Length = 376
Score = 37.2 bits (87), Expect = 0.001
Identities = 22/52 (42%), Positives = 31/52 (59%), Gaps = 2/52 (3%)
Query: 31 VMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHK-GERTFGEDA 81
++ +DLG+ VA++ G P I N E R TP++VAF K GER G+ A
Sbjct: 4 IIGIDLGTTNSCVAVMEGGEPTVIP-NAEGSRTTPSVVAFTKKGERLVGQPA 54
>gnl|CDD|212680 cd10238, HSPA14-like_NBD, Nucleotide-binding domain of human HSPA14
and similar proteins. Human HSPA14 (also known as
70-kDa heat shock protein 14, HSP70L1, HSP70-4; the gene
encoding HSPA14 maps to 10p13), is ribosome-associated
and belongs to the heat shock protein 70 (HSP70) family
of chaperones that assist in protein folding and
assembly, and can direct incompetent "client" proteins
towards degradation. Typically, HSP70s have a
nucleotide-binding domain (NBD) and a substrate-binding
domain (SBD). The nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. HSP70 chaperone
activity is regulated by various co-chaperones: J-domain
proteins and nucleotide exchange factors (NEFs). HSPA14
interacts with the J-protein MPP11 to form the mammalian
ribosome-associated complex (mRAC). HSPA14 participates
in a pathway along with Nijmegen breakage syndrome 1
(NBS1, also known as p85 or nibrin), heat shock
transcription factor 4b (HSF4b), and HSPA4 (belonging to
a different subfamily), that induces tumor migration,
invasion, and transformation. HSPA14 is a potent T
helper cell (Th1) polarizing adjuvant that contributes
to antitumor immune responses.
Length = 375
Score = 37.0 bits (86), Expect = 0.002
Identities = 24/90 (26%), Positives = 36/90 (40%), Gaps = 2/90 (2%)
Query: 53 EIALNKESKRKTPTLVAFHKGERTFGEDAQIIGTRFPSNSYGYFLDLLGKSIDSPVVQLF 112
++ N R TP +VAF E G A+ R +N+ +LG+S P Q
Sbjct: 23 DVVANDAGDRVTPAVVAFTDTEVIVGLAAKQGRIRNAANTIVKNKQILGRSYSDPFKQKE 82
Query: 113 KSRFPYYDIVADEERGTIVFKTNDNELYHV 142
K+ I D E +F + + HV
Sbjct: 83 KTESSCKIIEKDGEPKYEIFT--EEKTKHV 110
>gnl|CDD|140213 PTZ00186, PTZ00186, heat shock 70 kDa precursor protein;
Provisional.
Length = 657
Score = 37.0 bits (85), Expect = 0.002
Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 1/88 (1%)
Query: 31 VMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHKGERTFGEDAQIIGTRFPS 90
V+ VDLG+ + VA + + N E R TP++VAF E+ G A+ P
Sbjct: 29 VIGVDLGTTYSCVATMDGDKA-RVLENSEGFRTTPSVVAFKGSEKLVGLAAKRQAITNPQ 87
Query: 91 NSYGYFLDLLGKSIDSPVVQLFKSRFPY 118
+++ L+G+ + +Q PY
Sbjct: 88 STFYAVKRLIGRRFEDEHIQKDIKNVPY 115
>gnl|CDD|212688 cd11738, HSPA4L_NBD, Nucleotide-binding domain of HSPA4L. Human
HSPA4L (also known as 70-kDa heat shock protein 4-like,
APG-1, HSPH3, and OSP94; the human HSPA4L gene maps to
4q28) is expressed ubiquitously and predominantly in the
testis. It is required for normal spermatogenesis and
plays a role in osmotolerance. HSPA4L belongs to the
105/110 kDa heat shock protein (HSP105/110) subfamily of
the HSP70-like family. HSP105/110s are believed to
function generally as co-chaperones of HSP70 chaperones,
acting as nucleotide exchange factors (NEFs), to remove
ADP from their HSP70 chaperone partners during the ATP
hydrolysis cycle. HSP70 chaperones assist in protein
folding and assembly, and can direct incompetent
"client" proteins towards degradation. Like HSP70
chaperones, HSP105/110s have an N-terminal
nucleotide-binding domain (NBD) and a C-terminal
substrate-binding domain (SBD). For HSP70 chaperones,
the nucleotide sits in a deep cleft formed between the
two lobes of the NBD. The two subdomains of each lobe
change conformation between ATP-bound, ADP-bound, and
nucleotide-free states. ATP binding opens up the
substrate-binding site; substrate-binding increases the
rate of ATP hydrolysis. Hsp70 chaperone activity is also
regulated by J-domain proteins.
Length = 383
Score = 36.5 bits (84), Expect = 0.002
Identities = 27/89 (30%), Positives = 41/89 (46%), Gaps = 1/89 (1%)
Query: 30 AVMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHKGERTFGEDAQIIGTRFP 89
+V+ +DLG +A+ G +E N+ S R TP ++ R G A+
Sbjct: 1 SVVGIDLGFLNCYIAVARSG-GIETIANEYSDRCTPACISLGSRTRAIGNAAKSQIVTNV 59
Query: 90 SNSYGYFLDLLGKSIDSPVVQLFKSRFPY 118
N+ F L G+S D P+VQ + R PY
Sbjct: 60 RNTIHGFKKLHGRSFDDPIVQTERIRLPY 88
>gnl|CDD|184039 PRK13411, PRK13411, molecular chaperone DnaK; Provisional.
Length = 653
Score = 36.3 bits (84), Expect = 0.003
Identities = 21/53 (39%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 31 VMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHK-GERTFGEDAQ 82
V+ +DLG+ VA++ G P+ I N E R TP++V F K G+R G+ A+
Sbjct: 4 VIGIDLGTTNSCVAVLEGGKPIVIP-NSEGGRTTPSIVGFGKSGDRLVGQLAK 55
>gnl|CDD|233830 TIGR02350, prok_dnaK, chaperone protein DnaK. Members of this
family are the chaperone DnaK, of the DnaK-DnaJ-GrpE
chaperone system. All members of the seed alignment
were taken from completely sequenced bacterial or
archaeal genomes and (except for Mycoplasma sequence)
found clustered with other genes of this systems. This
model excludes DnaK homologs that are not DnaK itself,
such as the heat shock cognate protein HscA
(TIGR01991). However, it is not designed to distinguish
among DnaK paralogs in eukaryotes. Note that a number
of dnaK genes have shadow ORFs in the same reverse
(relative to dnaK) reading frame, a few of which have
been assigned glutamate dehydrogenase activity. The
significance of this observation is unclear; lengths of
such shadow ORFs are highly variable as if the
presumptive protein product is not conserved [Protein
fate, Protein folding and stabilization].
Length = 595
Score = 36.1 bits (84), Expect = 0.003
Identities = 22/52 (42%), Positives = 32/52 (61%), Gaps = 2/52 (3%)
Query: 31 VMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHK-GERTFGEDA 81
++ +DLG+ VA++ G P+ I N E R TP++VAF K GER G+ A
Sbjct: 2 IIGIDLGTTNSCVAVMEGGEPVVIP-NAEGARTTPSVVAFTKNGERLVGQPA 52
>gnl|CDD|212687 cd11737, HSPA4_NBD, Nucleotide-binding domain of HSPA4. Human
HSPA4 (also known as 70-kDa heat shock protein 4, APG-2,
HS24/P52, hsp70 RY, and HSPH2; the human HSPA4 gene maps
to 5q31.1) responds to acidic pH stress, is involved in
the radioadaptive response, is required for normal
spermatogenesis and is overexpressed in hepatocellular
carcinoma. It participates in a pathway along with NBS1
(Nijmegen breakage syndrome 1, also known as p85 or
nibrin), heat shock transcription factor 4b (HDF4b), and
HSPA14 (belonging to a different HSP70 subfamily) that
induces tumor migration, invasion, and transformation.
HSPA4 expression in sperm was increased in men with
oligozoospermia, especially in those with varicocele.
HSPA4 belongs to the 105/110 kDa heat shock protein
(HSP105/110) subfamily of the HSP70-like family.
HSP105/110s are believed to function generally as
co-chaperones of HSP70 chaperones, acting as nucleotide
exchange factors (NEFs), to remove ADP from their HSP70
chaperone partners during the ATP hydrolysis cycle.
HSP70 chaperones assist in protein folding and assembly,
and can direct incompetent "client" proteins towards
degradation. Like HSP70 chaperones, HSP105/110s have an
N-terminal nucleotide-binding domain (NBD) and a
C-terminal substrate-binding domain (SBD). For HSP70
chaperones, the nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. Hsp70 chaperone
activity is also regulated by J-domain proteins.
Length = 383
Score = 35.7 bits (82), Expect = 0.005
Identities = 25/89 (28%), Positives = 39/89 (43%), Gaps = 1/89 (1%)
Query: 30 AVMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHKGERTFGEDAQIIGTRFP 89
+V+ +DLG + VA+ G +E N+ S R TP ++F R+ G A+
Sbjct: 1 SVVGIDLGFQSCYVAVARAG-GIETIANEYSDRCTPACISFGPKNRSIGAAAKSQVISNA 59
Query: 90 SNSYGYFLDLLGKSIDSPVVQLFKSRFPY 118
N+ F G++ P VQ K Y
Sbjct: 60 KNTVQGFKRFHGRAFSDPFVQAEKPSLAY 88
>gnl|CDD|234715 PRK00290, dnaK, molecular chaperone DnaK; Provisional.
Length = 627
Score = 32.8 bits (76), Expect = 0.046
Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 43 VAIVSPGVPMEIALNKESKRKTPTLVAFHK-GERTFGEDA 81
VA++ G P I N E R TP++VAF K GER G+ A
Sbjct: 16 VAVMEGGEPKVIE-NAEGARTTPSVVAFTKDGERLVGQPA 54
>gnl|CDD|214360 CHL00094, dnaK, heat shock protein 70.
Length = 621
Score = 32.0 bits (73), Expect = 0.091
Identities = 20/53 (37%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 31 VMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHK-GERTFGEDAQ 82
V+ +DLG+ VA++ G P I N E R TP++VA+ K G+ G+ A+
Sbjct: 4 VVGIDLGTTNSVVAVMEGGKPTVIP-NAEGFRTTPSIVAYTKKGDLLVGQIAK 55
>gnl|CDD|212678 cd10236, HscA_like_NBD, Nucleotide-binding domain of HscA and
similar proteins. Escherichia coli HscA (heat shock
cognate protein A, also called Hsc66), belongs to the
heat shock protein 70 (HSP70) family of chaperones that
assist in protein folding and assembly and can direct
incompetent "client" proteins towards degradation.
Typically, HSP70s have a nucleotide-binding domain (NBD)
and a substrate-binding domain (SBD). The nucleotide
sits in a deep cleft formed between the two lobes of the
NBD. The two subdomains of each lobe change conformation
between ATP-bound, ADP-bound, and nucleotide-free
states. ATP binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
HSP70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs). HscA's partner J-domain protein is HscB;
it does not appear to require a NEF, and has been shown
to be induced by cold-shock. The HscA-HscB
chaperone/co-chaperone pair is involved in [Fe-S]
cluster assembly.
Length = 355
Score = 31.4 bits (72), Expect = 0.14
Identities = 32/110 (29%), Positives = 51/110 (46%), Gaps = 6/110 (5%)
Query: 34 VDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHKGERTFGEDAQIIGTRFPSNSY 93
+DLG+ VA V G ++I ++ + P++V + G + G DA + P N+
Sbjct: 5 IDLGTTNSLVASVLSG-KVKILPDENGRVLLPSVVHYGDGGISVGHDALKLAISDPKNTI 63
Query: 94 GYFLDLLGKSIDSPVVQLFKSRFPYYDIVADEERGTIVFKTNDNELYHVE 143
L+GKSI+ K FPY I+ + G I+F T + VE
Sbjct: 64 SSVKRLMGKSIEDI-----KKSFPYLPILEGKNGGIILFHTQQGTVTPVE 108
>gnl|CDD|131030 TIGR01975, isoAsp_dipep, isoaspartyl dipeptidase IadA. The
L-isoaspartyl derivative of Asp arises non-enzymatically
over time as a form of protein damage. In this
isomerization, the connectivity of the polypeptide
changes to pass through the beta-carboxyl of the side
chain. Much but not all of this damage can be repaired
by protein-L-isoaspartate (D-aspartate)
O-methyltransferase. This model describes the
isoaspartyl dipeptidase IadA, apparently one of two such
enzymes in E. coli, an enzyme that degrades isoaspartyl
dipeptides and may unblock degradation of proteins that
cannot be repaired. This model also describes closely
related proteins from other species (e.g. Clostridium
perfringens, Thermoanaerobacter tengcongensis) that we
assume to be equivalent in function. This family shows
homology to dihydroorotases [Protein fate, Degradation
of proteins, peptides, and glycopeptides].
Length = 389
Score = 29.4 bits (66), Expect = 0.63
Identities = 17/57 (29%), Positives = 27/57 (47%)
Query: 28 GIAVMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHKGERTFGEDAQII 84
G+ V S + E ++ A+ VP+E AL + L KGE + G DA ++
Sbjct: 302 GLGVGSFETLFEEVREAVKDGDVPLEKALRVITSNVAGVLNLTGKGEISPGNDADLV 358
>gnl|CDD|238633 cd01308, Isoaspartyl-dipeptidase, Isoaspartyl dipeptidase
hydrolyzes the beta-L-isoaspartyl linkages in
dipeptides, as part of the degradative pathway to
eliminate proteins with beta-L-isoaspartyl peptide
bonds, bonds whereby the beta-group of an aspartate
forms the peptide link with the amino group of the
following amino acid. Formation of this bond is a
spontaneous nonenzymatic reaction in nature and can
profoundly effect the function of the protein.
Isoaspartyl dipeptidase is an octameric enzyme that
contains a binuclear zinc center in the active site of
each subunit and shows a strong preference of
hydrolyzing Asp-Leu dipeptides.
Length = 387
Score = 29.3 bits (66), Expect = 0.71
Identities = 17/57 (29%), Positives = 27/57 (47%)
Query: 28 GIAVMSVDLGSEWMKVAIVSPGVPMEIALNKESKRKTPTLVAFHKGERTFGEDAQII 84
G+ V SVD ++ A+ +P+E+AL + L KGE G DA ++
Sbjct: 300 GLGVGSVDTLLREVREAVKCGDIPLEVALRVITSNVARILKLRKKGEIQPGFDADLV 356
>gnl|CDD|233016 TIGR00546, lnt, apolipoprotein N-acyltransferase. This enzyme
transfers the acyl group to lipoproteins in the
lgt/lsp/lnt system which is found broadly in bacteria
but not in archaea. This model represents one component
of the "lipoprotein lgt/lsp/lnt system" genome property
[Protein fate, Protein modification and repair].
Length = 391
Score = 27.3 bits (61), Expect = 2.8
Identities = 11/49 (22%), Positives = 21/49 (42%)
Query: 12 LCSSVVLLLTLFEHSYGIAVMSVDLGSEWMKVAIVSPGVPMEIALNKES 60
L +VV+LL + + + VA+V P +P ++ + E
Sbjct: 131 LAIAVVVLLAALGFLLYELKSATPVPGPTLNVALVQPNIPQDLKFDSEG 179
>gnl|CDD|177895 PLN02253, PLN02253, xanthoxin dehydrogenase.
Length = 280
Score = 26.7 bits (59), Expect = 4.6
Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 12/82 (14%)
Query: 1 MLCLMKISLVTLCSSVVLLLTLFEHSYGIAVMSV---------DLGSEWMKVAIVSP-GV 50
M+ L K S+V+LCS + L H+Y + +V +LG ++V VSP V
Sbjct: 142 MIPLKKGSIVSLCSVASAIGGLGPHAYTGSKHAVLGLTRSVAAELGKHGIRVNCVSPYAV 201
Query: 51 PMEIALNK--ESKRKTPTLVAF 70
P +AL E +R L F
Sbjct: 202 PTALALAHLPEDERTEDALAGF 223
>gnl|CDD|224208 COG1289, COG1289, Predicted membrane protein [Function unknown].
Length = 674
Score = 27.0 bits (60), Expect = 4.7
Identities = 6/30 (20%), Positives = 12/30 (40%)
Query: 5 MKISLVTLCSSVVLLLTLFEHSYGIAVMSV 34
++ +L L L + H Y I + +
Sbjct: 359 LRTALALLLGYAFWLALGWPHGYWILLTAA 388
>gnl|CDD|226555 COG4069, COG4069, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 367
Score = 26.7 bits (59), Expect = 5.0
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 2/46 (4%)
Query: 34 VDLGSEWMKVAIV--SPGVPMEIALNKESKRKTPTLVAFHKGERTF 77
VDL +K + SP P ++ KE+ ++ H ER++
Sbjct: 216 VDLARAVVKTGALRRSPDEPKKVKSRKENAHAVKVILIDHAAERSY 261
>gnl|CDD|173034 PRK14570, PRK14570, D-alanyl-alanine synthetase A; Provisional.
Length = 364
Score = 26.3 bits (58), Expect = 6.8
Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 81 AQIIGTRFPSNSYGYFLDLLGKSIDSPVVQLFKSRFPYYDIVADEE 126
A I+G+ N Y F LL KS + P+V F YD D+E
Sbjct: 119 AGILGSAISINKY--FCKLLLKSFNIPLVPFIG--FRKYDYFLDKE 160
>gnl|CDD|218211 pfam04683, Proteasom_Rpn13, Proteasome complex subunit Rpn13
ubiquitin receptor. This family was thought originally
to be involved in cell-adhesion, but the members are now
known to be proteasome subunit Rpn13, a novel ubiquitin
receptor. The 26S proteasome is a huge macromolecular
protein-degradation machine consisting of a
proteolytically active 20S core, in the form of four
disc-like proteins, and one or two 19S regulatory
particles. The regulatory particle(s) sit on the top and
or bottom of the core, de-ubiquitinate the substrate
peptides, unfold them and guide them into the narrow
channel through the centre of the core. Rpn13 and its
homologues dock onto the regulatory particle through the
N-terminal region which binds Rpn2. The C-terminal part
of the domain binds de-ubiquitinating enzyme Uch37/UCHL5
and enhances its isopeptidase activity. Rpn13 binds
ubiquitin via a conserved amino-terminal region called
the pleckstrin-like receptor for ubiquitin, termed Pru,
domain. The domain forms two contiguous anti-parallel
beta-sheets with a configuration similar to the
pleckstrin-homology domain (PHD) fold. Rpn13's ability
to bind ubiquitin and the proteasome subunit Rpn2/S1
simultaneously supports evidence of its role as a
ubiquitin receptor. Finally, when complexed to
di-ubiquitin, via the Pru, and Uch37 via the C-terminal
part, it frees up the distal ubiquitin for
de-ubiquitination by the Uch37.
Length = 84
Score = 24.9 bits (55), Expect = 8.2
Identities = 5/25 (20%), Positives = 11/25 (44%)
Query: 119 YDIVADEERGTIVFKTNDNELYHVE 143
+ D +G + +D+ L H +
Sbjct: 8 KTVTPDPRKGLLYLYKSDDGLLHFQ 32
>gnl|CDD|128971 smart00732, YqgFc, Likely ribonuclease with RNase H fold. YqgF
proteins are likely to function as an alternative to
RuvC in most bacteria, and could be the principal
holliday junction resolvases in low-GC Gram-positive
bacteria. In Spt6p orthologues, the catalytic residues
are substituted indicating that they lack enzymatic
functions.
Length = 99
Score = 25.2 bits (56), Expect = 9.1
Identities = 24/106 (22%), Positives = 39/106 (36%), Gaps = 12/106 (11%)
Query: 29 IAVMSVDLGSEWMKVAIVSPGVPMEIALNKES---KRKTPTLVAFHKGERTFGEDAQIIG 85
V+ +D G + + VA+V ++A E K K + + D +IG
Sbjct: 1 KRVLGLDPGRKGIGVAVVDE--TGKLADPLEVIPRTNKEADAARLKKLIKKYQPDLIVIG 58
Query: 86 TRFPSNSYGYFLDLLGKSIDSPVVQLFKSRFPYYDIVADEERGTIV 131
P N G + + +L K RF ++ D ER V
Sbjct: 59 --LPLNMNG----TASRETEEAFAELLKERFNLPVVLVD-ERLATV 97
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
0.321 0.138 0.400
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,404,825
Number of extensions: 664230
Number of successful extensions: 574
Number of sequences better than 10.0: 1
Number of HSP's gapped: 565
Number of HSP's successfully gapped: 44
Length of query: 146
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 58
Effective length of database: 7,034,450
Effective search space: 407998100
Effective search space used: 407998100
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: 54 (24.4 bits)