RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1347
(245 letters)
>gnl|CDD|215754 pfam00153, Mito_carr, Mitochondrial carrier protein.
Length = 96
Score = 72.3 bits (178), Expect = 1e-16
Identities = 26/96 (27%), Positives = 40/96 (41%), Gaps = 6/96 (6%)
Query: 95 GWTPVIQEVLSLYTTGVMGLLVGHPMDTIKTRTQTMPD------KTMIQIIANTFKLEGF 148
+ +L+ G + V +P+D +KTR Q+ K ++ +K EG
Sbjct: 1 SPLSFLASLLAGGIAGAIAATVTYPLDVVKTRLQSSAAGGSRKYKGILDCFKKIYKEEGI 60
Query: 149 RGFYKGFLAPMLTTGVTNAIFFGVYGNTIRYLRSIS 184
RG YKG L +L AI+FG Y + L
Sbjct: 61 RGLYKGLLPNLLRVAPAAAIYFGTYETLKKLLLKKL 96
Score = 42.6 bits (101), Expect = 1e-05
Identities = 17/40 (42%), Positives = 23/40 (57%)
Query: 199 PLWDWNEFFSGSIAGAIITAVGAPVEAIKTRLQANAGNYS 238
PL +G IAGAI V P++ +KTRLQ++A S
Sbjct: 2 PLSFLASLLAGGIAGAIAATVTYPLDVVKTRLQSSAAGGS 41
>gnl|CDD|203931 pfam08398, Parvo_coat_N, Parvovirus coat protein VP1. This is
the N-terminal region of the Parvovirus VP1 coat
protein. Also see Parvovirus coat protein VP2
(pfam00740).
Length = 64
Score = 53.9 bits (130), Expect = 4e-10
Identities = 18/33 (54%), Positives = 21/33 (63%)
Query: 3 FPFHNYLGPGNHLDNGPPIDDDDEIALRHDEAY 35
P + YLGPGN LDNG P++ D A HD AY
Sbjct: 1 LPGYKYLGPGNSLDNGEPVNPADAAAREHDFAY 33
>gnl|CDD|240302 PTZ00169, PTZ00169, ADP/ATP transporter on adenylate translocase;
Provisional.
Length = 300
Score = 32.8 bits (75), Expect = 0.12
Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 7/81 (8%)
Query: 103 VLSLYTTGVMGLLVGHPMDTIKTRTQTMPDKT-------MIQIIANTFKLEGFRGFYKGF 155
+LS G LL+ +P+D +TR + K + + K GF Y+GF
Sbjct: 117 ILSGGLAGASSLLIVYPLDFARTRLASDIGKGGDREFTGLFDCLMKISKQTGFLSLYQGF 176
Query: 156 LAPMLTTGVTNAIFFGVYGNT 176
+ V +FG+Y +
Sbjct: 177 GVSVQGIIVYRGAYFGLYDSA 197
Score = 29.4 bits (66), Expect = 1.9
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 9/62 (14%)
Query: 108 TTGVMGLLVGHPMDTIKTRTQTMPDKTMIQII--ANTF-------KLEGFRGFYKGFLAP 158
T ++ L+ +P DT++ R M + I T K EG GF+KG A
Sbjct: 219 TVTILAGLISYPFDTVRRRMMMMSGRKAKSEIQYTGTLDCWKKILKNEGLGGFFKGAWAN 278
Query: 159 ML 160
+L
Sbjct: 279 VL 280
>gnl|CDD|185494 PTZ00168, PTZ00168, mitochondrial carrier protein; Provisional.
Length = 259
Score = 32.2 bits (73), Expect = 0.20
Identities = 11/28 (39%), Positives = 20/28 (71%)
Query: 206 FFSGSIAGAIITAVGAPVEAIKTRLQAN 233
+G+++G I+ AV P+++IKT +QA
Sbjct: 7 LVTGALSGVIVDAVLYPIDSIKTNIQAK 34
Score = 31.8 bits (72), Expect = 0.27
Identities = 33/131 (25%), Positives = 53/131 (40%), Gaps = 23/131 (17%)
Query: 109 TGVMGLLVGHPMDTIKTRTQTMPDKTMIQIIANTFKLEGFRGFYKGFLAPMLTTGVTNAI 168
+GV+ V +P+D+IKT Q +F + Y G L ++ T +A
Sbjct: 13 SGVIVDAVLYPIDSIKTNIQA----------KKSFSFSDIKKLYSGILPTLVGTVPASAF 62
Query: 169 FFGVYGNTIRYLRSISESSEEYRCDGFLATPLWDWNEFFSGSIAGAIITAVGAPVEAIKT 228
F+ Y + + L E+ + T L+ S SIA V P E +K
Sbjct: 63 FYCFYELSKKLLTEYRENISK--------TNLY----LISTSIAEITACIVRLPFEIVKQ 110
Query: 229 RLQANAGNYSM 239
+Q +GN S+
Sbjct: 111 NMQV-SGNISV 120
>gnl|CDD|234746 PRK00394, PRK00394, transcription factor; Reviewed.
Length = 179
Score = 31.4 bits (72), Expect = 0.28
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 10/57 (17%)
Query: 42 EQVRQADIEAIRDFN---TNYVATGNWHSVVG----AIGLTWK---YEVEQFTGVLY 88
+++++ I+ I + N VA+ + + AIGL + YE EQF G++Y
Sbjct: 77 KKLKELGIKVIDEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVY 133
>gnl|CDD|119432 cd05172, PIKKc_DNA-PK, DNA-dependent protein kinase (DNA-PK),
catalytic domain; The DNA-PK catalytic domain subfamily
is part of a larger superfamily that includes the
catalytic domains of other kinases such as the typical
serine/threonine/tyrosine protein kinases (PKs),
aminoglycoside phosphotransferase, choline kinase, and
RIO kinases. DNA-PK is a member of the phosphoinositide
3-kinase-related protein kinase (PIKK) subfamily. PIKKs
have intrinsic serine/threonine kinase activity and are
distinguished from other PKs by their unique catalytic
domain, similar to that of lipid PI3K, and their large
molecular weight (240-470 kDa). DNA-PK is comprised of a
regulatory subunit, containing the Ku70/80 subunit, and
a catalytic subunit, which contains a NUC194 domain of
unknown function, a FAT (FRAP, ATM and TRRAP) domain, a
catalytic domain, and a FATC domain at the C-terminus.
It is part of a multi-component system involved in
non-homologous end joining (NHEJ), a process of
repairing double strand breaks (DSBs) by joining
together two free DNA ends of little homology. DNA-PK
functions as a molecular sensor for DNA damage that
enhances the signal via phosphorylation of downstream
targets. It may also act as a protein scaffold that aids
the localization of DNA repair proteins to the site of
DNA damage. DNA-PK also plays a role in the maintenance
of telomeric stability and the prevention of chromosomal
end fusion.
Length = 235
Score = 30.0 bits (68), Expect = 0.80
Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 5/52 (9%)
Query: 154 GFLAPMLTTGVTNAIFFGVYGNTIRYLRSISESSEEYRCDGFLATPLWDWNE 205
+ PM G+ + V+ T+R LR+ D F+ P DW
Sbjct: 189 NLMEPMKADGLLRSCM--VH--TLRALRNERHLLLST-MDVFVKEPSLDWKN 235
>gnl|CDD|226058 COG3527, AlsD, Alpha-acetolactate decarboxylase [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 234
Score = 29.6 bits (67), Expect = 1.1
Identities = 11/47 (23%), Positives = 19/47 (40%), Gaps = 5/47 (10%)
Query: 123 IKTRT---QTMPDKTMIQIIAN--TFKLEGFRGFYKGFLAPMLTTGV 164
+ R QT P + +++ F+ E +G GF P G+
Sbjct: 122 VHVRMVPKQTPPYTPLAEVVKIQPVFEFENVKGTIVGFWTPEYFEGL 168
>gnl|CDD|239954 cd04518, TBP_archaea, archaeal TATA box binding protein (TBP): TBPs
are transcription factors present in archaea and
eukaryotes, that recognize promoters and initiate
transcription. TBP has been shown to be an essential
component of three different transcription initiation
complexes: SL1, TFIID and TFIIIB, directing
transcription by RNA polymerases I, II and III,
respectively. TBP binds directly to the TATA box
promoter element, where it nucleates polymerase
assembly, thus defining the transcription start site.
TBP's binding in the minor groove induces a dramatic DNA
bending while its own structure barely changes. The
conserved core domain of TBP, which binds to the TATA
box, has a bipartite structure, with intramolecular
symmetry generating a saddle-shaped structure that sits
astride the DNA.
Length = 174
Score = 28.8 bits (65), Expect = 1.9
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 15/78 (19%)
Query: 43 QVRQADIEAIRDFN---TNYVATGNWHSVVG----AIGL-TWKYEVEQFTGVLYPPVDKS 94
+++ I+ I N VA+ + V AIGL +YE EQF G++Y +
Sbjct: 79 KLKDYGIKVIEKPEIKVQNIVASADLGREVNLDAIAIGLPNAEYEPEQFPGLVYRLDEPK 138
Query: 95 GWTPVIQEVLSLYTTGVM 112
VL L+++G M
Sbjct: 139 V-------VLLLFSSGKM 149
>gnl|CDD|221185 pfam11719, Drc1-Sld2, DNA replication and checkpoint protein.
Genome duplication is precisely regulated by
cyclin-dependent kinases CDKs, which bring about the
onset of S phase by activating replication origins and
then prevent relicensing of origins until mitosis is
completed. The optimum sequence motif for CDK
phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found
to have at least 11 potential phosphorylation sites.
Drc1 is required for DNA synthesis and S-M replication
checkpoint control. Drc1 associates with Cdc2 and is
phosphorylated at the onset of S phase when Cdc2 is
activated. Thus Cdc2 promotes DNA replication by
phosphorylating Drc1 and regulating its association with
Cut5. Sld2 and Sld3 represent the minimal set of S-CDK
substrates required for DNA replication.
Length = 397
Score = 29.4 bits (66), Expect = 2.0
Identities = 11/37 (29%), Positives = 14/37 (37%)
Query: 23 DDDEIALRHDEAYETATSPEQVRQADIEAIRDFNTNY 59
DD+ LR EA E P + D +A D
Sbjct: 247 DDELDVLREIEAEEAGIGPIEEEVVDSQAANDEPRRV 283
>gnl|CDD|153091 cd00125, PLA2c, PLA2c: Phospholipase A2, a family of secretory
and cytosolic enzymes; the latter are either Ca
dependent or Ca independent. PLA2 cleaves the sn-2
position of the glycerol backbone of phospholipids (PC
or phosphatidylethanolamine), usually in a
metal-dependent reaction, to generate lysophospholipid
(LysoPL) and a free fatty acid (FA). The resulting
products are either dietary or used in synthetic
pathways for leukotrienes and prostaglandins. Often,
arachidonic acid is released as a free fatty acid and
acts as second messenger in signaling networks.
Secreted PLA2s have also been found to specifically
bind to a variety of soluble and membrane proteins in
mammals, including receptors. As a toxin, PLA2 is a
potent presynaptic neurotoxin which blocks nerve
terminals by binding to the nerve membrane and
hydrolyzing stable membrane lipids. The products of the
hydrolysis (LysoPL and FA) cannot form bilayers leading
to a change in membrane conformation and ultimately to
a block in the release of neurotransmitters. PLA2 may
form dimers or oligomers.
Length = 115
Score = 28.0 bits (63), Expect = 2.3
Identities = 12/34 (35%), Positives = 14/34 (41%), Gaps = 3/34 (8%)
Query: 8 YLGPGNHLDNGPPIDDDDEIALRHDEAYETATSP 41
Y G G G P+DD D HD Y+ A
Sbjct: 26 YCGLGGS---GTPVDDTDRCCQVHDCCYDRAEKG 56
>gnl|CDD|107304 cd06309, PBP1_YtfQ_like, Periplasmic binding domain of ABC-type
YtfQ-like transport systems. Periplasmic binding domain
of ABC-type YtfQ-like transport systems. The YtfQ
protein from Escherichia coli is up-regulated under
glucose-limited conditions and shares homology with a
family of pentose/hexose sugar-binding proteins of the
type I periplasmic binding protein superfamily. Members
of this group are predicted to be involved in the
transport of sugar-containing molecules across cellular
and organellar membranes; however their ligand
specificity is not determined experimentally.
Length = 273
Score = 28.0 bits (63), Expect = 5.0
Identities = 30/138 (21%), Positives = 46/138 (33%), Gaps = 35/138 (25%)
Query: 39 TSPEQVRQADIEAIRDFNTNYVATGNWHSVVGAIGLTWKYEVEQFTGVLYPPVDKSGWTP 98
+Q ++ I AIR F +A G V I L PV ++GW P
Sbjct: 35 ADAQQKQENQISAIRSF----IAQG-----VDVIILA--------------PVVETGWDP 71
Query: 99 VIQEVLSLYTTGVMGLLVGHPMDTIKTRTQTMPDKTMIQIIANTFKLEGFRGFYKGFLAP 158
V++E + G P+ + D + I + F EG R +LA
Sbjct: 72 VLKEAKA----------AGIPVILVDRGVDVKDDSLYVTFIGSDFVEEGRRA--ADWLAK 119
Query: 159 MLTTGVTNAIFFGVYGNT 176
G G++
Sbjct: 120 ATGGKGNIVELQGTVGSS 137
>gnl|CDD|182299 PRK10199, PRK10199, alkaline phosphatase isozyme conversion
aminopeptidase; Provisional.
Length = 346
Score = 27.8 bits (62), Expect = 6.3
Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 5/24 (20%)
Query: 52 IRDFNTNYVATG-----NWHSVVG 70
IR FN+ Y+ T NWH+V G
Sbjct: 74 IRTFNSRYIYTARDNRKNWHNVTG 97
>gnl|CDD|216247 pfam01019, G_glu_transpept, Gamma-glutamyltranspeptidase.
Length = 495
Score = 27.6 bits (62), Expect = 7.4
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 3/21 (14%)
Query: 140 ANTFKL---EGFRGFYKGFLA 157
A T +L EG FY+G LA
Sbjct: 163 AKTLELIAEEGPEAFYRGELA 183
>gnl|CDD|200071 TIGR01041, ATP_syn_B_arch, ATP synthase archaeal, B subunit.
Archaeal ATP synthase shares extensive sequence
similarity with eukaryotic and prokaryotic V-type
(H+)-ATPases [Energy metabolism, ATP-proton motive force
interconversion].
Length = 458
Score = 27.4 bits (61), Expect = 7.4
Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 3/50 (6%)
Query: 10 GPGNHLDNGPPIDDDDEIALRHDEAYETATS--PEQVRQADIEAIRDFNT 57
G G +D GP I D+ + + PE+ Q I AI NT
Sbjct: 89 GSGEPIDGGPEIVPDERRDI-NGAPINPYAREYPEEFIQTGISAIDGMNT 137
>gnl|CDD|225012 COG2101, SPT15, TATA-box binding protein (TBP), component of TFIID
and TFIIIB [Transcription].
Length = 185
Score = 27.0 bits (60), Expect = 8.1
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 7/42 (16%)
Query: 58 NYVATGNWHSVVG----AIGL---TWKYEVEQFTGVLYPPVD 92
N VA+ + + AIGL +YE EQF G++Y +
Sbjct: 103 NIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDE 144
>gnl|CDD|133048 cd06426, NTP_transferase_like_2, NTP_trnasferase_like_2 is a member
of the nucleotidyl transferase family. This is a
subfamily of nucleotidyl transferases. Nucleotidyl
transferases transfer nucleotides onto phosphosugars.
The activated sugars are precursors for synthesis of
lipopolysaccharide, glycolipids and polysaccharides.
Other subfamilies of nucleotidyl transferases include
Alpha-D-Glucose-1-Phosphate Cytidylyltransferase,
Mannose-1-phosphate guanyltransferase, and
Glucose-1-phosphate thymidylyltransferase.
Length = 220
Score = 27.1 bits (61), Expect = 8.7
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 132 DKTMIQIIANTFKLEGFRGFY 152
K +++ I + F +GFR FY
Sbjct: 28 GKPILETIIDRFIAQGFRNFY 48
>gnl|CDD|163574 TIGR03862, flavo_PP4765, uncharacterized flavoprotein, PP_4765
family. This model describes a sharply distinctive
clade of proteins within the larger family of
flavoproteins described by pfam03486 and TIGRFAMs model
TIGR00275. The function is unknown.
Length = 376
Score = 27.1 bits (60), Expect = 8.8
Identities = 11/42 (26%), Positives = 17/42 (40%)
Query: 200 LWDWNEFFSGSIAGAIITAVGAPVEAIKTRLQANAGNYSMYG 241
L DW+ F+ AG + V A +TR + + G
Sbjct: 173 LVDWSAHFASRFAGEPLKRVNATAGTQQTRGEIVITARGLEG 214
>gnl|CDD|241367 cd13213, PH-GRAM_MTMR14, Myotubularian (MTM) related 14 protein
(MTMR14) Pleckstrin Homology-Glucosyltransferases,
Rab-like GTPase activators and Myotubularins (PH-GRAM)
domain. MTMR14 is a member of the myotubularin protein
phosphatase gene family. MTMR14 binds to
phosphoinositide lipids through its PH-GRAM domain, and
can hydrolyze phosphatidylinositol(3)-phosphate and
phosphatidylinositol(3,5)-biphosphate in vitro. MTMR14
plays a role in the regulation of autophagy and
mutations in MTMR14 result in autosomal dominant
centronuclear myopathy. MTMR14 contain a N-terminal
PH-GRAM domain, a Rac-induced recruitment domain (RID)
domain, an active PTP domain, a SET-interaction domain
(SID), a coiled-coil region, and a C-terminal PDZ
domain. Myotubularin-related proteins are a subfamily
of protein tyrosine phosphatases (PTPs) that
dephosphorylate D3-phosphorylated inositol lipids.
Mutations in this family cause the human neuromuscular
disorders myotubular myopathy and type 4B
Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs
5, 9-13) contain naturally occurring substitutions of
residues required for catalysis by PTP family enzymes.
Although these proteins are predicted to be
enzymatically inactive, they are thought to function as
antagonists of endogenous phosphatase activity or
interaction modules. Most MTMRs contain a N-terminal
PH-GRAM domain, a Rac-induced recruitment domain (RID)
domain, a PTP domain (which may be active or inactive),
a SET-interaction domain (SID), and a C-terminal
coiled-coil region. In addition some members contain
DENN domain N-terminal to the PH-GRAM domain and FYVE,
PDZ, and PH domains C-terminal to the coiled-coil
region. The GRAM domain, found in myotubularins,
glucosyltransferases, and other putative
membrane-associated proteins, is part of a larger motif
with a pleckstrin homology (PH) domain fold. The PH
domain family possesses multiple functions including
the ability to bind phosphoinositides via its
beta1/beta2, beta3/beta4, and beta6/beta7 connecting
loops and to other proteins. However, no
phosphoinositide binding sites have been found for the
MTMRs to date.
Length = 168
Score = 26.5 bits (59), Expect = 9.2
Identities = 9/54 (16%), Positives = 19/54 (35%), Gaps = 1/54 (1%)
Query: 7 NYLGPGNHLDNGPPIDDDDEIALRHDEAYETATSPEQVRQADIEAIRDFNTNYV 60
+YL G + + E + ++VR DI+ ++ N +
Sbjct: 42 DYLFSGFGSTPSSSDPSELQEQSEETENGDWQ-LFDKVRGQDIKLLKTLNVGTI 94
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
0.320 0.138 0.426
Gapped
Lambda K H
0.267 0.0689 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,002,313
Number of extensions: 1237035
Number of successful extensions: 1138
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1134
Number of HSP's successfully gapped: 26
Length of query: 245
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 151
Effective length of database: 6,768,326
Effective search space: 1022017226
Effective search space used: 1022017226
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: 58 (26.2 bits)