RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11404
(251 letters)
>gnl|CDD|241468 cd13314, PH_Rpn13, Regulatory Particle Non-ATPase 13 Pleckstrin
homology-like domain. Targeted protein degradation is
performed to a great extent by the ubiquitin-proteasome
pathway, in which substrate proteins are marked by
covalently attached ubiquitin chains that mediate
recognition by the proteasome. Rpn13(also called
ADRM1/ARM1) is one of the two major ubiquitin receptors
of the proteasome, the other being S5a/Rpn10 which is
not essential for ubiquitin-mediated protein degradation
in budding yeast2. S5a has two ubiquitin interacting
motifs (UIMs) that bind simultaneously to ubiquitin
moieties to increase affinity while Rpn13 binds
ubiquitin with a single, high affinity surface within
its N-terminal PH domain. Rpn13 also binds and activates
deubiquitinating enzyme Uch37, one of the proteasome's
three deubiquitinating enzymes. Recently it was
discovered that the ubiquitin-binding domain (BD) and
Uch37 BD of human (h) Rpn13 pack against each other when
it is not incorporated into the proteasome reducing
hRpn13's affinity for ubiquitin. However when hRpn13
binds to hRpn2/S1 this abrogates its interdomain
interactions, thus activating hRpn13 for ubiquitin
binding. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 105
Score = 198 bits (505), Expect = 2e-65
Identities = 72/98 (73%), Positives = 85/98 (86%)
Query: 1 MTMKGKMVHPDKRKGLVYVHQSDDSLMHFCWKDRQSGSVVEDLIIFPDDCEFKKVPQCTT 60
MT+KG V PD RKGLVY++Q DD L+HFCWKDR +G+V +DLIIFPDD EFKKVPQCTT
Sbjct: 8 MTLKGTTVTPDPRKGLVYLYQGDDGLIHFCWKDRTTGAVEDDLIIFPDDAEFKKVPQCTT 67
Query: 61 GRVYVLKFKSSNRKLFFWLQEPKTDKDDENARKVNEVL 98
GRVYVLKFKSS++K FFW+QEP TDKD+E +KVNE+L
Sbjct: 68 GRVYVLKFKSSSQKHFFWMQEPSTDKDEEICKKVNELL 105
>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 = 147 bits (372), Expect = 1e-45
Identities = 52/82 (63%), Positives = 66/82 (80%)
Query: 1 MTMKGKMVHPDKRKGLVYVHQSDDSLMHFCWKDRQSGSVVEDLIIFPDDCEFKKVPQCTT 60
M + GK V PD RKGL+Y+++SDD L+HF WK R +G V +DLI+FP + FK+VPQCTT
Sbjct: 3 MNLDGKTVTPDPRKGLLYLYKSDDGLLHFQWKPRDTGEVEDDLILFPGEATFKRVPQCTT 62
Query: 61 GRVYVLKFKSSNRKLFFWLQEP 82
GRVYVLKFKSS ++ FFW+QEP
Sbjct: 63 GRVYVLKFKSSGQRYFFWMQEP 84
>gnl|CDD|222294 pfam13658, UCH37_bd, Ubiquitin C-terminal hydrolase 37 receptor
binding site. This domain appears frequently at the
C-terminus of Proteasom_Rpn13, pfam04683. It is a
proteasome subunit that binds the de-ubiquitinating
enzyme, UCH37.
Length = 96
Score = 48.4 bits (116), Expect = 1e-07
Identities = 16/44 (36%), Positives = 27/44 (61%)
Query: 165 EAVSMFSAALQSGQLGPVVQQFDVSNEAVAATTQGNMEEFVRAL 208
+A++ S AL+SG L ++ Q ++ E V A G++E F+ AL
Sbjct: 53 QALASLSQALRSGGLPSLLSQLGLNPEEVFAANGGDVEAFLEAL 96
>gnl|CDD|240709 cd12263, RRM_ABT1_like, RNA recognition motif found in activator of
basal transcription 1 (ABT1) and similar proteins. This
subfamily corresponds to the RRM of novel nuclear
proteins termed ABT1 and its homologous counterpart,
pre-rRNA-processing protein ESF2 (eighteen S factor 2),
from yeast. ABT1 associates with the TATA-binding
protein (TBP) and enhances basal transcription activity
of class II promoters. Meanwhile, ABT1 could be a
transcription cofactor that can bind to DNA in a
sequence-independent manner. The yeast ABT1 homolog,
ESF2, is a component of 90S preribosomes and 5'
ETS-based RNPs. It is previously identified as a
putative partner of the TATA-element binding protein.
However, it is primarily localized to the nucleolus and
physically associates with pre-rRNA processing factors.
ESF2 may play a role in ribosome biogenesis. It is
required for normal pre-rRNA processing, as well as for
SSU processome assembly and function. Both ABT1 and ESF2
contain an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 98
Score = 29.1 bits (66), Expect = 0.73
Identities = 21/71 (29%), Positives = 30/71 (42%), Gaps = 13/71 (18%)
Query: 61 GRVYVLKFKSSNRKLFFWLQEPKTD---------KDDENARKVNEVLNNPPTPGSQRSDS 111
GR+Y+ + RK K +D + A++V E LNN P G +RS
Sbjct: 28 GRIYLQPEDPAKRKRRKKKGGNKKKKFTEGWVEFEDKKVAKRVAESLNNTPIGGKKRS-- 85
Query: 112 SGRVEGDIQNL 122
R D+ NL
Sbjct: 86 --RYRDDLWNL 94
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 29.9 bits (67), Expect = 1.4
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 4/64 (6%)
Query: 97 VLNNPPTPGSQRSDSSGRVEGDIQNLLSNMSQ-QQLMQFFGGQINQMGGLSSLLGTMRSK 155
V N P + R+E DI+ L + + Q +Q QI+ L+SL +++S
Sbjct: 393 VENCIPENKISTPSAIERLEQDIKKLQAELQQARQNESELRNQISL---LTSLERSLKSD 449
Query: 156 VQRV 159
+ ++
Sbjct: 450 LGQL 453
>gnl|CDD|217502 pfam03343, SART-1, SART-1 family. SART-1 is a protein involved in
cell cycle arrest and pre-mRNA splicing. It has been
shown to be a component of U4/U6 x U5 tri-snRNP complex
in human, Schizosaccharomyces pombe and Saccharomyces
cerevisiae. SART-1 is a known tumour antigen in a range
of cancers recognised by T cells.
Length = 603
Score = 29.0 bits (65), Expect = 2.6
Identities = 10/49 (20%), Positives = 22/49 (44%)
Query: 201 MEEFVRALQNASISGQQTHERPAPETTQPEKRLKSEEKKSPDDDDDDVN 249
EFVR+LQ + + ++ + E + +E+ D D +++
Sbjct: 396 TSEFVRSLQKEPLEEKPENKDESVEEISDAEEDDEDEEDEDGDGDVEMS 444
>gnl|CDD|222330 pfam13705, TRC8_N, TRC8 N-terminal domain. This region is found at
the N-terminus of the TRC8 protein. TRC8 is an E3
ubiquitin-protein ligase also known as RNF139. This
region contains 12 transmembrane domains. This region
has been suggested to contain a sterol sensing domain.
It has been found that TRC8 protein levels are sterol
responsive and that it binds and stimulates
ubiquitylation of the endoplasmic reticulum anchor
protein INSIG.
Length = 511
Score = 28.9 bits (65), Expect = 2.8
Identities = 11/25 (44%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 163 TTEAVSMFSAALQSGQLG-PVVQQF 186
TTEAV ALQ+G G Q+
Sbjct: 320 TTEAVLFLILALQTGLTGLQPEQRT 344
>gnl|CDD|220776 pfam10483, Hap2_elong, Histone acetylation protein 2. Hap2 is one
of three histone acetyltransferases proteins that, in
yeasts, are found associated with elongating forms of
RNA polymerase II (Elongator). The Haps can be isolated
in two forms, as a six-subunit complex with Elongator
and as a complex of the three proteins on their own. The
role of the Hap complex in transcription is still
speculative, being possibly to keep the HAT activity of
free Elongator in check, allowing histone acetylation
only in the presence of a transcribing polymerase, or
the interaction with Haps might render Elongator
susceptible to modifications thereby altering its
activity.
Length = 280
Score = 28.5 bits (64), Expect = 2.9
Identities = 28/110 (25%), Positives = 42/110 (38%), Gaps = 13/110 (11%)
Query: 62 RVYVLKFKSSNRKLFFW----LQEPK-TDKDDENARK-----VNEVLNNPPTPGSQRSDS 111
R ++ + K K+ F L +P+ D + K V EV + P+ ++ +
Sbjct: 30 REFIRRAKLRKEKVIFLSFETLNKPEGADSFIDARSKSLEEIVKEVKSALPSSMAKPTKK 89
Query: 112 SGRVEGDIQNLLSNMSQQQLMQFFGGQINQMGGLSSLLGTMRSKVQRVNN 161
S V D N L N QL QF G +LLGT + N
Sbjct: 90 S-LVIIDSLNYLLNHEPCQLTQFLSSIAASPG--VTLLGTYHQDLPDAQN 136
>gnl|CDD|222918 PHA02687, PHA02687, ORF061 late transcription factor VLTF-4;
Provisional.
Length = 231
Score = 28.4 bits (63), Expect = 3.1
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 223 APETTQPEKRLKSEEKKSPDDDDDDVNME 251
+ +PEK K+ EK P DD DD N E
Sbjct: 93 KAKADKPEKSPKAVEKLCPPDDRDDKNEE 121
>gnl|CDD|241442 cd13288, PH_Ses, Sesquipedalian family Pleckstrin homology (PH)
domain. The sesquipedalian family has 2 mammalian
members: Ses1 and Ses2, which are also callled 7 kDa
inositol polyphosphate phosphatase-interacting protein 1
and 2. They play a role in endocytic trafficking and are
required for receptor recycling from endosomes, both to
the trans-Golgi network and the plasma membrane. Members
of this family form homodimers and heterodimers.
Sesquipedalian interacts with inositol polyphosphate
5-phosphatase OCRL-1 (INPP5F) also known as Lowe
oculocerebrorenal syndrome protein, a phosphatase enzyme
that is involved in actin polymerization and is found in
the trans-Golgi network and INPP5B. Sesquipedalian
contains a single PH domain. PH domains have diverse
functions, but in general are involved in targeting
proteins to the appropriate cellular location or in the
interaction with a binding partner. They share little
sequence conservation, but all have a common fold, which
is electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 120
Score = 27.6 bits (62), Expect = 3.6
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 194 AATTQGNMEEFVRALQNASI 213
AA +Q +ME +++AL AS
Sbjct: 84 AAESQEDMESWMKALSRASY 103
>gnl|CDD|227699 COG5412, COG5412, Phage-related protein [Function unknown].
Length = 637
Score = 28.6 bits (64), Expect = 3.6
Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 3/71 (4%)
Query: 119 IQNLLSNMSQQQLMQFFGGQINQMGGLSSLLGTMRSKVQRVNNCTTEA---VSMFSAALQ 175
++NLL ++ F +GGL+S +G + VQ + N +++ +Q
Sbjct: 118 VKNLLESVINAIFGTAFDILSQIIGGLNSNIGGIVQAVQNIINFIKIFEGFLNLVGLVMQ 177
Query: 176 SGQLGPVVQQF 186
L + +F
Sbjct: 178 FIWLTIITAKF 188
>gnl|CDD|233560 TIGR01760, tape_meas_TP901, phage tail tape measure protein, TP901
family, core region. This model represents a reasonably
well conserved core region of a family of phage tail
proteins. The member from phage TP901-1 was
characterized as a tail length tape measure protein in
that a shortened form of the protein leads to phage with
proportionately shorter tails [Mobile and
extrachromosomal element functions, Prophage functions].
Length = 350
Score = 28.5 bits (64), Expect = 4.0
Identities = 21/94 (22%), Positives = 34/94 (36%), Gaps = 10/94 (10%)
Query: 124 SNMSQQQLMQFFGGQINQMGGLSSLLGTMRSKVQRVNNCTTEAVSMFSAALQSGQLGPVV 183
S+++ ++ +N G + + + N + ALQ GPV
Sbjct: 89 SDLTAEEAASILAKIMNAFGLTAKDSEKVADVLNYTANNSAATTRDMGDALQ--YAGPVA 146
Query: 184 QQFDVSNEAVAATTQGNMEEFVRALQNASISGQQ 217
+ VS E AA T AL +A I G+
Sbjct: 147 KSLGVSLEETAAATA--------ALASAGIEGEI 172
>gnl|CDD|202599 pfam03340, Pox_Rif, Poxvirus rifampicin resistance protein.
Length = 541
Score = 28.5 bits (64), Expect = 4.2
Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 8/28 (28%)
Query: 39 VVEDLII--------FPDDCEFKKVPQC 58
++EDL+I FP+ E +VP
Sbjct: 284 LLEDLVIVSDDKPKGFPEKAEIVEVPPD 311
>gnl|CDD|226341 COG3820, COG3820, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 230
Score = 27.2 bits (60), Expect = 7.7
Identities = 26/113 (23%), Positives = 49/113 (43%), Gaps = 16/113 (14%)
Query: 145 LSSLLGTMRSKVQRVNNCTTEAVSMFSAALQSGQLGPV----VQQFDVSNEA-VAATTQG 199
+S L+GT +S ++++ T SA + + PV Q D+ E A+ +
Sbjct: 124 ISKLIGTTKSTIEQIRTRT----HWNSANITP--MDPVTLGLCSQIDLDKEVERASRGRP 177
Query: 200 NMEEFVRALQNASISGQQTHERPAPETTQPE-----KRLKSEEKKSPDDDDDD 247
+E L AS + Q +E E + + +L S + + D++D+D
Sbjct: 178 TAKELGPTLLPASETEQLDYEEEREEERELDADAVFAKLSSLKSGNKDEEDED 230
>gnl|CDD|163497 TIGR03785, marine_sort_HK, proteobacterial dedicated sortase system
histidine kinase. This histidine kinase protein is
paired with an adjacent response regulator (TIGR03787)
gene. It co-occurs with a variant sortase enzyme
(TIGR03784), usually in the same gene neighborhood, in
proteobacterial species most of which are marine, and
with an LPXTG motif-containing sortase target conserved
protein (TIGR03788). Sortases and LPXTG proteins are far
more common in Gram-positive bacteria, where sortase
systems mediate attachment to the cell wall or
cross-linking of pilin structures. We give this
predicted sensor histidine kinase the gene symbol psdS,
for Proteobacterial Dedicated Sortase system Sensor
histidine kinase.
Length = 703
Score = 27.4 bits (61), Expect = 8.0
Identities = 12/46 (26%), Positives = 19/46 (41%)
Query: 110 DSSGRVEGDIQNLLSNMSQQQLMQFFGGQINQMGGLSSLLGTMRSK 155
DS GR+ G I S L + F + ++ + L M S+
Sbjct: 446 DSQGRISGAIPASRSRDEIGDLSRSFAQMVARLRQYTHYLENMSSR 491
>gnl|CDD|233990 TIGR02740, TraF-like, TraF-like protein. This protein is related
to the F-type conjugation system pilus assembly proteins
TraF (TIGR02739)and TrbB (TIGR02738) both of which
exhibit a thioredoxin fold. The protein represented by
this model has the same length and architecture as TraF,
but lacks the CXXC-motif found in TrbB and believed to
be responsible for the disulfide isomerase activity of
that protein.
Length = 271
Score = 27.4 bits (61), Expect = 8.2
Identities = 13/69 (18%), Positives = 27/69 (39%), Gaps = 6/69 (8%)
Query: 60 TGRVYVLKFKSSNRKLFFWLQEPKTDKDDENARKVNEVLNNPPTPGSQRSDSSGRVEGDI 119
T V F ++ +FW ++P +++E + PP P +Q+ +
Sbjct: 26 TPFVSGQAFYKDEKRGWFWYEDPPPKEEEE------PLEPAPPAPPAQQPAREELAPFSV 79
Query: 120 QNLLSNMSQ 128
L N+ +
Sbjct: 80 AWLRENLPE 88
>gnl|CDD|221866 pfam12935, Sec16_N, Vesicle coat trafficking protein Sec16
N-terminus. Sec16 is a multi-domain vesicle coat
protein. The overall function of Sec16 is in mediating
the movement of protein-cargo between the organelles of
the secretory pathway. Over-expression of truncated
mutants of only the N-terminus are lethal, and this
portion does not appear to be essential for function so
may act as a stabilising region.
Length = 246
Score = 27.2 bits (60), Expect = 8.3
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 190 NEAVAATTQGNMEEFVRALQNASISGQQTHE--RPAPETTQPEKRLKSEEKKSPDDDDDD 247
+ +AA+T GN E ++ ++ E E+T E L E ++ D+DDD
Sbjct: 136 SNVLAASTDGNPESESQSEPSSEEELAARAELSDDESESTPTEDDLA-ERWQAFLDNDDD 194
>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional.
Length = 333
Score = 27.3 bits (61), Expect = 8.5
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 229 PEKRLKSEEKKSPDDDDDDV 248
P KR+KS+ D+D +
Sbjct: 40 PLKRMKSKRDDDSYDEDVED 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
0.313 0.128 0.368
Gapped
Lambda K H
0.267 0.0663 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,149,222
Number of extensions: 1081137
Number of successful extensions: 865
Number of sequences better than 10.0: 1
Number of HSP's gapped: 863
Number of HSP's successfully gapped: 33
Length of query: 251
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 156
Effective length of database: 6,723,972
Effective search space: 1048939632
Effective search space used: 1048939632
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.3 bits)