RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11405
(76 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 = 94.3 bits (235), Expect = 4e-27
Identities = 33/48 (68%), Positives = 40/48 (83%)
Query: 21 VEFKAGKMTMKGKMVHPDKRKGLVYVHQSDDSLMHFCWKDRQSGSVVE 68
VEFKAGKMT+KG V PD RKGLVY++Q DD L+HFCWKDR +G+V +
Sbjct: 1 VEFKAGKMTLKGTTVTPDPRKGLVYLYQGDDGLIHFCWKDRTTGAVED 48
>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 = 66.5 bits (163), Expect = 1e-16
Identities = 24/43 (55%), Positives = 32/43 (74%)
Query: 26 GKMTMKGKMVHPDKRKGLVYVHQSDDSLMHFCWKDRQSGSVVE 68
GKM + GK V PD RKGL+Y+++SDD L+HF WK R +G V +
Sbjct: 1 GKMNLDGKTVTPDPRKGLLYLYKSDDGLLHFQWKPRDTGEVED 43
>gnl|CDD|166839 PRK00178, tolB, translocation protein TolB; Provisional.
Length = 430
Score = 28.1 bits (63), Expect = 0.32
Identities = 12/26 (46%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 41 KGLVYVHQSDDSLMHFCWKDRQSGSV 66
K LV VH+ D H +D Q GSV
Sbjct: 343 KTLVMVHR-QDGNFHVAAQDLQRGSV 367
>gnl|CDD|178050 PLN02431, PLN02431, ferredoxin--nitrite reductase.
Length = 587
Score = 25.9 bits (57), Expect = 2.4
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 8/46 (17%)
Query: 1 MPSGGALFGSTVSRSQSKNLVEFKAGKMTMKGKMVHPDKRKGLVYV 46
MP+G + R+ S++LV+ K + G VHP K++GL YV
Sbjct: 361 MPNG------ELERAASEDLVDKKWERRDYLG--VHPQKQEGLSYV 398
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
0.319 0.130 0.423
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,542,590
Number of extensions: 247105
Number of successful extensions: 214
Number of sequences better than 10.0: 1
Number of HSP's gapped: 214
Number of HSP's successfully gapped: 5
Length of query: 76
Length of database: 10,937,602
Length adjustment: 46
Effective length of query: 30
Effective length of database: 8,897,318
Effective search space: 266919540
Effective search space used: 266919540
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 (21.8 bits)
S2: 53 (24.4 bits)