RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15739
(95 letters)
>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 = 105 bits (264), Expect = 2e-29
Identities = 39/85 (45%), Positives = 55/85 (64%), Gaps = 3/85 (3%)
Query: 7 EPRQTTSNLGHLQKHSVQALIHGLNRHYYSISINYRKNELEQKMLLNLHKKTWMDGLSLQ 66
EPRQTTSN+GHL K ++ G N+ YYS+ I Y K+ L++K+LLNL K W++ LSL
Sbjct: 153 EPRQTTSNIGHLPKPKIE-DFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNKYWVNTLSLS 211
Query: 67 DYNEHCKLNEGTVNDMLELAKHYNK 91
E+ NE T+ +L+LA+ K
Sbjct: 212 PLLENS--NEYTIKQILDLAEKLEK 234
>gnl|CDD|205193 pfam13012, MitMem_reg, Maintenance of mitochondrial structure and
function. This is C-terminal to the Mov24 region of
the yeast proteasomal subunit Rpn11 and seems likely to
regulate the mitochondrial fission and tubulation
processes, ie the outer mitochondrial membrane
proteins. This function appears to be unrelated to the
proteasome activity of the N-terminal region.
Length = 115
Score = 71.1 bits (175), Expect = 1e-17
Identities = 33/89 (37%), Positives = 44/89 (49%), Gaps = 16/89 (17%)
Query: 6 QEPRQTTSNLGHLQKHSVQALIHGLNRHYYSISINYRKNELEQKMLLNLHKKTWMDGLSL 65
QE Q V+ L+ GLNRHYYS +++ RK ELEQK L NLHK+ W GL L
Sbjct: 1 QEAEQI----------GVEHLLRGLNRHYYS-TLS-RKLELEQKALKNLHKRLWTIGLYL 48
Query: 66 QDYN----EHCKLNEGTVNDMLELAKHYN 90
+D + +L L +Y+
Sbjct: 49 EDVIDGKLPPNHEILRKLQSLLNLLPNYD 77
>gnl|CDD|238514 cd01066, APP_MetAP, A family including aminopeptidase P,
aminopeptidase M, and prolidase. Also known as
metallopeptidase family M24. This family of enzymes is
able to cleave amido-, imido- and amidino-containing
bonds. Members exibit relatively narrow substrate
specificity compared to other metallo-aminopeptidases,
suggesting they play roles in regulation of biological
processes rather than general protein degradation.
Length = 207
Score = 27.4 bits (61), Expect = 1.1
Identities = 11/50 (22%), Positives = 17/50 (34%), Gaps = 5/50 (10%)
Query: 14 NLGHLQKHSVQALIHGLNRHYYSISINYRKNELEQKMLLNLHKKTWMDGL 63
N GH H + GL H + LE M+ + ++ G
Sbjct: 147 NFGHRTGHGI-----GLEIHEPPVLKAGDDTVLEPGMVFAVEPGLYLPGG 191
>gnl|CDD|181700 PRK09209, PRK09209, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 761
Score = 27.0 bits (60), Expect = 1.7
Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 36 SISIN-YRKNELEQKMLLNLHKKTWMDGL 63
SIS N Y + + LL+LH W +GL
Sbjct: 712 SISFNFYVPSTIRASELLDLHMTAWKEGL 740
>gnl|CDD|214910 smart00917, LeuA_dimer, LeuA allosteric (dimerisation) domain.
This is the C-terminal regulatory (R) domain of
alpha-isopropylmalate synthase, which catalyses the
first committed step in the leucine biosynthetic
pathway. This domain, is an internally duplicated
structure with a novel fold. It comprises two similar
units that are arranged such that the two -helices pack
together in the centre, crossing at an angle of 34
degrees, sandwiched between the two three-stranded,
antiparallel beta-sheets. The overall domain is thus
constructed as a beta-alpha-beta three-layer sandwich.
Length = 131
Score = 25.9 bits (58), Expect = 2.6
Identities = 6/11 (54%), Positives = 8/11 (72%)
Query: 22 SVQALIHGLNR 32
S +AL+ LNR
Sbjct: 120 SAKALVSALNR 130
>gnl|CDD|233854 TIGR02409, carnitine_bodg, gamma-butyrobetaine hydroxylase.
Members of this protein family are gamma-butyrobetaine
hydroxylase, both bacterial and eukarytotic. This enzyme
catalyzes the last step in the conversion of lysine to
carnitine. Carnitine can serve as a compatible solvent
in bacteria and also participates in fatty acid
metabolism.
Length = 366
Score = 26.3 bits (58), Expect = 3.1
Identities = 11/55 (20%), Positives = 20/55 (36%), Gaps = 6/55 (10%)
Query: 40 NYRKNELEQKMLLNLHKKTWMD-----GLSLQDYNEHCKLNEGTVNDMLELAKHY 89
Y K EL ++ L K+ W L D+ + ++ + D L +
Sbjct: 82 CYDKQELRERELFFPEKQRWGKATSELSLPTLDFEAVMR-DDSVLLDWLSAVRDV 135
>gnl|CDD|149159 pfam07925, RdRP_5, Reovirus RNA-dependent RNA polymerase lambda 3.
The sequences in this family are similar to the reoviral
minor core protein lambda 3, which functions as a
RNA-dependent RNA polymerase within the protein capsid.
It is organised into 3 domains. N- and C-terminal
domains create a 'cage' that encloses a conserved
central catalytic domain within a hollow centre; this
catalytic domain is arranged to form 'fingers', 'palm'
and 'thumb' subdomains. Unlike other RNA polymerases,
like HIV reverse transcriptase and T7 RNA polymerase,
lambda 3 protein binds template and substrate with only
localised rearrangements, and catalytic activity can
occur with little structural change. However, the
structure of the catalytic complex is similar to that of
other polymerase catalytic complexes with known
structure.
Length = 1271
Score = 26.0 bits (57), Expect = 3.4
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 61 DGLSLQDYNEHCKLNEGTVNDMLELAKHYNKG 92
DGL + N K++ + ++LEL Y +
Sbjct: 738 DGLLIIPGNTAGKISSEDIQELLELLSKYGEE 769
>gnl|CDD|238896 cd01915, CODH, Carbon monoxide dehydrogenase (CODH) is found in
acetogenic and methanogenic organisms and is responsible
for the synthesis and breakdown of acetyl-CoA,
respectively. CODH has two types of metal clusters, a
cubane [Fe4-S4] center (B-cluster) similar to that of
hybrid cluster protein (HCP) and a Ni-Fe-S center
(C-cluster) where carbon monoxide oxidation occurs.
Bifunctional CODH forms a heterotetramer with acetyl-CoA
synthase (ACS) consisting of two CODH and two ACS
subunits while monofunctional CODH forms a homodimer.
Bifunctional CODH reduces carbon dioxide to carbon
monoxide and ACS then synthesizes acetyl-CoA from carbon
monoxide, CoA, and a methyl group donated by another
protein (CoFeSP), while monofunctional CODH oxidizes
carbon monoxide to carbon dioxide. CODH and ACS each
have a metal cluster referred to as the C- and
A-clusters, respectively.
Length = 613
Score = 25.7 bits (57), Expect = 3.8
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 6 QEPRQTTSNLGHLQKHSVQALIHGLN 31
+P + +NLG L V +HG N
Sbjct: 228 PKPVVSEANLGVLDPDYVNIAVHGHN 253
>gnl|CDD|198361 cd07786, FGGY_EcGK_like, Escherichia coli glycerol kinase-like
proteins; belongs to the FGGY family of carbohydrate
kinases. This subgroup is composed of mostly bacterial
and archaeal glycerol kinases (GK), including the well
characterized proteins from Escherichia coli (EcGK),
Thermococcus kodakaraensis (TkGK), and Enterococcus
casseliflavus (EnGK). GKs contain two large domains
separated by a deep cleft that forms the active site.
This model includes both the N-terminal domain, which
adopts a ribonuclease H-like fold, and the structurally
related C-terminal domain. The high affinity ATP binding
site of EcGK is created only by a substrate-induced
conformational change, which is initiated by
protein-protein interactions through complex formation
with enzyme IIAGlc (also known as IIIGlc), the
glucose-specific phosphocarrier protein of the
phosphotransferase system (PTS). EcGK exists in a
dimer-tetramer equilibrium. IIAGlc binds to both EcGK
dimer and tetramer, and inhibits the uptake and
subsequent metabolism of glycerol and maltose. Another
well-known allosteric regulator of EcGK is fructose
1,6-bisphosphate (FBP), which binds to the EcGK tetramer
and plays an essential role in the stabilization of the
inactive tetrameric form. EcGK requires Mg2+ for its
enzymatic activity. Members in this subgroup belong to
the FGGY family of carbohydrate kinases.
Length = 486
Score = 25.9 bits (58), Expect = 3.9
Identities = 7/14 (50%), Positives = 8/14 (57%)
Query: 50 MLLNLHKKTWMDGL 63
ML N+H W D L
Sbjct: 186 MLFNIHTLEWDDEL 199
>gnl|CDD|217347 pfam03063, Prismane, Prismane/CO dehydrogenase family. This family
includes both hybrid-cluster proteins and the beta chain
of carbon monoxide dehydrogenase. The hybrid-cluster
proteins contain two Fe/S centres - a [4Fe-4S] cubane
cluster, and a hybrid [4Fe-2S-2O] cluster. The
physiological role of this protein is as yet unknown,
although a role in nitrate/nitrite respiration has been
suggested. The prismane protein from Escherichia coli
was shown to contain hydroxylamine reductase activity
(NH2OH + 2e + 2 H+ -> NH3 + H2O). This activity is
rather low. Hydroxylamine reductase activity was also
found in CO-dehydrogenase in which the active site Ni
was replaced by Fe. The CO dehydrogenase contains a
Ni-3Fe-2S-3O centre.
Length = 505
Score = 25.5 bits (57), Expect = 4.5
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 7 EPRQTTSNLGHLQKHSVQALIHG 29
EP T NLG L+K V L+ G
Sbjct: 155 EPVLTEVNLGVLKKDYVNILVSG 177
>gnl|CDD|236477 PRK09355, PRK09355, hydroxyethylthiazole kinase; Validated.
Length = 263
Score = 25.1 bits (56), Expect = 5.3
Identities = 7/22 (31%), Positives = 9/22 (40%)
Query: 74 LNEGTVNDMLELAKHYNKGKTP 95
L E + ML K N+ P
Sbjct: 65 LTEERIEAMLAAGKIANEAGKP 86
>gnl|CDD|223394 COG0317, SpoT, Guanosine polyphosphate
pyrophosphohydrolases/synthetases [Signal transduction
mechanisms / Transcription].
Length = 701
Score = 25.3 bits (56), Expect = 6.9
Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 18 LQKHSVQALIHGLNRHYYSISINYRK 43
L+ ++A + G +H YSI YRK
Sbjct: 229 LKAAGIKAEVSGRPKHIYSI---YRK 251
>gnl|CDD|132802 cd06892, PX_SNX5_like, The phosphoinositide binding Phox Homology
domain of Sorting Nexins 5 and 6. The PX domain is a
phosphoinositide (PI) binding module present in many
proteins with diverse functions. Sorting nexins (SNXs)
make up the largest group among PX domain containing
proteins. They are involved in regulating membrane
traffic and protein sorting in the endosomal system. The
PX domain of SNXs binds PIs and targets the protein to
PI-enriched membranes. SNXs differ from each other in
PI-binding specificity and affinity, and the presence of
other protein-protein interaction domains, which help
determine subcellular localization and specific function
in the endocytic pathway. Members of this subfamily
include SNX5, SNX6, and similar proteins. They contain a
Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane
curvature, C-terminal to the PX domain, similar to other
sorting nexins including SNX1-2. The PX-BAR structural
unit helps determine the specific membrane-targeting of
some SNXs. SNX5 and SNX6 may be components of the
retromer complex, a membrane coat multimeric complex
required for endosomal retrieval of lysosomal hydrolase
receptors to the Golgi, acting as a mammalian equivalent
of yeast Vsp17p.
Length = 141
Score = 24.7 bits (54), Expect = 8.2
Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 2/30 (6%)
Query: 43 KNELEQKMLLNLHKKT-WMDGLSLQDYNEH 71
K ELE + L + KKT M + L+ H
Sbjct: 97 KQELEAEYL-AIFKKTVAMHEVFLRRLASH 125
>gnl|CDD|218603 pfam05482, Serendipity_A, Serendipity locus alpha protein (SRY-A).
The Drosophila serendipity alpha (sry alpha) gene is
specifically transcribed at the blastoderm stage, from
nuclear cycle 11 to the onset of gastrulation, in all
somatic nuclei. SRY-A is required for the
cellularisation of the embryo and is involved in the
localisation of the actin filaments just prior to and
during plasma membrane invagination.
Length = 549
Score = 24.9 bits (54), Expect = 9.9
Identities = 10/36 (27%), Positives = 17/36 (47%)
Query: 55 HKKTWMDGLSLQDYNEHCKLNEGTVNDMLELAKHYN 90
H + +M+ L+ Q N L E +D+ +L N
Sbjct: 148 HLEAYMEILANQTQNSLHILEENDTDDIDQLGSIVN 183
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
0.315 0.131 0.388
Gapped
Lambda K H
0.267 0.0844 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,526,452
Number of extensions: 352514
Number of successful extensions: 327
Number of sequences better than 10.0: 1
Number of HSP's gapped: 325
Number of HSP's successfully gapped: 28
Length of query: 95
Length of database: 10,937,602
Length adjustment: 62
Effective length of query: 33
Effective length of database: 8,187,654
Effective search space: 270192582
Effective search space used: 270192582
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: 53 (24.0 bits)