RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16329
(215 letters)
>gnl|CDD|218936 pfam06201, PITH, PITH domain. This family was formerly known as
DUF1000. The full-length, Txnl1, protein which is a
probable component of the 26S proteasome, uses its
C-terminal, PITH, domain to associate specifically with
the 26S proteasome. PITH derives from
proteasome-interacting thioredoxin domain.
Length = 151
Score = 152 bits (387), Expect = 2e-47
Identities = 58/114 (50%), Positives = 77/114 (67%), Gaps = 3/114 (2%)
Query: 103 SLYKHIDTENVECLNETVDGSG-KTIFKPWEDRLNKEKFVESDVDSELLINIPFTSNIKL 161
SLY ID + VECLNE+ +GSG K++FKPW++RL+ E ++ESD D +LLINIPFT +KL
Sbjct: 1 SLYSQIDLDKVECLNESDEGSGAKSLFKPWDERLDPEPYLESDADEQLLINIPFTQPVKL 60
Query: 162 KGLRLIGGDSDSHPNRIKLFKNRPGMTFDDVN-ASPDQEFELNQDSD-ASIEYP 213
+ + G D DS P IKLF N P + FDD +P Q EL++ D +EYP
Sbjct: 61 HSILIRGLDDDSAPKTIKLFINPPNLDFDDAEDLTPTQTLELSESDDEGGVEYP 114
Score = 47.6 bits (114), Expect = 4e-07
Identities = 16/36 (44%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 10 RAAKFSNVYHLTCYFPTNFG-SDNTCLYYLGFRGES 44
+ KF NV LT +F NFG + T + Y+G RGE
Sbjct: 116 KYVKFQNVNSLTIFFEDNFGEDETTRIDYIGLRGEP 151
>gnl|CDD|240593 cd12936, GUCT_RHII_Gualpha_beta, RNA-binding GUCT domain found in
vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA
helicase II/Gubeta (RH-II/Gubeta) and similar proteins.
This subfamily corresponds to the Gu C-terminal (GUCT)
domain of RH-II/Gualpha and RH-II/Gubeta, two paralogues
found in vertebrates. RH-II/Gualpha, also termed
nucleolar RNA helicase 2, or DEAD box protein 21, or
nucleolar RNA helicase Gu, is a bifunctional enzyme that
displays independent RNA-unwinding and RNA-folding
activities. It unwinds double-stranded RNA in the 5' to
3' direction in the presence of Mg2+ through the domains
in its N-terminal region. In contrast, it folds
single-stranded RNA in an ATP-dependent manner and its
C-terminal region is responsible for the Mg2+
independent RNA-foldase activity. RH-II/Gualpha consists
of a DEAD box helicase domain (DEAD), a helicase
conserved C-terminal domain (helicase_C), and a GUCT
followed by three FRGQR repeats and one PRGQR sequence.
The DEAD and helicase_C domains may play critical roles
in the RNA-helicase activity of RH-II/Gualpha. The
function of GUCT domain remains unclear. The C-terminal
region responsible for the RNA-foldase activity does not
overlap with the GUCT domain. RH-II/Gubeta, also termed
ATP-dependent RNA helicase DDX50, or DEAD box protein
50, or nucleolar protein Gu2, shows significant sequence
homology with RH-II/Gualpha. It contains a DEAD domain,
a helicase_C domain, and a GUCT domain followed by an
arginine-serine-rich sequence but not (F/P)RGQR repeats
in RH-II/Gualpha. Both RH-II/Gualpha and RH-II/Gubeta
localize to nucleoli, suggesting roles in ribosomal RNA
production, but RH-II/Gubeta also localizes to nuclear
speckles containing the splicing factor SC35, suggesting
its possible involvement in pre-mRNA splicing. In
contrast to RH-II/Gualpha, RH-II/Gubeta has
RNA-unwinding activity, but no RNA-folding activity.
Length = 93
Score = 29.3 bits (66), Expect = 0.48
Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 10/62 (16%)
Query: 150 LINIPFTS----NIKLKGLRLIGGDSDSHPNRIKLFKNRPGMTFDDVNASPDQEFELN-Q 204
IP S +K K G D+D+H +R+ L K R G+ F DV + + +
Sbjct: 28 SEEIPNRSYAWKELKEKL----GVDADAHISRMCLLKGRMGVCF-DVPTAEVESIQAEWH 82
Query: 205 DS 206
DS
Sbjct: 83 DS 84
>gnl|CDD|201483 pfam00873, ACR_tran, AcrB/AcrD/AcrF family. Members of this family
are integral membrane proteins. Some are involved in
drug resistance. AcrB cooperates with a membrane fusion
protein, AcrA, and an outer membrane channel TolC. The
structure shows the AcrB forms a homotrimer.
Length = 1021
Score = 29.9 bits (68), Expect = 1.3
Identities = 12/90 (13%), Positives = 22/90 (24%), Gaps = 23/90 (25%)
Query: 122 GSGKTIFKPWEDRLNKEKFVE-------SDVDSELLINIPFTSNIKLKGLRLIGGDSDSH 174
G KPW++R E+ VE + N+ ++ L G
Sbjct: 614 GDVFITLKPWKERPGPEQTVEAIIERLRKALAKIPGANVFLFQPPAIRELGTASGFR--- 670
Query: 175 PNRIKLFKNRPGMTFDDVNASPDQEFELNQ 204
+ L++
Sbjct: 671 ------------SDLQVKIFGDGLD-ALDE 687
>gnl|CDD|176268 cd04266, DUF619-NAGS-FABP, DUF619 domain of N-acetylglutamate
Synthase of the fungal arginine-biosynthetic pathway.
DUF619-NAGS-FABP: This family includes the DUF619
domain of N-acetylglutamate synthase (NAGS) of the
fungal arginine-biosynthetic pathway (FABP). This NAGS
(also known as arginine-requiring protein 2 or ARG2)
consists of an N-terminal NAG kinase-like domain and a
C-terminal DUF619 domain. NAGS catalyzes the formation
of NAG from acetylcoenzyme A and L-glutamate. The
DUF619 domain, yet to be characterized, is predicted to
function in NAGS association in fungi.
Length = 108
Score = 27.8 bits (62), Expect = 1.8
Identities = 7/33 (21%), Positives = 12/33 (36%)
Query: 51 GVTICNYETTPSLADHKVDNMNSFPVMAHNHGG 83
G I +E K+ ++ F V+ G
Sbjct: 22 GAAILTWEGPDGSTPEKIAYLDKFAVLPKAQGS 54
>gnl|CDD|227832 COG5545, COG5545, Predicted P-loop ATPase and inactivated
derivatives [General function prediction only].
Length = 517
Score = 29.2 bits (65), Expect = 1.9
Identities = 19/79 (24%), Positives = 28/79 (35%), Gaps = 10/79 (12%)
Query: 120 VDGSGKTIFKPWE-DRLNKEKFVESDVDSELLINIPFTSNIKLKGLRLIGGDSDSHPNRI 178
V+G+ K I E D K F +D +++ + P KL G D + +
Sbjct: 56 VEGTMKNIITAIENDERLKGLFWLNDSSNQVEMARPA----KLHGSTRDEFV-DLDSSEL 110
Query: 179 K----LFKNRPGMTFDDVN 193
R GM D N
Sbjct: 111 AAWLEHDPERYGMKCSDDN 129
>gnl|CDD|165700 PLN00131, PLN00131, hypothetical protein; Provisional.
Length = 218
Score = 28.5 bits (63), Expect = 2.5
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 9/41 (21%)
Query: 164 LRLIGGDSDSHPNRIKLFKNRPGMTFDDVNASPDQEFELNQ 204
L + GG SD+ P+R RP + D+N++P E +LNQ
Sbjct: 81 LSIGGGGSDAGPSR------RPVL---DLNSTPQPELDLNQ 112
>gnl|CDD|236558 PRK09545, znuA, high-affinity zinc transporter periplasmic
component; Reviewed.
Length = 311
Score = 28.4 bits (64), Expect = 2.7
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 79 HNHGGHCCGEEDHSHDDTELGIQYS 103
H+H GH +EDH H + + I S
Sbjct: 126 HDHAGHEKSDEDHHHGEYNMHIWLS 150
>gnl|CDD|221927 pfam13116, DUF3971, Protein of unknown function. Some members of
this family are related to the AsmA family proteins.
Length = 289
Score = 28.0 bits (63), Expect = 3.2
Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 6/55 (10%)
Query: 141 VESDVDSELLINIPFTSNIKLKGLRLIGGDSDSHPNRIKLFKNRPGMTFDDVNAS 195
V VD +L ++IP +K GD N + + PG+ +V+
Sbjct: 156 VSGKVDGDLNLDIPLDGEEVVK----AKGDLTLKNNSLSI--APPGLKLKNVSGQ 204
>gnl|CDD|131530 TIGR02477, PFKA_PPi, diphosphate--fructose-6-phosphate
1-phosphotransferase. Diphosphate--fructose-6-phosphate
1-phosphotransferase catalyzes the addition of phosphate
from diphosphate (PPi) to fructose 6-phosphate to give
fructose 1,6-bisphosphate (EC 2.7.1.90). The enzyme is
also known as pyrophosphate-dependent
phosphofructokinase. The usage of PPi-dependent enzymes
in glycolysis presumably frees up ATP for other
processes. TIGR02482 represents the ATP-dependent
6-phosphofructokinase enzyme contained within Pfam
pfam00365: Phosphofructokinase. This model hits
primarily bacterial, plant alpha, and plant beta
sequences [Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 539
Score = 26.9 bits (60), Expect = 9.1
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 7/34 (20%)
Query: 12 AKFSNVYHL-----TCYFPTNFGSDNTCLYYLGF 40
KFS V H C FP+NF D+ Y LG+
Sbjct: 403 GKFSAVSHFFGYEGRCAFPSNF--DSDYCYALGY 434
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 0.138 0.427
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,755,220
Number of extensions: 968319
Number of successful extensions: 712
Number of sequences better than 10.0: 1
Number of HSP's gapped: 709
Number of HSP's successfully gapped: 17
Length of query: 215
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 122
Effective length of database: 6,812,680
Effective search space: 831146960
Effective search space used: 831146960
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 (21.7 bits)
S2: 57 (25.7 bits)