RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2584
(397 letters)
>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 = 278 bits (713), Expect = 4e-93
Identities = 115/243 (47%), Positives = 147/243 (60%), Gaps = 43/243 (17%)
Query: 85 FLVALGVPSKWQIVDVYGTDPDMLAIVPQPVLALIMLFPCTEKYEEHCKEQEKEIEEKGQ 144
FL LGV W+ VDVYG DP++LA VP+PVLA+++LFP T+ YEE KE+E+EI+EKGQ
Sbjct: 14 FLHKLGVSPGWEFVDVYGLDPELLAFVPRPVLAVLLLFPITKAYEEFRKEEEEEIKEKGQ 73
Query: 145 TISSELFFMKQFVHNACGTIALIHSYEEHCKEQEKEIEEKGQTISSELFFMKQFVHNACG 204
E S ++FMKQ + NACG
Sbjct: 74 ---------------------------EV---------------SESVYFMKQTIGNACG 91
Query: 205 TIALIHSVANNLNNVK-LEDGKLKSFLDEAKDLSPERRGKLLDENQSISDVHKVIAQEGQ 263
TIALIH+VANN + + LE LK FL+EAK LSPE R KLL++++++ H A EGQ
Sbjct: 92 TIALIHAVANNEDRINILEGSFLKKFLEEAKGLSPEERAKLLEKSEALEKAHAAAATEGQ 151
Query: 264 TAPPEDREPVPYHFVALVHKEGALYELDGRKGFPINHGATSPETLLADATQVAKKYMQRD 323
T P E V HF+A V K+G LYELDGRK PINHG TS ETLL DA +V +K+++R+
Sbjct: 152 TEAPSADEKVNLHFIAFVKKDGHLYELDGRKPGPINHGPTSEETLLKDAAKVCRKFIERE 211
Query: 324 PDN 326
PD
Sbjct: 212 PDE 214
Score = 79.6 bits (197), Expect = 3e-17
Identities = 31/49 (63%), Positives = 40/49 (81%)
Query: 349 QYEEHCKEQEKEIEEKGQTISSELFFMKQFVHNACGTIALIHSVANNLN 397
YEE KE+E+EI+EKGQ +S ++FMKQ + NACGTIALIH+VANN +
Sbjct: 56 AYEEFRKEEEEEIKEKGQEVSESVYFMKQTIGNACGTIALIHAVANNED 104
>gnl|CDD|216294 pfam01088, Peptidase_C12, Ubiquitin carboxyl-terminal hydrolase,
family 1.
Length = 211
Score = 239 bits (612), Expect = 4e-78
Identities = 98/248 (39%), Positives = 131/248 (52%), Gaps = 45/248 (18%)
Query: 78 STPGSL-AFLVALGVPSKWQIVDVYGTDPDMLAIVPQPVLALIMLFPCTEKYEEHCKEQE 136
S PG L LGV Q DVY D ++LA++P+PV ALI LFP TE
Sbjct: 7 SNPGVFTELLEKLGV-KGVQFEDVYSLDDELLAMLPRPVYALIFLFPWTE---------- 55
Query: 137 KEIEEKGQTISSELFFMKQFVHNACGTIALIHSYEEHCKEQEKEIEEKGQTISSELFFMK 196
+YEE +E++ I+EK Q S +FF K
Sbjct: 56 --------------------------------AYEEFREEEDATIKEKDQAASEGVFFAK 83
Query: 197 QFVHNACGTIALIHSVANNLNNVKLEDG-KLKSFLDEAKDLSPERRGKLLDENQSISDVH 255
Q + NACGT AL+H++ NN + +++E G +LK FL+ K LSPE RGK L+ ++ I + H
Sbjct: 84 QTIGNACGTQALLHALLNNEDKIEIELGSELKKFLEFTKGLSPEERGKALENSEEIREAH 143
Query: 256 KVIAQEGQTAPPEDREPVPYHFVALVHKEGALYELDGRKGFPINHGATSPETLLADATQV 315
A+EGQT P + V +HF+A V +G LYELDG K PINHG TS E L DA V
Sbjct: 144 NSFAREGQTEAPSAEDDVDFHFIAFVPVDGHLYELDGLKPGPINHGETSDEDFLEDAAPV 203
Query: 316 AKKYMQRD 323
+K ++R
Sbjct: 204 IQKRIERY 211
Score = 69.9 bits (172), Expect = 7e-14
Identities = 23/50 (46%), Positives = 33/50 (66%)
Query: 348 TQYEEHCKEQEKEIEEKGQTISSELFFMKQFVHNACGTIALIHSVANNLN 397
YEE +E++ I+EK Q S +FF KQ + NACGT AL+H++ NN +
Sbjct: 55 EAYEEFREEEDATIKEKDQAASEGVFFAKQTIGNACGTQALLHALLNNED 104
>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 = 88.1 bits (219), Expect = 3e-20
Identities = 49/157 (31%), Positives = 73/157 (46%), Gaps = 13/157 (8%)
Query: 175 KEQEKEIEEKG---QTISSELFFMKQFVHNACGTIALIHSVANNLNNVKLEDGKLKSFLD 231
K QE E +E I S +FF Q + NAC T AL+ + N + V L + L F +
Sbjct: 50 KWQEGEEDEGSVVDDEIPSNIFFANQVIPNACATQALLSVLLNCSDEVDLGE-TLSEFKE 108
Query: 232 EAKDLSPERRGKLLDENQSISDVHKVIAQ------EGQTAPPEDREPVPYHFVALVHKEG 285
K PE +G+ + ++ I VH A+ + + +E +HF++ V G
Sbjct: 109 FTKGFDPEMKGEAIGNSEEIRKVHNSFARPEPFLLDEKLNKKATKEEDAFHFISYVPIGG 168
Query: 286 ALYELDGRKGFPINHGATSPETLLADATQVAKKYMQR 322
LYELDG K PI+HG S D + A+ +Q
Sbjct: 169 RLYELDGLKEGPIDHGPCSEG---EDWLEKARPVIQA 202
Score = 34.1 bits (79), Expect = 0.068
Identities = 19/44 (43%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 355 KEQEKEIEEKG---QTISSELFFMKQFVHNACGTIALIHSVANN 395
K QE E +E I S +FF Q + NAC T AL+ SV N
Sbjct: 50 KWQEGEEDEGSVVDDEIPSNIFFANQVIPNACATQALL-SVLLN 92
>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 = 56.3 bits (135), Expect = 4e-09
Identities = 72/132 (54%), Positives = 91/132 (68%), Gaps = 1/132 (0%)
Query: 192 LFFMKQFVHNACGTIALIHSVANNLNNVKLEDGK-LKSFLDEAKDLSPERRGKLLDENQS 250
++FMKQ + NACGTI LIH++ANN + + E G LK FL+E+ +SPE R + L+ +
Sbjct: 79 VYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDA 138
Query: 251 ISDVHKVIAQEGQTAPPEDREPVPYHFVALVHKEGALYELDGRKGFPINHGATSPETLLA 310
I H+ A EGQT P E V HF+ALVH +G LYELDGRK FPINHG TS ETLL
Sbjct: 139 IRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLE 198
Query: 311 DATQVAKKYMQR 322
DA +V KK+M+R
Sbjct: 199 DAIEVCKKFMER 210
>gnl|CDD|182127 PRK09874, PRK09874, drug efflux system protein MdtG; Provisional.
Length = 408
Score = 30.3 bits (68), Expect = 2.1
Identities = 29/110 (26%), Positives = 44/110 (40%), Gaps = 13/110 (11%)
Query: 150 LFFMKQFVHNACGTIALIHSYEEHCKEQEKEIEEKGQTISS--------ELFFMKQFVHN 201
+FF+ V C + L E +KE+ + ++S LF +
Sbjct: 174 VFFITASVLFLCFLVTLFCIRENFQPVSKKEMLHMREVVTSLKNPKLVLSLFVTTLIIQV 233
Query: 202 ACGTIALI-----HSVANNLNNVKLEDGKLKSFLDEAKDLSPERRGKLLD 246
A G+IA I +A N++N+ G + S A LS R GKL D
Sbjct: 234 ATGSIAPILTLYVRELAGNVSNIAFISGMIASVPGVAALLSAPRLGKLGD 283
>gnl|CDD|223363 COG0286, HsdM, Type I restriction-modification system
methyltransferase subunit [Defense mechanisms].
Length = 489
Score = 30.1 bits (68), Expect = 2.3
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 160 ACGTIALIHSYEEHCKEQEKEIEEKGQTISSE---LFFMKQFVHNACGTIALIHSVANNL 216
ACG+ ++ ++ K + EI GQ I+ L M +H G + H + L
Sbjct: 194 ACGSGGMLLQAAKYLKRHQDEIFIYGQEINDTTYRLAKMNLILHGIEGDANIRH--GDTL 251
Query: 217 NNVKLEDGKLKSFLD 231
+N K +D K D
Sbjct: 252 SNPKHDDKDDKGKFD 266
>gnl|CDD|221833 pfam12889, DUF3829, Protein of unknown function (DUF3829). This is
a small family of proteins from several bacterial
species, whose function is not known. It may, however,
be related to the GvpL_GvpF family of proteins,
pfam06386.
Length = 277
Score = 29.3 bits (66), Expect = 3.3
Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 8/81 (9%)
Query: 170 YEEHCKEQEKEIEEKGQTISSELFFMKQFVHNACGTIALIHSVANNLNNVKLEDGKLKSF 229
+E EQ +E++++G+ I+ ++ + + A + L S + D L
Sbjct: 143 NDERLLEQLEELKKEGKKIA---YYTLELLLEAEQLLNLFSSKDVAKKDAADLDAALAEL 199
Query: 230 LDEAKDLSPERRGKLLDENQS 250
+DL KL E+
Sbjct: 200 EKALEDLK-----KLTKEDGD 215
>gnl|CDD|215229 PLN02413, PLN02413, choline-phosphate cytidylyltransferase.
Length = 294
Score = 28.8 bits (64), Expect = 4.5
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 127 KYEEHCKEQEKEIEEKGQTISSELFFMK-QFVHNACGTIA-LIHSYEEHCKEQEKEIEEK 184
K E KEQ++++ EK QT++ + ++V NA +A + +EE C + I+++
Sbjct: 201 KLREKVKEQQEKVGEKIQTVAKTAGMHRNEWVENADRWVAGFLEKFEEGCHKMGTAIKDR 260
Query: 185 GQT 187
Q
Sbjct: 261 IQE 263
>gnl|CDD|206034 pfam13863, DUF4200, Domain of unknown function (DUF4200). This
family is found in eukaryotes. It is a coiled-coil
domain of unknwon function.
Length = 126
Score = 27.6 bits (62), Expect = 5.9
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 126 EKYEEHCKEQEKEIEEKGQTISSELFFMKQFV-HNACGTIALIHSYEE---HCKEQEKEI 181
E+ EE K++E+E+E+K + + L +F+ N EE KE+E+EI
Sbjct: 24 ERREELLKQREEELEKKEEELQESLIKFDKFLKENEAKRRRAEKKAEEEKKLRKEKEEEI 83
Query: 182 EEKGQTIS 189
+E +
Sbjct: 84 KELKAELE 91
>gnl|CDD|215868 pfam00343, Phosphorylase, Carbohydrate phosphorylase. The members
of this family catalyze the formation of glucose
1-phosphate from one of the following polyglucoses;
glycogen, starch, glucan or maltodextrin.
Length = 712
Score = 28.5 bits (64), Expect = 7.4
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 200 HNACGTIALIHSVANNLNNVKLEDGKLK 227
+ A I LI+SVA+ +NN KLK
Sbjct: 497 YMAKRIIKLINSVADVVNNDPAVGDKLK 524
>gnl|CDD|217270 pfam02889, Sec63, Sec63 Brl domain. This domain (also known as the
Brl domain) is required for assembly of functional
endoplasmic reticulum translocons.
Length = 309
Score = 28.3 bits (64), Expect = 7.5
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 220 KLEDGKLKSFLDEAKDLSPERRGKLLDENQS-ISDVHKVIAQ 260
KLE + S ++ DL PE G+LL N D+ + + +
Sbjct: 163 KLEKKGISSL-EDLMDLDPEELGELLGNNPKQGKDIAEFVNR 203
>gnl|CDD|202254 pfam02491, SHS2_FTSA, SHS2 domain inserted in FTSA. FtsA is
essential for bacterial cell division, and co-localises
to the septal ring with FtsZ. The SHS2 domain is
inserted in to the RNAseH fold of FtsA, and is involved
in protein-protein interaction.
Length = 80
Score = 26.0 bits (58), Expect = 9.3
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 10/51 (19%)
Query: 247 ENQSI--SDVHKVIAQEGQTAPPEDREPVPYHFVALVHKEGALYELDGRKG 295
E++ + DV +V+ A P DRE +H Y +DG++G
Sbjct: 17 EDREVTQEDVERVLEAAKAVAIPPDREI--------LHVLPQEYIVDGQEG 59
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
0.317 0.135 0.399
Gapped
Lambda K H
0.267 0.0773 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,546,618
Number of extensions: 2012269
Number of successful extensions: 1943
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1933
Number of HSP's successfully gapped: 34
Length of query: 397
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 298
Effective length of database: 6,546,556
Effective search space: 1950873688
Effective search space used: 1950873688
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: 60 (26.8 bits)