RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy396
(239 letters)
>gnl|CDD|227514 COG5187, RPN7, 26S proteasome regulatory complex component,
contains PCI domain [Posttranslational modification,
protein turnover, chaperones].
Length = 412
Score = 167 bits (423), Expect = 2e-49
Identities = 77/231 (33%), Positives = 120/231 (51%), Gaps = 18/231 (7%)
Query: 5 GGDWSARNKLKAYEGVYCLAIRQYCRAAELFVDVVPTFESYELAEFGTIIRYTVLACMIA 64
GGDW RN+ K Y+G++ + R + AA L D++PTFES EL + +RY + ++
Sbjct: 185 GGDWERRNRYKVYKGIFKMMRRNFKEAAILLSDILPTFESSELISYSRAVRYAIFCGLLR 244
Query: 65 LPRYNLRKKLMHHGVMAQALHS--QYRDLREYFVSLYDGHYFEFLKCLAAVE-QDMKRDP 121
L R +++ K++ + + S + L + SLY+ Y L + ++ D
Sbjct: 245 LERRDIKTKILDSPEVLDVIGSSEKLGSLVQLATSLYECDYGGDFMNLLYLFCNSLQDDV 304
Query: 122 LLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCK 181
L H +V+EMR R Y Q+L++YR LSL+ MAQ FGVSVE++++++ F GRL C
Sbjct: 305 FLGRHVDLFVREMRRRVYAQLLESYRLLSLESMAQTFGVSVEYVDRDLGEFIPEGRLNCV 364
Query: 182 IDSVAGNVVTTSHISEKGDCRSEAPEASLDRGILYQTTVKRGDIFLNRLKK 232
ID V G V T + Y + VK+GD L +L+K
Sbjct: 365 IDRVNGVVETNRPDEKNQQ---------------YSSVVKQGDDLLRKLQK 400
>gnl|CDD|220821 pfam10602, RPN7, 26S proteasome subunit RPN7. RPN7 (known as the
non ATPase regulatory subunit 6 in higher eukaryotes) is
one of the lid subunits of the 26S proteasome and has
been shown in Saccharomyces cerevisiae to be required
for structural integrity. The 26S proteasome is is
involved in the ATP-dependent degradation of
ubiquitinated proteins.
Length = 174
Score = 89.9 bits (224), Expect = 2e-22
Identities = 33/70 (47%), Positives = 45/70 (64%)
Query: 4 SGGDWSARNKLKAYEGVYCLAIRQYCRAAELFVDVVPTFESYELAEFGTIIRYTVLACMI 63
GGDW RN+LK YEG+ LAIR + AA+LF+D + TF S EL + + Y VL +
Sbjct: 105 KGGDWERRNRLKVYEGLALLAIRDFKEAAKLFLDSLSTFTSTELISYEDVAIYGVLCALA 164
Query: 64 ALPRYNLRKK 73
+L R +L+KK
Sbjct: 165 SLDRVDLKKK 174
>gnl|CDD|216479 pfam01399, PCI, PCI domain. This domain has also been called the
PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).
Length = 100
Score = 75.3 bits (186), Expect = 8e-18
Identities = 32/104 (30%), Positives = 55/104 (52%), Gaps = 4/104 (3%)
Query: 88 YRDLREYFVSLYDGHYFEFLKCLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYR 147
YRDL + Y G +F + LA E ++ D L +++R +++ + Y
Sbjct: 1 YRDLLR---AFYSGDLSDFEEILADNEDELL-DDGLAELLEDLRRKIRELNLRRLAKPYS 56
Query: 148 SLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDSVAGNVVT 191
S+SL +A+ G+SV+ +EK +++ GR++ KID V G VV
Sbjct: 57 SISLSDLAKLLGLSVDEVEKILSKLIRDGRIRGKIDQVNGIVVF 100
>gnl|CDD|214803 smart00753, PAM, PCI/PINT associated module.
Length = 88
Score = 69.6 bits (171), Expect = 1e-15
Identities = 21/69 (30%), Positives = 34/69 (49%)
Query: 125 PHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDS 184
+++RL Q+ + Y S+SL +A+ G+SV +EK V++ G + KID
Sbjct: 1 QLVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQ 60
Query: 185 VAGNVVTTS 193
V G V
Sbjct: 61 VNGIVEFEE 69
>gnl|CDD|214509 smart00088, PINT, motif in proteasome subunits, Int-6, Nip-1 and
TRIP-15. Also called the PCI (Proteasome, COP9,
Initiation factor 3) domain. Unknown function.
Length = 88
Score = 69.6 bits (171), Expect = 1e-15
Identities = 21/69 (30%), Positives = 34/69 (49%)
Query: 125 PHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAAAGRLQCKIDS 184
+++RL Q+ + Y S+SL +A+ G+SV +EK V++ G + KID
Sbjct: 1 QLVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQ 60
Query: 185 VAGNVVTTS 193
V G V
Sbjct: 61 VNGIVEFEE 69
>gnl|CDD|176133 cd08442, PBP2_YofA_SoxR_like, The C-terminal substrate binding
domain of LysR-type transcriptional regulators, YofA and
SoxR, contains the type 2 periplasmic binding fold.
YofA is a LysR-like transcriptional regulator of cell
growth in Bacillus subtillis. YofA controls cell
viability and the formation of constrictions during cell
division. YofaA positively regulates expression of the
cell division gene ftsW, and thus is essential for cell
viability during stationary-phase growth of Bacillus
substilis. YofA shows significant homology to SoxR from
Arthrobacter sp. TE1826. SoxR is a negative regulator
for the sarcosine oxidase gene soxA. Sarcosine oxidase
catalyzes the oxidative demethylation of sarcosine,
which is involved in the metabolism of creatine and
choline. The topology of this substrate-binding domain
is most similar to that of the type 2 periplasmic
binding proteins (PBP2), which are responsible for the
uptake of a variety of substrates such as phosphate,
sulfate, polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 193
Score = 29.9 bits (68), Expect = 0.81
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 8/54 (14%)
Query: 49 EFGTIIRYTVLACMIA------LPRYNLRKKLMHHGVMAQALHSQYRDLREYFV 96
EFG+ + +L C+ A LPR L V L + D+ + V
Sbjct: 125 EFGSY--HAILGCVAAGMGIALLPRSVLDSLQGRGSVSIHPLPEPFADVTTWLV 176
>gnl|CDD|217534 pfam03399, SAC3_GANP, SAC3/GANP/Nin1/mts3/eIF-3 p25 family. This
large family includes diverse proteins involved in large
complexes. The alignment contains one highly conserved
negatively charged residue and one highly conserved
positively charged residue that are probably important
for the function of these proteins. The family includes
the yeast nuclear export factor Sac3, and mammalian
GANP/MCM3-associated proteins, which facilitate the
nuclear localisation of MCM3, a protein that associates
with chromatin in the G1 phase of the cell-cycle. The
26S protease (or 26S proteasome) is responsible for
degrading ubiquitin conjugates. It consists of 19S
regulatory complexes associated with the ends of 20S
proteasomes. The 19S regulatory complex is composed of
about 20 different polypeptides and confers
ATP-dependence and substrate specificity to the 26S
enzyme. The conserved region occurs at the C-terminal of
the Nin1-like regulatory subunit. This family includes
several eukaryotic translation initiation factor 3
subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation
factor 3 (eIF3) is a multisubunit complex that is
required for binding of mRNA to 40 S ribosomal subunits,
stabilisation of ternary complex binding to 40 S
subunits, and dissociation of 40 and 60 S subunits.
Length = 155
Score = 29.5 bits (67), Expect = 0.82
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 129 HYVQEMRLRAYKQILQAYRSLSLKYMAQ 156
++ +R A K I +AYRS+ L Y+A+
Sbjct: 125 RFLDRIRKEALKAISKAYRSIPLSYLAE 152
>gnl|CDD|239163 cd02762, MopB_1, The MopB_1 CD includes a group of related
uncharacterized bacterial molybdopterin-binding
oxidoreductase-like domains with a putative N-terminal
iron-sulfur [4Fe-4S] cluster binding site and
molybdopterin cofactor binding site. These members
belong to the molybdopterin_binding (MopB) superfamily
of proteins.
Length = 539
Score = 28.5 bits (64), Expect = 3.2
Identities = 15/75 (20%), Positives = 25/75 (33%), Gaps = 4/75 (5%)
Query: 109 CLAAVEQDMKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKE 168
LAA+ + + L + R + ++ A + + A GV E I +
Sbjct: 222 LLAAMLAVLLAEGLTD--RRFLAE--HCDGLDEVRAALAEFTPEAYAPRCGVPAETIRRL 277
Query: 169 VARFAAAGRLQCKID 183
FAAA
Sbjct: 278 AREFAAAPSAAVYGR 292
>gnl|CDD|225566 COG3022, COG3022, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 253
Score = 27.7 bits (62), Expect = 5.5
Identities = 9/46 (19%), Positives = 17/46 (36%)
Query: 129 HYVQEMRLRAYKQILQAYRSLSLKYMAQCFGVSVEFIEKEVARFAA 174
Q L +++L+ R LS ++ +S + RF
Sbjct: 21 ELTQPELLDYSQELLKILRKLSPNQISSLMKISDKLAGLNAQRFQD 66
>gnl|CDD|130808 TIGR01747, diampropi_NH3ly, diaminopropionate ammonia-lyase family.
This small subfamily includes diaminopropionate
ammonia-lyase from Salmonella typhimurium and a small
number of close homologs, about 50 % identical in
sequence. The enzyme is a pyridoxal phosphate-binding
homodimer homologous to threonine dehydratase (threonine
deaminase) [Energy metabolism, Other].
Length = 376
Score = 27.6 bits (61), Expect = 6.1
Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 20/85 (23%)
Query: 137 RAYKQILQAYRSL---SLKYMAQCFGVSVEFIEKEVARFA----------------AAGR 177
A+ + + YR +L ++A G+ ++ E RF A +
Sbjct: 11 LAFHKKIPGYRPTPLCALDHLANLLGLKKILVKDESKRFGLNAFKMLGGSYAIAQYLAEK 70
Query: 178 LQCKIDSVAGNVVTTSHISEK-GDC 201
L I++++ + I EK G
Sbjct: 71 LHLDIETLSFEHLKNDAIGEKMGQA 95
>gnl|CDD|224460 COG1543, COG1543, Uncharacterized conserved protein [Function
unknown].
Length = 504
Score = 27.3 bits (61), Expect = 7.3
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 117 MKRDPLLNPHYRHYVQEMRLRAYKQILQAYRSLSLKYMAQ 156
M DP L Y Y+ E ++ ++ + Y SL+ +A+
Sbjct: 67 MLADPYLQDRYLRYL-EWKIELSEKEEKRYADQSLRELAE 105
>gnl|CDD|176695 cd08347, PcpA_C_like, C-terminal domain of Sphingobium
chlorophenolicum 2,6-dichloro-p-hydroquinone
1,2-dioxygenase (PcpA), and similar proteins. The
C-terminal domain of Sphingobium chlorophenolicum
(formerly Sphingomonas chlorophenolica)
2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and
similar proteins. PcpA is a key enzyme in the
pentachlorophenol (PCP) degradation pathway, catalyzing
the conversion of 2,6-dichloro-p-hydroquinone to
2-chloromaleylacetate. This domain belongs to a
conserved domain superfamily that is found in a variety
of structurally related metalloproteins, including the
bleomycin resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases.
Length = 157
Score = 26.7 bits (60), Expect = 7.6
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 5/30 (16%)
Query: 70 LRKKLMHHGVMAQALHSQYRDLREYFVSLY 99
+++L G+ S D R YF SLY
Sbjct: 82 WKERLEALGLP----VSGIVD-RFYFKSLY 106
>gnl|CDD|215047 PLN00070, PLN00070, aconitate hydratase.
Length = 936
Score = 27.5 bits (61), Expect = 9.2
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 187 GNVVTTSHISEKGDCRSEAPEAS--LDRGI 214
G+ +TT HIS G ++P A ++RG+
Sbjct: 714 GDSITTDHISPAGSIHKDSPAAKYLMERGV 743
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
0.326 0.138 0.412
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,452,616
Number of extensions: 1186178
Number of successful extensions: 1326
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1324
Number of HSP's successfully gapped: 29
Length of query: 239
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 145
Effective length of database: 6,768,326
Effective search space: 981407270
Effective search space used: 981407270
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 57 (25.7 bits)