RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17875
(107 letters)
>gnl|CDD|163699 cd08068, MPN_BRCC36, Mov34/MPN/PAD-1 family: BRCC36, a subunit of
BRCA1-A complex. BRCC36 (BRCA1-A complex subunit
BRCC36; BRCA1/BRCA2-containing complex subunit 36;
BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC
complex subunit BRCC36; BRCC36 isopeptidase complex;
Lys-63-specific deubiquitinase BRCC36) and BRCC36-like
domains are members of JAMM/MPN+ deubiquitinases (DUBs),
possibly with Zn2+-dependent ubiquitin isopeptidase
activity. BRCC36 is part of the
BRCA1/BRCA2/BARD1-containing nuclear complex that
displays an E3 ubiquitin ligase activity. It is targeted
to DNA damage foci after irradiation; RAP80 recruits the
Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand
breaks (DSBs) for DNA repair through specific
recognition of Lys 63-linked polyubiquitinated proteins
by its tandem ubiquitin-interacting motifs. A new
protein, MERIT40 (mediator of RAP80 interactions and
targeting 40 kDa), also named NBA1 (new component of the
BRCA1 A complex), exists in the same BRCA1-containing
complex and is essential for the integrity of the
complex. There are studies suggesting that MERIT40/NBA1
ties BRCA1 complex integrity, DSB recognition, and
ubiquitin chain activities to the DNA damage response.
It has also been shown that BRCA1-containing complex
resembles the lid complex of the 26S proteasome.
Length = 244
Score = 115 bits (291), Expect = 1e-33
Identities = 52/104 (50%), Positives = 68/104 (65%), Gaps = 3/104 (2%)
Query: 7 YISEDVYFSMFYLALSNDKLEVLSMLIGETKEEKG---VKSVHVYTMVIPLRLTSKHDRV 63
++S DVY ALS +K EV+ +LIGE + K V VH+ ++I R + DRV
Sbjct: 5 HLSADVYLVCLTHALSTEKEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRV 64
Query: 64 EASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHITVWPSDV 107
E SPEQL A TEAE+L++ R +RV+GW+HSHPHITVWPS V
Sbjct: 65 EISPEQLSAASTEAERLTEETGRPMRVVGWYHSHPHITVWPSHV 108
>gnl|CDD|163689 cd08058, MPN_euk_mb, Mpr1p, Pad1p N-terminal (MPN) domains with
catalytic isopeptidase activity (metal-binding);
eukaryotic. This family contains eukaryotic MPN (also
known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in
proteins with a variety of functions, including AMSH
(associated molecule with the Src homology 3 domain
(SH3) of STAM), H2A-DUB (histone H2A deubiquitinase),
BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as
well as Rpn11 (regulatory particle number 11) and CSN5
(COP9 signalosome complex subunit 5). These domains
contain the signature JAB1/MPN/Mov34 metalloenzyme
(JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc
ion coordination and provides the active site for
isopeptidase activity. Rpn11 is responsible for
substrate deubiquitination during proteasomal
degradation. It is essential for maintaining a correct
cell cycle and normal mitochondrial morphology and
physiology. CSN5 is critical for nuclear export and the
degradation of several tumor suppressor proteins,
including p53, p27, and Smad4. Over-expression of CSN5
has been implicated in cancer initiation and
progression. AMSH specifically cleaves Lys 63 and not
Lys48-linked polyubiquitin (poly-Ub) chains, thus
facilitating the recycling and subsequent trafficking of
receptors to the cell surface. It is involved in the
degradation of EGF receptor (EGFR) and possibly other
ubiquitinated endocytosed proteins. BRCC36 is part of
the BRCA1/BRCA2/BARD1-containing nuclear complex that
displays an E3 ubiquitin ligase activity; it is targeted
to DNA damage foci after irradiation. 2A-DUB is specific
for monoubiquitinated H2A (uH2A), regulating
transcription by coordinating histone acetylation and
deubiquitination, and destabilizing the association of
linker histone H1 with nucleosomes. It is a positive
regulator of androgen receptor (AR) transactivation
activity on a reporter gene and serves as a marker in
prostate tumors.
Length = 119
Score = 65.3 bits (159), Expect = 5e-15
Identities = 28/99 (28%), Positives = 35/99 (35%), Gaps = 17/99 (17%)
Query: 11 DVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKH-DRVEASPEQ 69
D M A SN +EV+ +L GE T KH + S
Sbjct: 1 DALLKMLQHAESNTGIEVMGLLCGELTHN---------------EFTDKHVIVPKQSAGP 45
Query: 70 LFEAVTE-AEKLSKLYNRELRVIGWFHSHPHITVWPSDV 107
E + R L V+GW+HSHP T W S V
Sbjct: 46 DSCTGENVEELFNVQTGRPLLVVGWYHSHPTFTAWLSSV 84
>gnl|CDD|216478 pfam01398, JAB, JAB1/Mov34/MPN/PAD-1 ubiquitin protease. Members
of this family are found in proteasome regulatory
subunits, eukaryotic initiation factor 3 (eIF3) subunits
and regulators of transcription factors. This family is
also known as the MPN domain and PAD-1-like domain,
JABP1 domain or JAMM domain. These are metalloenzymes
that function as the ubiquitin isopeptidase/
deubiquitinase in the ubiquitin-based signaling and
protein turnover pathways in eukaryotes. Versions of the
domain in prokaryotic cognates of the
ubiquitin-modification pathway are predicted to have a
similar role.
Length = 117
Score = 50.9 bits (122), Expect = 1e-09
Identities = 26/100 (26%), Positives = 43/100 (43%), Gaps = 7/100 (7%)
Query: 8 ISEDVYFSMFYLALSN--DKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEA 65
I V + A EV+ +L+G + ++ + V + + D VEA
Sbjct: 7 IHPLVLLKIVDHARRGGKSGEEVMGVLLGTLEGDR---VIEVTNSFALPQSET-EDDVEA 62
Query: 66 SPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHITVWPS 105
E E + + ++ K NR+ V+GW+HSHP W S
Sbjct: 63 -VELDHEYMEKMLEMLKKVNRDEEVVGWYHSHPGYGCWLS 101
>gnl|CDD|214573 smart00232, JAB_MPN, JAB/MPN domain. Domain in Jun kinase
activation domain binding protein and proteasomal
subunits. Domain at Mpr1p and Pad1p N-termini. Domain of
unknown function.
Length = 135
Score = 50.8 bits (122), Expect = 2e-09
Identities = 24/101 (23%), Positives = 47/101 (46%), Gaps = 8/101 (7%)
Query: 7 YISEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEAS 66
+ V ++ A+ + EV +L+G++ ++ V V + + D V+
Sbjct: 3 KVHPLVPLNILKHAIRDGPEEVCGVLLGKSNKD----RPEVKE-VFAVPNEPQDDSVQEY 57
Query: 67 PEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHITVWPSDV 107
E + E K N++L ++GW+HSHP + +PS+V
Sbjct: 58 DEDYSHLMDEELKKV---NKDLEIVGWYHSHPDESPFPSEV 95
>gnl|CDD|163701 cd08070, MPN_like, Mpr1p, Pad1p N-terminal (MPN) domains with
catalytic isopeptidase activity (metal-binding). This
family contains archaeal and bacterial MPN (also known
as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These
domains contain the signature JAB1/MPN/Mov34
metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is
involved in zinc ion coordination and provides the
active site for isopeptidase activity for the release of
ubiquitin from ubiquitinated proteins (thus having
deubiquitinating (DUB) activity) that are tagged for
degradation. The JAMM proteins likely hydrolyze
ubiquitin conjugates in a manner similar to thermolysin,
in which the zinc-polarized aqua ligand serves as the
nucleophile, compared with the classical DUBs that do so
with a cysteine residue in the active site.
Length = 128
Score = 41.1 bits (97), Expect = 1e-05
Identities = 23/76 (30%), Positives = 31/76 (40%), Gaps = 13/76 (17%)
Query: 32 LIGETKEEKGVKSVHVYTMVIPLR--LTSKHDRVEASPEQLFEAVTEAEKLSKLYNRELR 89
L+G+ + T V P+R S R E P + A EA + R L
Sbjct: 23 LLGKGGGVTAIV-----TEVYPVRNVAESPRRRFEIDPAEQLAAQREARE------RGLE 71
Query: 90 VIGWFHSHPHITVWPS 105
V+G +HSHP PS
Sbjct: 72 VVGIYHSHPDGPARPS 87
>gnl|CDD|163700 cd08069, MPN_RPN11_CSN5, Mov34/MPN/PAD-1 family: proteasomal
regulatory protein Rpn11 and signalosome complex subunit
CSN5. This family contains proteasomal regulatory
protein Rpn11 (26S proteasome regulatory subunit rpn11;
PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the
19S-proteasome; regulatory particle number 11) and
signalosomal CSN5 (COP9 signalosome complex subunit 5;
COP9 complex homolog subunit 5; c-Jun activation
domain-binding protein-1; CSN5/JAB1; JAB1). COP9
signalosome (CSN) and the proteasome lid are paralogous
complexes and their respective subunits CSN5 and Rpn11
are most closely related between the two complexes, both
containing the conserved JAMM (JAB1/MPN/Mov34
metalloenzyme) motif involved in zinc ion coordination
and providing the active site for isopeptidase activity.
Rpn11 is responsible for substrate deubiquitination
during proteasomal degradation. It is essential for
maintaining a correct cell cycle and normal
mitochondrial morphology and physiology; mutations in
Rpn11 cause cell cycle and mitochondrial defects,
temperature sensitivity and sensitivity to DNA damaging
reagents such as UV. It has been shown that the
C-terminal region of Rpn11 is involved in the regulation
of the mitochondrial fission and tubulation processes.
CSN5, one of the eight subunits of CSN, is critical for
nuclear export and the degradation of several tumor
suppressor proteins, including p53, p27, and Smad4. Its
MPN+ domain is critical for the physical interaction of
RUNX3 and Jab1. It has been suggested that the direct
interaction of CSN5/JAB1 with p27 provides p27 with a
leucine-rich nuclear export signal (NES), which is
required for binding to chromosomal region maintenance 1
(CRM1), and facilitates nuclear export. The
over-expression of CSN5/JAB1 also has been implicated in
cancer initiation and progression, including cancer of
the lung, pancreas, mouth, thyroid, and breast,
suggesting that the oncogenic activity of CSN5 is
associated with the down-regulation of RUNX3.
Length = 268
Score = 41.9 bits (99), Expect = 1e-05
Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 15/86 (17%)
Query: 26 LEVLSMLIGETKEEKGVKSVHVYTMVI----PLRLTSKHDRVEASPEQLFEAVTEAEKLS 81
+EV+ +++G+ + YT+++ L + RV A E F+ ++
Sbjct: 32 IEVMGLMLGKVDD---------YTIIVVDVFALPVEGTETRVNAQDE--FQEYMVQYEML 80
Query: 82 KLYNRELRVIGWFHSHPHITVWPSDV 107
K R V+GW+HSHP W S +
Sbjct: 81 KQTGRPENVVGWYHSHPGYGCWLSGI 106
>gnl|CDD|163698 cd08067, MPN_2A_DUB, Mov34/MPN/PAD-1 family: Histone H2A
deubiquitinase. This family includes histone H2A
deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM
and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or
KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases
(DUBs), with possible Zn2+-dependent ubiquitin
isopeptidase activity. It contains the SWIRM (Swi3p,
Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR,
TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain
can bind directly to DNA. 2A-DUB is specific for
monoubiquitinated H2A (uH2A), regulating transcription
by coordinating histone acetylation and
deubiquitination, and destabilizing the association of
linker histone H1 with nucleosomes. 2A-DUB interacts
with p/CAF (p300/CBP-associated factor) in a
co-regulatory protein complex, where the status of
acetylation of nucleosomal histones modulates its
deubiquitinase activity. 2A-DUB is a positive regulator
of androgen receptor (AR) transactivation activity on a
reporter gene; it participates in transcriptional
regulation events in androgen receptor-dependent gene
activation. In prostate tumors, the levels of uH2A are
dramatically decreased, thus 2A-DUB serving as a
cancer-related marker.
Length = 187
Score = 33.4 bits (77), Expect = 0.008
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 73 AVTEAEKLSKLYNRELRVIGWFHSHPHITVWPS 105
V+E E L +R L V+GW+HSHP PS
Sbjct: 64 PVSETEIRESLESRGLSVVGWYHSHPTFPPNPS 96
>gnl|CDD|224229 COG1310, COG1310, Predicted metal-dependent protease of the
PAD1/JAB1 superfamily [General function prediction
only].
Length = 134
Score = 32.5 bits (74), Expect = 0.016
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 88 LRVIGWFHSHPHITVWPSDV 107
V+GW+HSHP +PS+
Sbjct: 69 EVVVGWYHSHPGGPPYPSEA 88
>gnl|CDD|176856 cd07814, SRPBCC_CalC_Aha1-like, Putative hydrophobic ligand-binding
SRPBCC domain of Micromonospora echinospora CalC, human
Aha1, and related proteins. This family includes the
SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
of Micromonospora echinospora CalC, human Aha1, and
related proteins. Proteins in this group belong to the
SRPBCC domain superfamily of proteins, which bind
hydrophobic ligands. SRPBCC domains have a deep
hydrophobic ligand-binding pocket. MeCalC confers
resistance to the enediyne, calicheamicin gamma 1 (CLM),
by a self sacrificing mechanism which results in
inactivation of both CalC and the highly reactive
diradical enediyne species. MeCalC can also inactivate
two other enediynes, shishijimicin and namenamicin. A
crucial Gly of the MeCalC CLM resistance mechanism is
not conserved in this subgroup. This family also
includes the C-terminal, Bet v1-like domain of Aha1, one
of several co-chaperones, which regulate the dimeric
chaperone Hsp90. Aha1 promotes dimerization of the
N-terminal domains of Hsp90, and stimulates its low
intrinsic ATPase activity, and may regulate the dwell
time of Hsp90 with client proteins. Aha1 can act as
either a positive or negative regulator of
chaperone-dependent activation, depending on the client
protein, but the mechanisms by which these opposing
functions are achieved are unclear. Aha1 is upregulated
in a number of tumor lines co-incident with the
activation of several signaling kinases.
Length = 139
Score = 29.3 bits (66), Expect = 0.23
Identities = 9/40 (22%), Positives = 17/40 (42%), Gaps = 10/40 (25%)
Query: 63 VEASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHITV 102
+A PE ++ A+T+ E L++ WF +
Sbjct: 8 FDAPPELVWRALTDPELLAQ----------WFGPTTTAEM 37
>gnl|CDD|219798 pfam08327, AHSA1, Activator of Hsp90 ATPase homolog 1-like
protein. This family includes eukaryotic, prokaryotic
and archaeal proteins that bear similarity to a
C-terminal region of human activator of 90 kDa heat
shock protein ATPase homolog 1 (AHSA1/p38). This
protein is known to interact with the middle domain of
Hsp90, and stimulate its ATPase activity. It is
probably a general upregulator of Hsp90 function,
particularly contributing to its efficiency in
conditions of increased stress. p38 is also known to
interact with the cytoplasmic domain of the VSV G
protein, and may thus be involved in protein transport.
It has also been reported as being underexpressed in
Down's syndrome. This region is found repeated in two
members of this family.
Length = 125
Score = 29.2 bits (66), Expect = 0.24
Identities = 11/36 (30%), Positives = 20/36 (55%), Gaps = 5/36 (13%)
Query: 65 ASPEQLFEAVTEAEKLSKLYNR-----ELRVIGWFH 95
A PE+++ A+T+ E L++ + +LR G F
Sbjct: 2 APPERVWRALTDPELLARWFTTTEAEMDLRPGGRFR 37
>gnl|CDD|163690 cd08059, MPN_prok_mb, Mpr1p, Pad1p N-terminal (MPN) domains with
catalytic isopeptidase activity (metal-binding);
prokaryotic. This family contains bacterial and
archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB,
MPN+)-like domains. These catalytically active domains
contain the signature JAB1/MPN/Mov34 metalloenzyme
(JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc
ion coordination and provides the active site for
isopeptidase activity for the release of ubiquitin from
ubiquitinated proteins (thus having deubiquitinating
(DUB) activity) that are tagged for degradation. The
JAMM proteins likely hydrolyze ubiquitin conjugates in a
manner similar to thermolysin, in which the
zinc-polarized aqua ligand serves as the nucleophile,
compared with the classical DUBs that do so with a
cysteine residue in the active site.
Length = 101
Score = 28.7 bits (64), Expect = 0.27
Identities = 10/46 (21%), Positives = 18/46 (39%), Gaps = 2/46 (4%)
Query: 61 DRVEASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHITVWPSD 106
D + P + + ++V+G HSHP + PS+
Sbjct: 31 DELIFLPFVSGSVSAVIDLAAL--EIGMKVVGLVHSHPSGSCRPSE 74
>gnl|CDD|226353 COG3832, COG3832, Uncharacterized conserved protein [Function
unknown].
Length = 149
Score = 27.8 bits (62), Expect = 0.87
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 10/38 (26%)
Query: 62 RVEASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPH 99
++A PE++FEA+T+ E L++ WF
Sbjct: 15 LIDAPPEKVFEALTDPELLAR----------WFMPGGA 42
>gnl|CDD|163686 cd07767, MPN, Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also
known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are
found in the N-terminal termini of proteins with a
variety of functions; they are components of the
proteasome regulatory subunits, the signalosome (CSN),
eukaryotic translation initiation factor 3 (eIF3)
complexes, and regulators of transcription factors.
These domains are isopeptidases that release ubiquitin
from ubiquitinated proteins (thus having
deubiquitinating (DUB) activity) that are tagged for
degradation. Catalytically active MPN domains contain a
metalloprotease signature known as the JAB1/MPN/Mov34
metalloenzyme (JAMM) motif. For example, Rpn11 (also
known as POH1 or PSMD14), a subunit of the 19S
proteasome lid is involved in the ATP-dependent
degradation of ubiquitinated proteins, contains the
conserved JAMM motif involved in zinc ion coordination.
Poh1 is a regulator of c-Jun, an important regulator of
cell proliferation, differentiation, survival and death.
JAB1 is a component of the COP9 signalosome (CSN), a
regulatory particle of the ubiquitin (Ub)/26S proteasome
system occurring in all eukaryotic cells; it cleaves the
ubiquitin-like protein NEDD8 from the cullin subunit of
the SCF (Skp1, Cullins, F-box proteins) family of E3
ubiquitin ligases. AMSH (associated molecule with the
SH3 domain of STAM, also known as STAMBP), a member of
JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves
Lys 63-linked polyubiquitin (poly-Ub) chains, thus
facilitating the recycling and subsequent trafficking of
receptors to the cell surface. Similarly, BRCC36, part
of the nuclear complex that includes BRCA1 protein and
is targeted to DNA damage foci after irradiation,
specifically disassembles K63-linked polyUb. BRCC36 is
aberrantly expressed in sporadic breast tumors,
indicative of a potential role in the pathogenesis of
the disease. Some variants of the JAB1/MPN domains lack
key residues in their JAMM motif and are unable to
coordinate a metal ion. Comparisons of key catalytic and
metal binding residues explain why the MPN-containing
proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the
translation initiation factor 3 subunits f (p47) and h
(p40) do not show catalytic isopeptidase activity. It
has been proposed that the MPN domain in these proteins
has a primarily structural function.
Length = 116
Score = 27.1 bits (60), Expect = 1.1
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 85 NRELRVIGWFHSHPHITVWPS 105
N LR++GW+H+HP + + S
Sbjct: 60 NAGLRIVGWYHTHPKPSCFLS 80
>gnl|CDD|222766 pfam14464, Prok-JAB, Prokaryotic homologs of the JAB domain. These
are metalloenzymes that function as the ubiquitin
isopeptidase/ deubiquitinase in the ubiquitin-based
signaling and protein turnover pathways in eukaryotes.
Prokaryotic JAB domains are predicted to have a similar
role in their cognates of the ubiquitin modification
pathway. The domain is widely found in bacteria, archaea
and phages where they are present in several gene
contexts in addition to those that correspond to the
prokaryotic cognates of the eukaryotic Ub pathway. Other
contexts in which JAB domains are present include gene
neighbor associations with ubiquitin fold domains in
cysteine and siderophore biosynthesis, and phage tail
morphogenesis, where they are shown or predicted to
process the associated ubiquitin. A distinct family, the
RadC-like JAB domains are widespread in bacteria and are
predicted to function as nucleases. In halophilic
archaea the JAB domain shows strong gene-neighborhood
associations with a nucleotidyltransferase suggesting a
role in nucleotide metabolism.
Length = 98
Score = 27.0 bits (60), Expect = 1.1
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 4/46 (8%)
Query: 61 DRVEASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHITVWPSD 106
+ PE F A E R L ++G +HSHP +PS+
Sbjct: 37 PLLALDPEDSFAAAREDA----ARERGLELVGIYHSHPGGPAYPSE 78
>gnl|CDD|221666 pfam12617, LdpA_C, Iron-Sulfur binding protein C terminal. This
domain family is found in bacteria and eukaryotes, and
is typically between 179 and 201 amino acids in length.
The family is found in association with pfam00037. LdpA
(light-dependent period) plays a role in controlling the
redox state in cyanobacteria to modulate its. circadian
clock. LdpA is a protein with Iron-Sulfur
cluster-binding motifs.
Length = 182
Score = 27.5 bits (62), Expect = 1.2
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 58 SKHDRVEASPEQLFEAVTEAEKL 80
S+ +E PE L++AV A L
Sbjct: 156 SQGVSLEDWPELLWQAVALARSL 178
>gnl|CDD|163697 cd08066, MPN_AMSH_like, Mov34/MPN/PAD-1 family. AMSH (associated
molecule with the Src homology 3 domain (SH3) of STAM
(signal-transducing adapter molecule, also known as
STAMBP)) and AMSH-like proteins (AMSH-LP) are members
of JAMM/MPN+ deubiquitinases (DUBs), with
Zn2+-dependent ubiquitin isopeptidase activity. AMSH
specifically cleaves Lys 63 and not Lys48-linked
polyubiquitin (poly-Ub) chains, thus facilitating the
recycling and subsequent trafficking of receptors to
the cell surface. AMSH and AMSH-LP are anchored on the
early endosomal membrane via interaction with the
clathrin coat. AMSH shares a common SH3-binding site
with another endosomal DUB, UBPY (ubiquitin-specific
protease Y; also known as USP8), the latter being a
cysteine protease that does not discriminate between
Lys48 and Lys63-linked ubiquitin. AMSH is involved in
the degradation of EGF receptor (EGFR) and possibly
other ubiquitinated endocytosed proteins. AMSH also
interacts with CHMP1, CHMP2, and CHMP3 proteins, all of
which are components of ESCRT-III, suggested to be
required for EGFR down-regulation. The function of
AMSH-LP has not been elucidated; however, it exhibits
two fundamentally distinct features from AMSH: first,
there is a substitution in the critical amino acid
residue in the SH3-binding motif (SBM) in the human
AMSH-LP, but not in its mouse ortholog, and lacks
STAM-binding ability; second, AMSH-LP lacks the ability
to interact with CHMP proteins. It is therefore likely
that AMSH and AMSH-LP play different roles on early
endosomes.
Length = 173
Score = 27.2 bits (61), Expect = 1.5
Identities = 9/31 (29%), Positives = 15/31 (48%), Gaps = 9/31 (29%)
Query: 68 EQLFEAVTEAEKLSKLYNRELRVIGWFHSHP 98
E+LF+ + +L +GW H+HP
Sbjct: 64 EELFDFQDQ---------HDLITLGWIHTHP 85
>gnl|CDD|187612 cd05354, SDR_c7, classical (c) SDR, subgroup 7. These proteins are
members of the classical SDR family, with a canonical
active site triad (and also an active site Asn) and a
typical Gly-rich NAD-binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 235
Score = 27.0 bits (60), Expect = 1.6
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 39 EKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEA 77
+G + V+ I R+ + + SPE + EAV +A
Sbjct: 167 AQGTLVLSVHPGPIDTRMAAGAGGPKESPETVAEAVLKA 205
>gnl|CDD|234368 TIGR03835, termin_org_DnaJ, terminal organelle assembly protein
TopJ. This model describes TopJ (MG_200, CbpA), a DnaJ
homolog and probable assembly protein of the Mycoplasma
terminal organelle. The terminal organelle is involved
in both cytadherence and gliding motility [Cellular
processes, Chemotaxis and motility].
Length = 871
Score = 27.1 bits (59), Expect = 2.0
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 7/74 (9%)
Query: 23 NDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSK 82
ND++ + + +TK +KG VH+Y + K+DR +Q + KL K
Sbjct: 785 NDQVIFKDLGLTKTKYDKGSLIVHLYYSSVM----KKNDRTNVQVQQFNKLALREYKLLK 840
Query: 83 LYNRELRVIGWFHS 96
+EL+ F S
Sbjct: 841 YNQKELQ---NFQS 851
>gnl|CDD|212659 cd07770, FGGY_GntK, Gluconate kinases; a subfamily of the FGGY
family of carbohydrate kinases. This subfamily is
composed of a group of gluconate kinases (GntK, also
known as gluconokinase; EC 2.7.1.12) encoded by the
gntK gene, which catalyzes the ATP-dependent
phosphorylation of D-gluconate and produce
6-phospho-D-gluconate and ADP. The presence of Mg2+
might be required for catalytic activity. The
prototypical member of this subfamily is GntK from
Lactobacillus acidophilus. Unlike Escherichia coli
GntK, which belongs to the superfamily of P-loop
containing nucleoside triphosphate hydrolases, members
in this subfamily are homologous to glycerol kinase,
xylulose kinase, and rhamnulokinase from Escherichia
coli. They have been classified as members of the FGGY
family of carbohydrate kinases, which contain two large
domains separated by a deep cleft that forms the active
site. This model spans both the N-terminal domain,
which adopts a ribonuclease H-like fold, and the
structurally related C-terminal domain. Some
uncharacterized homologous sequences are also included
in this subfamily. The Lactobacillus gnt operon
contains a single gntK gene. The gnt operons of some
bacteria, such as Corynebacterium glutamicum, have two
gntK genes. For example, the C. glutamicum gnt operon
has both a gluconate kinase gntV gene (also known as
gntK) and a second hypothetical gntK gene (also known
as gntK2). Both gluconate kinases encoded by these
genes belong to this family, however the protein
encoded by C. glutamicum gntV is not included in this
model as it is truncated in the C-terminal domain.
Length = 440
Score = 26.8 bits (60), Expect = 2.2
Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 6/59 (10%)
Query: 43 KSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEA--EKLSKLYNRELRVIGW---FHS 96
+ V + PL T E P+++F+AV E E ++K + + + HS
Sbjct: 22 RIVAGVSKRYPL-ETPPDGAAEQDPDEIFDAVLEILDEVVAKALGGRIAAVSFSSAMHS 79
>gnl|CDD|176902 cd08893, SRPBCC_CalC_Aha1-like_GntR-HTH, Putative hydrophobic
ligand-binding SRPBCC domain of an uncharacterized
subgroup of CalC- and Aha1-like proteins; some contain
an N-terminal GntR family winged HTH DNA-binding
domain. SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a
functionally uncharacterized subgroup of CalC- and
Aha1-like proteins. This group shows similarity to the
SRPBCC domains of Micromonospora echinospora CalC (a
protein which confers resistance to enediynes) and
human Aha1 (one of several co-chaperones which regulate
the dimeric chaperone Hsp90), and belongs to the SRPBCC
domain superfamily of proteins that bind hydrophobic
ligands. SRPBCC domains have a deep hydrophobic
ligand-binding pocket and they bind diverse ligands.
Some proteins in this subgroup contain an N-terminal
winged helix-turn-helix DNA-binding domain found in the
GntR family of proteins which include bacterial
transcriptional regulators and their putative homologs
from eukaryota and archaea.
Length = 136
Score = 26.4 bits (59), Expect = 2.2
Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 20/52 (38%)
Query: 46 HVYTMVIPLRLTSKHDRVEASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSH 97
VY I A+PE++++A+T+ E ++ Y W +
Sbjct: 2 FVYVTYI-----------RATPEKVWQALTDPE-FTRQY--------WGGTT 33
>gnl|CDD|219010 pfam06406, StbA, StbA protein. This family consists of several
bacterial StbA plasmid stability proteins.
Length = 318
Score = 26.6 bits (59), Expect = 2.4
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 64 EASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHITV 102
E + + + EA K KL R +R + F + H+ V
Sbjct: 242 EDKRDSVMNVINEAVK--KLQERVIRALSRFSGYTHVMV 278
>gnl|CDD|225752 COG3211, PhoX, Predicted phosphatase [General function prediction
only].
Length = 616
Score = 26.7 bits (59), Expect = 2.9
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 5 VAYISEDVYFSMFYLALSNDK 25
V Y+ +D FY +SN +
Sbjct: 326 VVYLGDDERGEYFYKFVSNGR 346
>gnl|CDD|239161 cd02760, MopB_Phenylacetyl-CoA-OR, The MopB_Phenylacetyl-CoA-OR CD
contains the phenylacetyl-CoA:acceptor oxidoreductase,
large subunit (PadB2), and other related proteins. The
phenylacetyl-CoA:acceptor oxidoreductase has been
characterized as a membrane-bound molybdenum-iron-sulfur
enzyme involved in anaerobic metabolism of phenylalanine
in the denitrifying bacterium Thauera aromatica. Members
of this CD belong to the molybdopterin_binding (MopB)
superfamily of proteins.
Length = 760
Score = 26.5 bits (58), Expect = 3.2
Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 6/51 (11%)
Query: 54 LRLTSKHDRVEASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHITVWP 104
L + +HD E +++A+ A S E+ + WF H T P
Sbjct: 646 LDESQEHDV-----EYIWDAICRASSASLSKGGEVHGLEWFKEHGFYT-VP 690
>gnl|CDD|218748 pfam05787, DUF839, Bacterial protein of unknown function (DUF839).
This family consists of several bacterial proteins of
unknown function that contain a predicted beta-propeller
repeats.
Length = 515
Score = 26.4 bits (58), Expect = 3.2
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 5 VAYISEDVYFSMFYLALSNDKL 26
V Y+ +D F FY + ND+
Sbjct: 253 VVYLGDDERFEYFYRFVPNDRY 274
>gnl|CDD|223334 COG0256, RplR, Ribosomal protein L18 [Translation, ribosomal
structure and biogenesis].
Length = 125
Score = 26.0 bits (58), Expect = 3.3
Identities = 14/47 (29%), Positives = 17/47 (36%), Gaps = 9/47 (19%)
Query: 31 MLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRVEASPEQLFEAVTEA 77
LI E KG++ V V H RV A L + EA
Sbjct: 84 KLIAERALAKGIEEV-----VFDRGGYKYHGRVAA----LADGAREA 121
>gnl|CDD|176908 cd08899, SRPBCC_CalC_Aha1-like_6, Putative hydrophobic
ligand-binding SRPBCC domain of an uncharacterized
subgroup of CalC- and Aha1-like proteins. SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a
functionally uncharacterized subgroup of CalC- and
Aha1-like proteins. This group shows similarity to the
SRPBCC domains of Micromonospora echinospora CalC (a
protein which confers resistance to enediynes) and
human Aha1 (one of several co-chaperones which regulate
the dimeric chaperone Hsp90), and belongs to the SRPBCC
domain superfamily of proteins that bind hydrophobic
ligands. SRPBCC domains have a deep hydrophobic
ligand-binding pocket and they bind diverse ligands.
Length = 157
Score = 25.7 bits (57), Expect = 4.4
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 65 ASPEQLFEAVTEAEKLSK---LYNRELRVIG 92
A E ++ A+T+ E+L++ +LRV G
Sbjct: 21 APIEDVWAALTDPERLARWFAPGTGDLRVGG 51
>gnl|CDD|202536 pfam03103, DUF243, Domain of unknown function (DUF243). This
family of uncharacterized proteins is only found in fly
proteins. It is found associated with YLP motifs
pfam02757 in some proteins.
Length = 97
Score = 24.9 bits (55), Expect = 5.2
Identities = 8/34 (23%), Positives = 13/34 (38%)
Query: 58 SKHDRVEASPEQLFEAVTEAEKLSKLYNRELRVI 91
KH V +PE+ E + + RV+
Sbjct: 3 YKHFYVHVAPEEPEEHEIAVGVPAGPPQKHYRVV 36
>gnl|CDD|235053 PRK02610, PRK02610, histidinol-phosphate aminotransferase;
Provisional.
Length = 374
Score = 25.1 bits (55), Expect = 8.3
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 10/41 (24%)
Query: 68 EQLFEAVTE--AEKLSKLYNRELRVIGWFHSHPHITVWPSD 106
++L A+ E E+ +LY P + VWPS
Sbjct: 281 QELLAAIPEILQER-DRLYQ-------ALQELPQLRVWPSA 313
>gnl|CDD|223055 PHA03361, PHA03361, UL7 tegument protein; Provisional.
Length = 302
Score = 25.3 bits (56), Expect = 8.4
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 6 AYISEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLT 57
A +S + YF+ LA + ++L T E V S+ V +V+P RL
Sbjct: 88 AEVSSEDYFAQ-CLAQPAFRGFAFAVL---TAAEDRVHSLAVPPLVLPHRLV 135
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
0.318 0.133 0.384
Gapped
Lambda K H
0.267 0.0698 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,322,042
Number of extensions: 434282
Number of successful extensions: 505
Number of sequences better than 10.0: 1
Number of HSP's gapped: 501
Number of HSP's successfully gapped: 48
Length of query: 107
Length of database: 10,937,602
Length adjustment: 72
Effective length of query: 35
Effective length of database: 7,744,114
Effective search space: 271043990
Effective search space used: 271043990
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: 53 (24.3 bits)