RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15695
(299 letters)
>gnl|CDD|218295 pfam04858, TH1, TH1 protein. TH1 is a highly conserved but
uncharacterized metazoan protein. No homologue has been
identified in Caenorhabditis elegans. TH1 binds
specifically to A-Raf kinase.
Length = 582
Score = 328 bits (842), Expect = e-109
Identities = 129/204 (63%), Positives = 158/204 (77%), Gaps = 1/204 (0%)
Query: 93 ESDLFAIEKVHSI-CNSSKSSNELIAEITTLFHCIRYPVVSVGVIRWVECTVTEPSYFKL 151
+S + AIEK H+I CN+ + +ELIAE++TL++CIR+PVV GVI WV VTEPSYF+L
Sbjct: 377 KSTIKAIEKAHAIICNAKRGKSELIAELSTLYNCIRFPVVGAGVIAWVRSAVTEPSYFRL 436
Query: 152 CTEHTPTHLALLDEVVTCHTFLHHKVLQLFIELFESKQDELEILVQLEMRKMLLDRMVNL 211
T P HLA+LDEV H L +VL+L + LFES DELEILVQLE++KMLLDRMV L
Sbjct: 437 VTNSNPVHLAVLDEVARKHVALQGQVLELLVALFESHGDELEILVQLELKKMLLDRMVEL 496
Query: 212 LCRGCVVPVVKYVKQCWQRGDTDISLIRYFVTEVLEAITPPYTPEFVQLFLPIVENDEIT 271
L RG VVPV+ Y QCW+R DTDISLIRYFVTEVLE PPY+ +FVQLFLP++EN+ I
Sbjct: 497 LARGHVVPVITYACQCWRRLDTDISLIRYFVTEVLEIAGPPYSRDFVQLFLPLLENENIR 556
Query: 272 GTMRGDGENDPVSEFIVHCKAHFV 295
GTMRG+G++DPV EFIVHCK +
Sbjct: 557 GTMRGEGDSDPVDEFIVHCKRRYT 580
>gnl|CDD|221818 pfam12868, DUF3824, Domain of unknwon function (DUF3824). This
is a repeating domain found in fungal proteins. It is
proline-rich, and the function is not known.
Length = 135
Score = 33.7 bits (77), Expect = 0.043
Identities = 15/35 (42%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 39 SSMYESIYEPINPRPPSDLSSRSNYSLYSSNIPPP 73
S YE Y+P P PPS S Y S+ PPP
Sbjct: 47 SDSYEEPYDP-TPYPPSPPVSDPRYYPNSNYFPPP 80
>gnl|CDD|224296 COG1378, COG1378, Predicted transcriptional regulators
[Transcription].
Length = 247
Score = 32.4 bits (74), Expect = 0.22
Identities = 18/116 (15%), Positives = 46/116 (39%), Gaps = 5/116 (4%)
Query: 176 KVLQLFIELFESKQDELEILVQLEMRKMLLDRMVNLLCRGCVVPVVKYVKQCWQRGDTDI 235
++++ E+ + E+ I++ E+ K L + ++ L RG V ++ + +
Sbjct: 120 EIIEKIKEVINEAEKEIIIVLPYEIFKELKEPLIRALKRGVRVLILVFPI---RDVPLAF 176
Query: 236 SLIRYFVTEVLEAITPPYTPEFV--QLFLPIVENDEITGTMRGDGENDPVSEFIVH 289
+ ++F+ +++ V + I+ T+ G + FI H
Sbjct: 177 IVNKFFLDALIDIRFGDPLAGEVIISDRIRILIVPSDGETVEGVIYSFDEIAFITH 232
>gnl|CDD|99862 cd06109, BsCS-I_like, Bacillus subtilis (Bs) citrate synthase
CS-I_like. CS catalyzes the condensation of acetyl
coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate
and coenzyme A (CoA), the first step in the citric acid
cycle (TCA or Krebs cycle). 2MCS catalyzes the
condensation of propionyl-coenzyme A (PrCoA) and OAA to
form 2-methylcitrate and coenzyme A (CoA) during
propionate metabolism. The overall CS reaction is
thought to proceed through three partial reactions and
involves both closed and open conformational forms of
the enzyme: a) the carbanion or equivalent is generated
from AcCoA by base abstraction of a proton, b) the
nucleophilic attack of this carbanion on OAA to generate
citryl-CoA, and c) the hydrolysis of citryl-CoA to
produce citrate and CoA. This group contains proteins
similar to BsCS-I, one of two CS isozymes in the
gram-positive B. subtilis. The majority of CS activity
in B. subtilis is provided by the other isozyme, BsCS-II
(not included in this group). BsCS-I has a lower
catalytic activity than BsCS-II, and has a Glu in place
of a key catalytic Asp residue. This change is conserved
in other members of this group. For E. coli CS (not
included in this group), site directed mutagenesis of
the key Asp residue to a Glu converts the enzyme into
citryl-CoA lyase which cleaves citryl-CoA to AcCoA and
OAA. A null mutation in the gene encoding BsCS-I (citA)
had little effect on B. subtilis CS activity or on
sporulation. However, disruption of the citA gene in a
strain null for the gene encoding BsCS-II resulted in a
sporulation deficiency, a characteristic of strains
defective in the Krebs cycle. This group contains
proteins which functions exclusively as either a CS or a
2MCS, as well as those with relaxed specificity which
have dual functions as both a CS and a 2MCS. Many of the
gram-negative species represented in this group have a
second CS isozyme which is in another group.
Length = 349
Score = 31.1 bits (71), Expect = 0.74
Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 15/66 (22%)
Query: 46 YEPINPRPPSDLSSRSNYSLYSSNIPPPEAEVDALTDLLV----HSLDT---------SS 92
+PI P P LS ++Y + PP EA V AL LV H ++ S+
Sbjct: 127 KQPIAPDP--SLSHAADYLRMLTGEPPSEAHVRALDAYLVTVADHGMNASTFTARVIAST 184
Query: 93 ESDLFA 98
E+DL +
Sbjct: 185 EADLTS 190
>gnl|CDD|233185 TIGR00918, 2A060602, The Eukaryotic (Putative) Sterol Transporter
(EST) Family.
Length = 1145
Score = 31.4 bits (71), Expect = 0.78
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 49 INPRPPSDLSSRSNYSLYSSNIPPPEAEVDALTDLLVHSLDTSSESDLFAIEKVHSICN 107
I P PP L +++Y + IP E A ++ L +S+ + AIE V +ICN
Sbjct: 881 IYPHPPEWLHDKNDYDPENLRIPAAEPLEYAQFPFYLNGLRETSQF-VEAIEHVRAICN 938
>gnl|CDD|176458 cd03468, PolY_like, DNA Polymerase Y-family. Y-family DNA
polymerases are a specialized subset of polymerases that
facilitate translesion synthesis (TLS), a process that
allows the bypass of a variety of DNA lesions. Unlike
replicative polymerases, TLS polymerases lack
proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. The active
sites of TLS polymerases are large and flexible to allow
the accomodation of distorted bases. Expression of
Y-family polymerases is often induced by DNA damage and
is believed to be highly regulated. TLS is likely
induced by the monoubiquitination of the replication
clamp PCNA, which provides a scaffold for TLS
polymerases to bind in order to access the lesion.
Because of their high error rates, TLS polymerases are
potential targets for cancer treatment and prevention.
Length = 335
Score = 30.8 bits (70), Expect = 0.88
Identities = 15/65 (23%), Positives = 22/65 (33%), Gaps = 2/65 (3%)
Query: 197 QLEMRKMLLDRMVNLLCRGCVVPVVKYVKQCWQRGDTDISLIRYFVTEVLEAITPPYTPE 256
L +R + R+ L R V V R D + + E LE + P
Sbjct: 267 FLALRGLGARRLSLTLFR--EDGRVTRVLVGLARPSRDDLPLLRLLRERLERLALPRGIA 324
Query: 257 FVQLF 261
V+L
Sbjct: 325 PVRLL 329
>gnl|CDD|220720 pfam10371, EKR, Domain of unknown function. EKR is a short, 33
residue, domain found in bacterial and some lower
eukaryotic species which lies between a POR (pyruvate
ferredoxin/flavodoxin oxidoreductase) pfam01558 and the
4Fe-4S binding domain Fer4 pfam00037. It contains a
characteristic EKR sequence motif. The exact function of
this domain is not known.
Length = 60
Score = 28.0 bits (63), Expect = 0.99
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 10/35 (28%)
Query: 255 PEFVQLFLPIVENDEITGTM-RGDGENDPVSEFIV 288
PEFV+ + M G+G++ PVS F
Sbjct: 17 PEFVK---------NVLAPMNAGEGDDLPVSAFPE 42
>gnl|CDD|188963 cd09564, SAM_kazrin_repeat1, SAM domain of kazrin proteins repeat
1. SAM (sterile alpha motif) domain repeat 1 of kazrin
proteins is a protein-protein interaction domain. The
long isoform of kazrin contains three copies (repeats)
of SAM domain. Kazrin can interact with periplakin. It
is involved into interplay between desmosomes and in
adheren junctions. Additionally kazrins play a role in
regulation of intercellular differentiation, junction
assembly, and cytoskeletal organization.
Length = 70
Score = 27.8 bits (62), Expect = 1.7
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 7/56 (12%)
Query: 135 VIRWVECTVTEPSYFKLCTEHTPTHLALLD----EVVTC---HTFLHHKVLQLFIE 183
V+ W+E + P Y K C E+ + LL E+ + LH + L+L IE
Sbjct: 9 VLAWLEVVMHMPMYSKACAENVKSGKVLLGLSDSELESGLGISNVLHRRKLRLAIE 64
>gnl|CDD|187835 cd09704, Csx12, CRISPR/Cas system-associated protein Cas9. CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; Very large protein
containing McrA/HNH-nuclease related domain and a
RuvC-like nuclease domain; signature gene for type II.
Length = 804
Score = 30.0 bits (67), Expect = 1.9
Identities = 8/36 (22%), Positives = 16/36 (44%)
Query: 83 LLVHSLDTSSESDLFAIEKVHSICNSSKSSNELIAE 118
+L LD D + +++ S K +E++A
Sbjct: 400 ILQRILDRVKAIDELLLNEIYFKLESGKKLDEVLAN 435
>gnl|CDD|234096 TIGR03031, cas_csx12, CRISPR-associated protein Cas9/Csx12, subtype
II-B/NMENI. Members of this family of CRISPR-associated
(cas) protein are found, so far, in CRISPR/cas loci in
Wolinella succinogenes DSM 1740, Legionella pneumophila
str. Paris, and Francisella tularensis, where the last
probably is an example of a degenerate CRISPR locus,
having neither repeats nor a functional Cas1. The
characteristic repeat length is 37 base pairs and period
is about 72. One region of this large protein shows
sequence similarity to pfam01844, HNH endonuclease
[Mobile and extrachromosomal element functions, Other].
Length = 802
Score = 30.0 bits (67), Expect = 2.0
Identities = 10/36 (27%), Positives = 16/36 (44%)
Query: 83 LLVHSLDTSSESDLFAIEKVHSICNSSKSSNELIAE 118
+L LD + + D F ++K S K E + E
Sbjct: 400 ILQRYLDLNKKIDKFKLKKQLSFLGQGKKLPENLIE 435
>gnl|CDD|176879 cd08870, START_STARD2_7-like, Lipid-binding START domain of
mammalian STARD2, -7, and related proteins. This
subfamily includes the steroidogenic acute regulatory
protein (StAR)-related lipid transfer (START) domains of
STARD2 (also known as phosphatidylcholine transfer
protein/PC-TP), and STARD7 (also known as gestational
trophoblastic tumor 1/GTT1). The START domain family
belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. STARD2 is a cytosolic phosphatidycholine
(PtdCho) transfer protein, which traffics PtdCho, the
most common class of phospholipids in eukaryotes,
between membranes. It represents a minimal START domain
structure. STARD2 plays roles in hepatic cholesterol
metabolism, in the development of atherosclerosis, and
may also have a mitochondrial function. The gene
encoding STARD7 is overexpressed in choriocarcinoma.
STARD7 appears to be involved in the intracellular
trafficking of PtdCho to mitochondria. STARD7 was shown
to be surface active and to interact differentially with
phospholipid monolayers. It showed a preference for
phosphatidylserine, cholesterol, and
phosphatidylglycerol.
Length = 209
Score = 29.3 bits (66), Expect = 2.1
Identities = 19/81 (23%), Positives = 25/81 (30%), Gaps = 24/81 (29%)
Query: 226 QCWQRGDTDISLIRYFVTEVLEAITPP----------YTPEFVQLF--LPIVENDEITGT 273
Q W+R L Y V V E TP Y ++ + +E DE +GT
Sbjct: 38 QAWRRKPKGTGLYEYLVRGVFEDCTPELLRDFYWDDEYRKKWDETVIEHETLEEDEKSGT 97
Query: 274 MRGDGENDPVSEFIVHCKAHF 294
IV F
Sbjct: 98 E------------IVRWVKKF 106
>gnl|CDD|218236 pfam04735, Baculo_helicase, Baculovirus DNA helicase.
Length = 1173
Score = 29.5 bits (67), Expect = 2.5
Identities = 22/76 (28%), Positives = 27/76 (35%), Gaps = 3/76 (3%)
Query: 162 LLDEVVTCHTFLHHKVLQLFIELFESKQDELEILVQLEMRKMLLDRMVNLLCRGCVVPVV 221
L C K+ LF EL+ EL IL K + D + NL C C
Sbjct: 593 LFGNCANCKIEEQDKLNDLFRELWNYDHSELIILGLYLNDKKMSDLIHNLKCSECKESA- 651
Query: 222 KYVKQCWQRGDTDISL 237
K+C DI L
Sbjct: 652 --SKKCDCLKKIDIDL 665
>gnl|CDD|225749 COG3208, GrsT, Predicted thioesterase involved in non-ribosomal
peptide biosynthesis [Secondary metabolites
biosynthesis, transport, and catabolism].
Length = 244
Score = 28.4 bits (64), Expect = 3.9
Identities = 20/58 (34%), Positives = 24/58 (41%), Gaps = 10/58 (17%)
Query: 215 GCVVPVVKYVKQCWQRGDTDI--SLIRYFVT--EVLEAITPPYTPEFVQLFLPIVEND 268
GC P KQ D D L+ T E+LE PE + LFLPI+ D
Sbjct: 109 GCRAPHYDRGKQIHHLDDADFLADLVDLGGTPPELLE------DPELMALFLPILRAD 160
>gnl|CDD|182326 PRK10240, PRK10240, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 229
Score = 28.4 bits (63), Expect = 4.4
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 63 YSLYSSNIPPPEAEVDALTDLLVHSLDTSSES 94
Y+ S N P EV AL +L V +LD+ +S
Sbjct: 44 YAFSSENWNRPAQEVSALMELFVWALDSEVKS 75
>gnl|CDD|216296 pfam01094, ANF_receptor, Receptor family ligand binding region.
This family includes extracellular ligand binding
domains of a wide range of receptors. This family also
includes the bacterial amino acid binding proteins of
known structure.
Length = 343
Score = 28.2 bits (63), Expect = 5.3
Identities = 9/64 (14%), Positives = 22/64 (34%), Gaps = 6/64 (9%)
Query: 29 VIFQPQSTQSSSMYESIYEPIN------PRPPSDLSSRSNYSLYSSNIPPPEAEVDALTD 82
+ P + + + +LS ++ Y ++ +P + A+ D
Sbjct: 53 AVIGPSCSSVAIAVARLAGAFGIPMISYGATSPELSDKTRYPTFARTVPSDSKQARAIAD 112
Query: 83 LLVH 86
+L H
Sbjct: 113 ILKH 116
>gnl|CDD|153201 cd04929, ACT_TPH, ACT domain of the nonheme iron-dependent aromatic
amino acid hydroxylase, tryptophan hydroxylases (TPH),
both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT
domain of the nonheme iron-dependent aromatic amino acid
hydroxylase, tryptophan hydroxylases (TPH), both
peripheral (TPH1) and neuronal (TPH2) enzymes. TPH
catalyses the hydroxylation of L-Trp to
5-hydroxytryptophan, the rate limiting step in the
biosynthesis of 5-hydroxytryptamine (serotonin) and the
first reaction in the synthesis of melatonin. Very
little is known about the role of the ACT domain in TPH,
which appears to be regulated by phosphorylation but not
by its substrate or cofactor. Members of this CD belong
to the superfamily of ACT regulatory domains.
Length = 74
Score = 26.2 bits (58), Expect = 5.4
Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 11/50 (22%)
Query: 176 KVLQLFIEL------FESKQ-----DELEILVQLEMRKMLLDRMVNLLCR 214
K L+LF EL ES++ E EI V E + LD +V LL R
Sbjct: 16 KALKLFQELGINVVHIESRKSKRRSSEFEIFVDCECDQRRLDELVQLLKR 65
>gnl|CDD|201250 pfam00476, DNA_pol_A, DNA polymerase family A.
Length = 383
Score = 28.1 bits (63), Expect = 5.5
Identities = 12/60 (20%), Positives = 20/60 (33%), Gaps = 1/60 (1%)
Query: 23 PPVTYTVIFQPQSTQSSSMYESIYEPINPRPPSDLSSRSNYSLYSSNIPPPEAEVDALTD 82
P T +ST + + ES+ E + L R L S+ + +D
Sbjct: 51 PKTKKTDKTGARSTNADVL-ESLREDAHEIIKIILEYRQLSKLQSTYVDKLPLMIDPDDG 109
>gnl|CDD|227361 COG5028, COG5028, Vesicle coat complex COPII, subunit SEC24/subunit
SFB2/subunit SFB3 [Intracellular trafficking and
secretion].
Length = 861
Score = 28.2 bits (63), Expect = 6.1
Identities = 25/107 (23%), Positives = 40/107 (37%), Gaps = 10/107 (9%)
Query: 14 PMYQTGEFHPPVTYTV-IFQPQSTQSSSMYESIYEPINPRP-----PSDLSSRSNYSLYS 67
M+ TG +P + FQ Q SS S+ + P+P P DL +
Sbjct: 65 AMHNTGANNPAPSVMSPAFQSQQKFSSPYGGSMADGTAPKPTNPLVPVDLFEDQPPPISD 124
Query: 68 SNIPPPEAEVDALTDLLVHSLDTSS----ESDLFAIEKVHSICNSSK 110
+PPP T+ + S S ++AI + + + SK
Sbjct: 125 LFLPPPPIVPPLTTNFVGSEQSNCSPKYVRSTMYAIPETNDLLKKSK 171
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
0.321 0.136 0.411
Gapped
Lambda K H
0.267 0.0604 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,996,236
Number of extensions: 1395603
Number of successful extensions: 1194
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1193
Number of HSP's successfully gapped: 34
Length of query: 299
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 203
Effective length of database: 6,679,618
Effective search space: 1355962454
Effective search space used: 1355962454
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: 59 (26.8 bits)