RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6731
(258 letters)
>gnl|CDD|187738 cd09617, Peptidase_C12_UCH37_BAP1, Cysteine peptidase C12
containing ubiquitin carboxyl-terminal hydrolase (UCH)
families UCH37 (UCH-L5) and BAP1. This ubiquitin
C-terminal hydrolase (UCH) family includes UCH37 (also
known as UCH-L5) and BRCA1-associated protein-1 (BAP1).
They contain a UCH catalytic domain as well as an
additional C-terminal extension which plays a role in
protein-protein interactions. UCH37 is responsible for
ubiquitin (Ub) isopeptidase activity in the 19S
proteasome regulatory complex; it disassembles
Lys48-linked poly-ubiquitin from the distal end of the
chain. It is also associated with the human Ino80
chromatin-remodeling complex (hINO80) in the nucleus and
can be activated through transient association of hINO80
with hRpn13 that is bound to the 19S regulatory particle
or the proteasome. UCH37 possibly plays a role in
oncogenesis; it competes with Smad ubiquitination
regulatory factor 2 (Smurf2, ubiquitin ligase) in
binding concurrently to Smad7 in order to deubiquitinate
the activated type I transforming growth factor beta
(TGF-beta) receptor, thus rescuing it from proteasomal
degradation. BAP1 binds to the wild-type BRCA1 RING
finger domain, localized in the nucleus. In addition to
the UCH catalytic domain, BAP1 contains a UCH37-like
domain (ULD), binding domains for BRCA1 and BARD1, which
form a tumor suppressor heterodimeric complex, and a
binding domain for HCFC1, which interacts with
histone-modifying complexes during cell division. The
full-length human BRCA1 is a ubiquitin ligase. However,
BAP1 does not appear to function in the deubiquitination
of autoubiquitinated BRCA1. BAP1 exhibits tumor
suppressor activity in cancer cells, and gene mutations
have been reported in a small number of breast and lung
cancer samples. In metastasis of uveal melanoma, the
most common primary cancer of the eye, inactivating
somatic mutations have been identified in the gene
encoding BAP1 on chromosome 3p21.1. These mutations
include several that cause premature protein termination
as well as affect its UCH domain, thus implicating loss
of BAP1 and suggesting that the BAP1 pathway may be a
valuable therapeutic target.
Length = 219
Score = 240 bits (616), Expect = 2e-80
Identities = 87/138 (63%), Positives = 105/138 (76%), Gaps = 1/138 (0%)
Query: 7 WCLIESDPGVFTELIRGFGVQGVQVEELWSLEPENLKILQPVHGLIFLFKLREDTEPAGS 66
WC IESDPGVFTEL+ FGV+GVQVEEL+SL+ ++L+ L PV+GLIFLFK +E E GS
Sbjct: 1 WCEIESDPGVFTELLEEFGVKGVQVEELYSLDADSLEQLPPVYGLIFLFKWQEGEEDEGS 60
Query: 67 IVQDSRLETIFFAKQVVNNACATQAILSILLNNSDPEVKLGSVLTEFKDFCQSFDPTMKG 126
+V D IFFA QV+ NACATQA+LS+LL N EV LG L+EFK+F + FDP MKG
Sbjct: 61 VVDDEIPSNIFFANQVIPNACATQALLSVLL-NCSDEVDLGETLSEFKEFTKGFDPEMKG 119
Query: 127 YALSNSQPIRTVHNSFAR 144
A+ NS+ IR VHNSFAR
Sbjct: 120 EAIGNSEEIRKVHNSFAR 137
Score = 31.4 bits (72), Expect = 0.32
Identities = 12/15 (80%), Positives = 13/15 (86%)
Query: 143 ARYSSEEIRFNLLAV 157
ARYS EIRFNL+AV
Sbjct: 205 ARYSEGEIRFNLMAV 219
>gnl|CDD|216294 pfam01088, Peptidase_C12, Ubiquitin carboxyl-terminal hydrolase,
family 1.
Length = 211
Score = 200 bits (511), Expect = 1e-64
Identities = 72/153 (47%), Positives = 94/153 (61%), Gaps = 9/153 (5%)
Query: 6 NWCLIESDPGVFTELIRGFGVQGVQVEELWSLEPENLK-ILQPVHGLIFLFKLRED---- 60
WC +ES+PGVFTEL+ GV+GVQ E+++SL+ E L + +PV+ LIFLF E
Sbjct: 1 GWCPLESNPGVFTELLEKLGVKGVQFEDVYSLDDELLAMLPRPVYALIFLFPWTEAYEEF 60
Query: 61 --TEPAGSIVQDSRL-ETIFFAKQVVNNACATQAILSILLNNSDP-EVKLGSVLTEFKDF 116
E A +D E +FFAKQ + NAC TQA+L LLNN D E++LGS L +F +F
Sbjct: 61 REEEDATIKEKDQAASEGVFFAKQTIGNACGTQALLHALLNNEDKIEIELGSELKKFLEF 120
Query: 117 CQSFDPTMKGYALSNSQPIRTVHNSFARYSSEE 149
+ P +G AL NS+ IR HNSFAR E
Sbjct: 121 TKGLSPEERGKALENSEEIREAHNSFAREGQTE 153
>gnl|CDD|187736 cd02255, Peptidase_C12, Cysteine peptidase C12 contains ubiquitin
carboxyl-terminal hydrolase (UCH) families L1, L3, L5
and BAP1. The ubiquitin C-terminal hydrolase (UCH;
ubiquitinyl hydrolase; ubiquitin thiolesterase) family
of deubiquitinating enzymes (DUBs) consists of four
members to date: UCH-L1, UCH-L3, UCH-L5 (UCH37) and
BRCA1-associated protein-1 (BAP1), all containing a
conserved catalytic domain with cysteine peptidase
activity. UCH-L1 hydrolyzes carboxyl terminal esters
and amides of ubiquitin (Ub). Dysfunction of this
hydrolase activity can lead to an accumulation of
alpha-synuclein, which is linked to Parkinson's disease
(PD) and neurofibrillary tangles, linked to Alzheimer's
disease (AD). UCH-L1, in its dimeric form, has
additional enzymatic activity as a ubiquitin ligase.
UCH-L3 hydrolyzes isopeptide bonds at the C-terminal
glycine of either Ub or Nedd8, a ubiquitin-like protein.
UCH-L3 can also interact with Lys48-linked Ub dimers to
protect it from degradation while inhibiting its
hydrolase activity at the same time. UCH-L1 and UCH-L3
are the most closely related of the UCH members. UCH-L5
(UCH37) is involved in the deubiquitinating activity in
the 19S proteasome regulatory complex. It is also
associated with the human Ino80 chromatin-remodeling
complex (hINO80) in the nucleus. BAP1 binds to the
wild-type BRCA1 RING finger domain, localized in the
nucleus. It consists of the N-terminal UCH domain and
two predicted nuclear localization signals (NLSs), only
one of which is functional. The full-length human BRCA1
is a ubiquitin ligase. However, BAP1 does not appear to
function in the deubiquitination of autoubiquitinated
BRCA1. There is growing evidence that UCH enzymes and
human malignancies are closely correlated. Studies show
that UCH enzymes play a crucial role in some signaling
pathways and in cell-cycle regulation.
Length = 222
Score = 191 bits (486), Expect = 5e-61
Identities = 36/148 (24%), Positives = 68/148 (45%), Gaps = 10/148 (6%)
Query: 7 WCLIESDPGVFTELIRGFGVQ-GVQVEELWSLEPENLKILQP-VHGLIFLFKLREDTEPA 64
W +E++P V + ++ G+ Q +++ ++PE L ++ V ++ LF + E E
Sbjct: 1 WLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVF 60
Query: 65 GSIVQDSRL-------ETIFFAKQVVNNACATQAILSILLNNSDPEVK-LGSVLTEFKDF 116
+ ++ +++F KQ ++NAC T ++ + NN D GS L +F +
Sbjct: 61 RTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEE 120
Query: 117 CQSFDPTMKGYALSNSQPIRTVHNSFAR 144
S P + L N IR H + A
Sbjct: 121 SVSMSPEERARYLENYDAIRVTHETSAH 148
>gnl|CDD|187737 cd09616, Peptidase_C12_UCH_L1_L3, Cysteine peptidase C12 containing
ubiquitin carboxyl-terminal hydrolase (UCH) families L1
and L3. This ubiquitin C-terminal hydrolase (UCH)
family includes UCH-L1 and UCH-L3, the two members
sharing around 53% sequence identity as well as
conserved catalytic residues. Both enzymes hydrolyze
carboxyl terminal esters and amides of ubiquitin (Ub).
UCH-L1, in dimeric form, has additional enzymatic
activity as a ubiquitin ligase. It is highly abundant in
the brain, constituting up to 2% of total protein, and
is expressed exclusively in neurons and testes. Abnormal
expression of UCH-L1 has been shown to correlate with
several forms of cancer, including several primary lung
tumors, lung tumor cell lines, and colorectal cancers.
Mutations in the UCH-L1 gene have been linked to
susceptibility to and protection from Parkinson's
disease (PD); dysfunction of the hydrolase activity can
lead to an accumulation of alpha-synuclein, which is
linked to Parkinson's disease (PD), while accumulation
of neurofibrillary tangles is linked to Alzheimer's
disease (AD). UCH-L3 hydrolyzes isopeptide bonds at the
C-terminal glycine of either Ub or Nedd8, a
ubiquitin-like protein. It can also interact with
Lys48-linked Ub dimers to protect them from degradation
while inhibiting its hydrolase activity at the same
time. Unlike UCH-L1, neither dimerization nor ligase
activity have been observed for UCH-L3. It has been
shown that levels of Nedd8 and the apoptotic protein p53
and Bax are elevated in UCH-L3 knockout mice upon
cryptorchid injury, possibly contributing to profound
germ cell loss via apoptosis.
Length = 222
Score = 83.1 bits (206), Expect = 3e-19
Identities = 41/150 (27%), Positives = 71/150 (47%), Gaps = 14/150 (9%)
Query: 7 WCLIESDPGVFTELIRGFGVQ-GVQVEELWSLEPENLK-ILQPVHGLIFLF--------- 55
W +ES+P V + + GV G + +++ L+PE L + +PV ++ LF
Sbjct: 1 WIPLESNPEVMNKFLHKLGVSPGWEFVDVYGLDPELLAFVPRPVLAVLLLFPITKAYEEF 60
Query: 56 KLREDTEPAGSIVQDSRLETIFFAKQVVNNACATQAILSILLNNSDPEVKL-GSVLTEFK 114
+ E+ E + S E+++F KQ + NAC T A++ + NN D L GS L +F
Sbjct: 61 RKEEEEEIKEKGQEVS--ESVYFMKQTIGNACGTIALIHAVANNEDRINILEGSFLKKFL 118
Query: 115 DFCQSFDPTMKGYALSNSQPIRTVHNSFAR 144
+ + P + L S+ + H + A
Sbjct: 119 EEAKGLSPEERAKLLEKSEALEKAHAAAAT 148
>gnl|CDD|227492 COG5163, NOP7, Protein required for biogenesis of the 60S ribosomal
subunit [Translation, ribosomal structure and
biogenesis].
Length = 591
Score = 30.4 bits (68), Expect = 1.1
Identities = 16/59 (27%), Positives = 31/59 (52%)
Query: 160 DKKMKYEKELAAATQALKDPSLDAATKTAKQNEVVQLKILIEEEAAKLESYRIENIRRK 218
D++++ +KEL Q +K A K +++ + K+ EEE KL+ + N ++K
Sbjct: 497 DEELQAQKELELEAQGIKYSETSEADKDVNKSKNKKRKVDEEEEEKKLKMIMMSNKQKK 555
>gnl|CDD|203963 pfam08503, DapH_N, Tetrahydrodipicolinate succinyltransferase
N-terminal. This domain is found at the N-terminus of
tetrahydrodipicolinate N-succinyltransferase (DapH)
which catalyzes the acylation of L-2-amino-6-oxopimelate
to 2-N-succinyl-6-oxopimelate in the
meso-diaminopimelate/lysine biosynthetic pathway of
bacteria, blue-green algae, and plants. The N-terminal
domain as defined here contains three alpha-helices and
two twisted hairpin loops.
Length = 82
Score = 27.9 bits (63), Expect = 1.4
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 196 LKILIEEEAAKLESYRIENIRR 217
+K +E K+E Y IEN RR
Sbjct: 52 IKPFLEANKDKIEDYVIENDRR 73
>gnl|CDD|222430 pfam13874, Nup54, Nucleoporin complex subunit 54. This is the
human Nup54 subunit of the nucleoporin complex,
equivalent to Nup57 of yeast. Nup54, Nup58 and Nup62 all
have similar affinities for importin-beta. It seems
likely that they are the only FG-repeat nucleoporins of
the central channel, and as such they would form a zone
of equal affinity spanning the central channel. The
diffusion of importin-beta import complexes through the
central channel may be a stochastic process as the
affinities are similar, whereas movement from
cytoplasmic fibrils to the central channel and from the
central channel to the nuclear basket would be
facilitated by the subtle differences in affinity
between them.
Length = 141
Score = 27.2 bits (61), Expect = 6.1
Identities = 22/64 (34%), Positives = 29/64 (45%), Gaps = 11/64 (17%)
Query: 186 KTAKQNEVVQLKILIEEEAAKLE---------SYRIENIRRKHNYLPLIMNLLKLLAKQG 236
++ EV QL+ + E KL+ S RIE +R+H L LLKL AK
Sbjct: 39 VKLQREEVKQLRERLHEINDKLKELQKHDLETSARIEEAKRRH--TELSHRLLKLAAKLE 96
Query: 237 QLVN 240
L N
Sbjct: 97 ILRN 100
>gnl|CDD|118197 pfam09665, RE_Alw26IDE, Type II restriction endonuclease
(RE_Alw26IDE). Members of this entry are type II
restriction endonucleases of the Alw26I/Eco31I/Esp3I
family. characterized specificities of the three members
are GGTCTC, CGTCTC and the shared subsequence GTCTC.
Length = 511
Score = 27.8 bits (62), Expect = 6.3
Identities = 23/98 (23%), Positives = 39/98 (39%), Gaps = 8/98 (8%)
Query: 135 IRTVHNSFARYSSEEIRFNLLAVVCDKKMKYEKELAAATQALKDPSLDAATKTAKQNEVV 194
IR S Y+S+E R N V+ + E++++ A Q L + K NE +
Sbjct: 409 IRIAFESLKDYNSKENR-NAKEVLTEN---EEQKISEAVQNLSSLPEA----SNKLNEKI 460
Query: 195 QLKILIEEEAAKLESYRIENIRRKHNYLPLIMNLLKLL 232
LK+ E+ + + ++ K KLL
Sbjct: 461 SLKLSSSVESEEEIRSLVTDLPTKEPEKETFTLCRKLL 498
>gnl|CDD|233346 TIGR01295, PedC_BrcD, bacteriocin transport accessory protein,
putative. This model describes a small family of
proteins believed to aid in the export of various class
II bacteriocins, which are ribosomally-synthesized,
non-lantibiotic bacterial peptide antibiotics. Members
of this family are found in operons for pediocin PA-1
from Pediococcus acidilactici and brochocin-C from
Brochothrix campestris.
Length = 122
Score = 26.8 bits (59), Expect = 7.3
Identities = 9/33 (27%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 116 FCQSFDPTMKGYALSNSQPIRTVHNSFARYSSE 148
+C+ F T+ G PI + +S S E
Sbjct: 37 YCRKFSGTLSGVVAQTKAPIYYI-DSENNGSFE 68
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
0.316 0.132 0.369
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,809,548
Number of extensions: 1214201
Number of successful extensions: 1086
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1074
Number of HSP's successfully gapped: 36
Length of query: 258
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 163
Effective length of database: 6,723,972
Effective search space: 1096007436
Effective search space used: 1096007436
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 (21.6 bits)
S2: 58 (26.2 bits)