RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9523
(107 letters)
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor of
a mutation in RCC1. Biochemical analysis revealed that
Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 113 bits (284), Expect = 1e-32
Identities = 43/79 (54%), Positives = 60/79 (75%), Gaps = 2/79 (2%)
Query: 19 LSFHLTSIYDHSIFEAFSKVIQKLIPQLPTLENLLNILINNSGIEKAFLFDVVSKIYIAT 78
L+F LTSI+DHS+++A+SK++QKLIP L TLENLL L ++S E+ FLF+ + + IAT
Sbjct: 152 LTFFLTSIWDHSLYKAWSKIVQKLIPNLSTLENLLKKLGSSSNAEEVFLFERSTFLVIAT 211
Query: 79 DS-SPVD-MQSYELCCDMV 95
DS SPVD Q YE C +++
Sbjct: 212 DSRSPVDIPQRYEKCSNII 230
>gnl|CDD|206745 cd11385, RagC_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins C and D. RagC
and RagD are closely related Rag GTPases (ras-related
GTP-binding protein C and D) that constitute a unique
subgroup of the Ras superfamily, and are functional
homologs of Saccharomyces cerevisiae Gtr2. These domains
form heterodimers with RagA or RagB, and similarly, Gtr2
dimerizes with Gtr1 in order to function. They play an
essential role in regulating amino acid-induced target
of rapamycin complex 1 (TORC1) kinase signaling,
exocytic cargo sorting at endosomes, and epigenetic
control of gene expression. In response to amino acids,
the Rag GTPases guide the TORC1 complex to activate the
platform containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 175
Score = 68.0 bits (167), Expect = 1e-15
Identities = 23/31 (74%), Positives = 28/31 (90%)
Query: 13 GYDQITLSFHLTSIYDHSIFEAFSKVIQKLI 43
G + + +SF+LTSIYDHSIFEAFSKV+QKLI
Sbjct: 145 GLEDVQISFYLTSIYDHSIFEAFSKVVQKLI 175
>gnl|CDD|206742 cd09915, Rag, Rag GTPase subfamily of Ras-related GTPases. Rag
GTPases (ras-related GTP-binding proteins) constitute a
unique subgroup of the Ras superfamily, playing an
essential role in regulating amino acid-induced target
of rapamycin complex 1 (TORC1) kinase signaling,
exocytic cargo sorting at endosomes, and epigenetic
control of gene expression. This subfamily consists of
RagA and RagB as well as RagC and RagD that are closely
related. Saccharomyces cerevisiae encodes single
orthologs of metazoan RagA/B and RagC/D, Gtr1 and Gtr2,
respectively. Dimer formation is important for their
cellular function; these domains form heterodimers, as
RagA or RagB dimerizes with RagC or RagD, and similarly,
Gtr1 dimerizes with Gtr2. In response to amino acids,
the Rag GTPases guide the TORC1 complex to activate the
platform containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 175
Score = 50.3 bits (120), Expect = 7e-09
Identities = 20/31 (64%), Positives = 27/31 (87%)
Query: 13 GYDQITLSFHLTSIYDHSIFEAFSKVIQKLI 43
G + LSF+LTSI+DHSI+EAFS+++QKLI
Sbjct: 145 GLEFPNLSFYLTSIWDHSIYEAFSQIVQKLI 175
>gnl|CDD|206744 cd11384, RagA_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins A and B. RagA
and RagB are closely related Rag GTPases (ras-related
GTP-binding protein A and B) that constitute a unique
subgroup of the Ras superfamily, and are functional
homologs of Saccharomyces cerevisiae Gtr1. These domains
function by forming heterodimers with RagC or RagD, and
similarly, Gtr1 dimerizes with Gtr2, through the
carboxy-terminal segments. They play an essential role
in regulating amino acid-induced target of rapamycin
complex 1 (TORC1) kinase signaling, exocytic cargo
sorting at endosomes, and epigenetic control of gene
expression. In response to amino acids, the Rag GTPases
guide the TORC1 complex to activate the platform
containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 286
Score = 40.7 bits (96), Expect = 3e-05
Identities = 18/70 (25%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 24 TSIYDHSIFEAFSKVIQKLIPQLPTLENLLNILINNSGIEKAFLFDVVSKIYIATDSSP- 82
TSI+D ++++A+S ++ LIP + LE+ L + ++ LF+ + + I+ S
Sbjct: 154 TSIWDETLYKAWSSIVYSLIPNIQVLESNLKKFADICEADEVVLFERATFLVISHSSRKE 213
Query: 83 ---VDMQSYE 89
+D +E
Sbjct: 214 ASALDPHRFE 223
>gnl|CDD|233590 TIGR01830, 3oxo_ACP_reduc, 3-oxoacyl-(acyl-carrier-protein)
reductase. This model represents 3-oxoacyl-[ACP]
reductase, also called 3-ketoacyl-acyl carrier protein
reductase, an enzyme of fatty acid biosynthesis [Fatty
acid and phospholipid metabolism, Biosynthesis].
Length = 239
Score = 27.6 bits (62), Expect = 1.1
Identities = 11/37 (29%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 28 DHSIFEAFSKVIQKLIPQLPTLENLLNILINNSGIEK 64
D S E V++++ +L ++ IL+NN+GI +
Sbjct: 56 DVSDREDVKAVVEEIEEELGPID----ILVNNAGITR 88
>gnl|CDD|187628 cd05370, SDR_c2, classical (c) SDR, subgroup 2. Short-chain
dehydrogenases/reductases (SDRs, aka Tyrosine-dependent
oxidoreductases) are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 228
Score = 27.3 bits (61), Expect = 1.6
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 28 DHSIFEAFSKVIQKLIPQLPTLENLLNILINNSGI 62
D EA + L+ + P L +ILINN+GI
Sbjct: 61 DAESVEAL---AEALLSEYPNL----DILINNAGI 88
>gnl|CDD|240285 PTZ00135, PTZ00135, 60S acidic ribosomal protein P0; Provisional.
Length = 310
Score = 26.9 bits (60), Expect = 2.1
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 35 FSKVIQKLIPQLPTLENLLNILINNSGIEKAFLF 68
K +++ + +LP LE LL + N G F+F
Sbjct: 61 IRKALKQRLEELPELEKLLPHVKGNVG----FVF 90
>gnl|CDD|187585 cd05324, carb_red_PTCR-like_SDR_c, Porcine testicular carbonyl
reductase (PTCR)-like, classical (c) SDRs. PTCR is a
classical SDR which catalyzes the NADPH-dependent
reduction of ketones on steroids and prostaglandins.
Unlike most SDRs, PTCR functions as a monomer. This
subgroup also includes human carbonyl reductase 1
(CBR1) and CBR3. CBR1 is an NADPH-dependent SDR with
broad substrate specificity and may be responsible for
the in vivo reduction of quinones, prostaglandins, and
other carbonyl-containing compounds. In addition it
includes poppy NADPH-dependent salutaridine reductase
which catalyzes the stereospecific reduction of
salutaridine to 7(S)-salutaridinol in the biosynthesis
of morphine, and Arabidopsis SDR1,a menthone reductase,
which catalyzes the reduction of menthone to
neomenthol, a compound with antimicrobial activity;
SDR1 can also carry out neomenthol oxidation. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Extended SDRs have
additional elements in the C-terminal region, and
typically have a TGXXGXXG cofactor binding motif.
Complex (multidomain) SDRs such as ketoreductase
domains of fatty acid synthase have a GGXGXXG
NAD(P)-binding motif and an altered active site motif
(YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 225
Score = 26.4 bits (59), Expect = 2.7
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 7/42 (16%)
Query: 21 FHLTSIYDHSIFEAFSKVIQKLIPQLPTLENLLNILINNSGI 62
FH + D + EA + +++ L+IL+NN+GI
Sbjct: 54 FHQLDVTDDASIEAAADFVEEKY-------GGLDILVNNAGI 88
>gnl|CDD|188475 TIGR03960, rSAM_fuse_unch, radical SAM family uncharacterized
protein. This model describes a radical SAM protein, or
protein region, regularly found paired with or fused to
a region described by TIGR03936. PSI-BLAST analysis of
TIGR03936 suggests a relationship to the tRNA
pseudouridine synthase TruA, suggesting that this system
may act in RNA modification [Unknown function, Enzymes
of unknown specificity].
Length = 605
Score = 26.5 bits (59), Expect = 3.0
Identities = 23/76 (30%), Positives = 29/76 (38%), Gaps = 30/76 (39%)
Query: 10 DSGGYDQITLSFHLTSIYDHSIFEAFSKVIQKLIPQLPTLENLLNILINNSGIEK----- 64
+ GYD+I+LS TS Y LE LL+ LI+ E
Sbjct: 295 KNTGYDEISLSSLSTSDYSQ-------------------LEELLDFLIDEFKPEHVNISL 335
Query: 65 ------AFLFDVVSKI 74
AF DV+SKI
Sbjct: 336 PSLRIDAFSLDVMSKI 351
>gnl|CDD|112616 pfam03812, KdgT, 2-keto-3-deoxygluconate permease.
Length = 314
Score = 26.3 bits (58), Expect = 3.4
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 28 DHSIFEAFSKVIQKLIPQLP-TLENLLNI-LINNSGIEKAFL 67
D + + FSKV+Q LIP L N +N+ +I +G+ FL
Sbjct: 188 DPDLRDLFSKVVQTLIPFFAFALGNTINLGVIIQTGLLGIFL 229
>gnl|CDD|213560 TIGR00793, kdgT, 2-keto-3-deoxygluconate transporter. This family
includes the characterized 2-Keto-3-Deoxygluconate
transporters from Bacillus subtilis and Erwinia
chrysanthemi. There are homologs of this protein found
in both gram-positive and gram-negative bacteria
[Transport and binding proteins, Carbohydrates, organic
alcohols, and acids].
Length = 314
Score = 26.4 bits (58), Expect = 3.6
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 28 DHSIFEAFSKVIQKLIPQLP-TLENLLNI-LINNSGIEKAFL 67
D + + FSK +Q LIP L N +++ +I +G+ L
Sbjct: 188 DPELRDFFSKAVQTLIPFFAFALGNTIDLGVIIQTGLLGILL 229
>gnl|CDD|226476 COG3967, DltE, Short-chain dehydrogenase involved in D-alanine
esterification of lipoteichoic acid and wall teichoic
acid (D-alanine transfer protein) [Cell envelope
biogenesis, outer membrane].
Length = 245
Score = 25.9 bits (57), Expect = 4.0
Identities = 8/13 (61%), Positives = 12/13 (92%)
Query: 53 LNILINNSGIEKA 65
LN+LINN+GI++
Sbjct: 79 LNVLINNAGIQRN 91
>gnl|CDD|223472 COG0395, UgpE, ABC-type sugar transport system, permease
component [Carbohydrate transport and metabolism].
Length = 281
Score = 26.0 bits (58), Expect = 4.6
Identities = 12/38 (31%), Positives = 14/38 (36%)
Query: 30 SIFEAFSKVIQKLIPQLPTLENLLNILINNSGIEKAFL 67
E FS L P TLEN + G + FL
Sbjct: 39 PSAEIFSGPPPSLWPSSFTLENYRTVFSGGPGFLRYFL 76
>gnl|CDD|225404 COG2848, COG2848, Uncharacterized conserved protein [Function
unknown].
Length = 445
Score = 25.9 bits (57), Expect = 5.0
Identities = 14/68 (20%), Positives = 22/68 (32%)
Query: 17 ITLSFHLTSIYDHSIFEAFSKVIQKLIPQLPTLENLLNILINNSGIEKAFLFDVVSKIYI 76
IT+ L I E + +K+ + L L G+ V+ I I
Sbjct: 23 ITIGISLLDCISSDIEELAENIYEKITTKALKLVETAEELTAELGVPIVNKRISVTPISI 82
Query: 77 ATDSSPVD 84
S+ D
Sbjct: 83 VAASTADD 90
>gnl|CDD|130052 TIGR00979, fumC_II, fumarate hydratase, class II. Putative
fumarases from several species (Mycobacterium
tuberculosis, Streptomyces coelicolor, Pseudomonas
aeruginosa) branch deeply, although within the same
branch of a phylogenetic tree rooted by aspartate
ammonia-lyase sequences, and score between the trusted
and noise cutoffs [Energy metabolism, TCA cycle].
Length = 458
Score = 25.5 bits (56), Expect = 6.9
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 8/41 (19%)
Query: 34 AFSKVIQKLIPQLPTLENLLNILINNSGIEKAFLFDVVSKI 74
A + +LIP L L+ L+ K+ F + KI
Sbjct: 149 AVLAIKNQLIPALENLKKTLD--------AKSKEFAHIVKI 181
>gnl|CDD|204372 pfam09999, DUF2240, Uncharacterized protein conserved in archaea
(DUF2240). This domain, found in various hypothetical
archaeal proteins, has no known function.
Length = 144
Score = 24.9 bits (55), Expect = 8.8
Identities = 14/60 (23%), Positives = 28/60 (46%), Gaps = 7/60 (11%)
Query: 15 DQITLSFHLTSIYDHSIFEAFSKVIQKLIPQLPTLENLLNILINNSGIEKAFLFDVVSKI 74
+F S+ I F K + ++ + E +L+ + ++GIEK +VV++I
Sbjct: 57 GDYVPNFDPASV---RIPLGF-KPDESILQEKSPFERILDRIAASAGIEKQ---EVVAEI 109
>gnl|CDD|222690 pfam14336, DUF4392, Domain of unknown function (DUF4392). This
family of proteins is found in bacteria, archaea and
eukaryotes. Proteins in this family are typically
between 282 and 585 amino acids in length. There are
two completely conserved G residues that may be
functionally important.
Length = 278
Score = 24.9 bits (55), Expect = 9.1
Identities = 9/53 (16%), Positives = 15/53 (28%), Gaps = 11/53 (20%)
Query: 48 TLENLLNILINNSGIEKAFLFDVVSK-----------IYIATDSSPVDMQSYE 89
LE+L+ GI K + + + + I T E
Sbjct: 1 QLEDLIATDRGGRGILKLYEPGYLLRAARLLLSSAGRVLIVTGFPVPPAPPAE 53
>gnl|CDD|113491 pfam04723, GRDA, Glycine reductase complex selenoprotein A. Found
in clostridia, this protein contains one active site
selenocysteine and catalyzes the reductive deamination
of glycine, which is coupled to the esterification of
orthophosphate resulting in the formation of ATP. A
member of this family may also exist in Treponema
denticola.
Length = 150
Score = 24.9 bits (54), Expect = 9.6
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 83 VDMQSYELCCDMVDLVIDVSGI 104
VD Y+ C M+++V+DV GI
Sbjct: 120 VDEAIYDDQCGMMEMVLDVDGI 141
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
0.322 0.139 0.406
Gapped
Lambda K H
0.267 0.0764 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,467,388
Number of extensions: 464538
Number of successful extensions: 583
Number of sequences better than 10.0: 1
Number of HSP's gapped: 581
Number of HSP's successfully gapped: 35
Length of query: 107
Length of database: 10,937,602
Length adjustment: 72
Effective length of query: 35
Effective length of database: 7,744,114
Effective search space: 271043990
Effective search space used: 271043990
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 (21.9 bits)
S2: 53 (24.1 bits)