RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10471
(318 letters)
>gnl|CDD|227508 COG5181, HSH155, U2 snRNP spliceosome subunit [RNA processing and
modification].
Length = 975
Score = 411 bits (1058), Expect = e-137
Identities = 157/296 (53%), Positives = 197/296 (66%), Gaps = 13/296 (4%)
Query: 23 ILPHLKNLVEIIEHGLVDEQQKVQENCIDLVGRIADRGPEYVSAREWMRICFELLELLKA 82
+ P L+N + QKV N I LVG I PEY+ REWMRICFEL++ LK+
Sbjct: 693 LTPILRN-----------KHQKVVANTIALVGTICMNSPEYIGVREWMRICFELVDSLKS 741
Query: 83 HKKAIRRATVNTFGYIAKAIGPHDVLATLLNNLKVQERQNRVCTTVAIAIVAETCSPFTV 142
K IRR TFG I++AIGP DVL LLNNLKVQERQ RVCT+VAI+IVAE C PF+V
Sbjct: 742 WNKEIRRNATETFGCISRAIGPQDVLDILLNNLKVQERQQRVCTSVAISIVAEYCGPFSV 801
Query: 143 LPALMNEYRVPELNVQNGVLKALSFLFEYIGEMGKDYIYAVTPLLEDALMDRDLVHRQTA 202
LP LM++Y PE NVQNGVLKA+ F+FEYIG+ DY+Y++TPLLEDAL DRD VHRQTA
Sbjct: 802 LPTLMSDYETPEANVQNGVLKAMCFMFEYIGQASLDYVYSITPLLEDALTDRDPVHRQTA 861
Query: 203 CATIKHMALGVYGFGCEDALTHLLNYVWPNIFETSPHLVQAFMDAVEGLRVALGPVRILQ 262
I+H+ L G G EDA HLLN +WPNI E SPH++Q+F + +E LG +++
Sbjct: 862 MNVIRHLVLNCPGTGDEDAAIHLLNLLWPNILEPSPHVIQSFDEGMESFATVLGSGAMMK 921
Query: 263 YVLQGLFHPARKVRDVYWKIYNSLYIGGQDALISAYPRIQNDMKNVYLRYELDYVL 318
YV QGLFHP+ VR YW +YN +Y+ DA++ YP ++ N L L +
Sbjct: 922 YVQQGLFHPSSTVRKRYWTVYNIMYVFDSDAMVPCYPVEEDL--NPELARTLHICI 975
Score = 58.4 bits (141), Expect = 2e-09
Identities = 16/39 (41%), Positives = 23/39 (58%)
Query: 8 GIKIVQQIAILMGCAILPHLKNLVEIIEHGLVDEQQKVQ 46
GI+I QQI L+G + L HL L++ I L D + V+
Sbjct: 337 GIRIAQQICELLGRSRLSHLGPLLKCISKLLKDRSRFVR 375
>gnl|CDD|237987 cd00020, ARM, Armadillo/beta-catenin-like repeats. An approximately
40 amino acid long tandemly repeated sequence motif
first identified in the Drosophila segment polarity gene
armadillo; these repeats were also found in the
mammalian armadillo homolog beta-catenin, the junctional
plaque protein plakoglobin, the adenomatous polyposis
coli (APC) tumor suppressor protein, and a number of
other proteins. ARM has been implicated in mediating
protein-protein interactions, but no common features
among the target proteins recognized by the ARM repeats
have been identified; related to the HEAT domain; three
consecutive copies of the repeat are represented by this
alignment model.
Length = 120
Score = 33.4 bits (77), Expect = 0.045
Identities = 15/90 (16%), Positives = 30/90 (33%), Gaps = 7/90 (7%)
Query: 6 NLGIKIVQQIAILMGCAILPHLKNLVEIIEHGLVDEQQKVQENCIDLVGRIADRGPEYVS 65
NL I ++ LP L L L E ++V + + + +A +
Sbjct: 33 NLSAGNNDNIQAVVEAGGLPALVQL-------LKSEDEEVVKAALWALRNLAAGPEDNKL 85
Query: 66 AREWMRICFELLELLKAHKKAIRRATVNTF 95
+L+ LL + + I++
Sbjct: 86 IVLEAGGVPKLVNLLDSSNEDIQKNATGAL 115
>gnl|CDD|105710 PRK12514, PRK12514, RNA polymerase sigma factor; Provisional.
Length = 179
Score = 30.6 bits (69), Expect = 0.79
Identities = 20/54 (37%), Positives = 25/54 (46%), Gaps = 8/54 (14%)
Query: 50 IDLVGRIAD--RGPE--YVSAREWMRI--CFELLELLKAHKKAIRRATVNTFGY 97
ID +AD GPE ++ E RI C E EL K A+RRA + Y
Sbjct: 97 IDEAHDLADPSPGPEAEVIAGDEGQRIDACLE--ELEKDRAAAVRRAYLEGLSY 148
>gnl|CDD|233161 TIGR00870, trp, transient-receptor-potential calcium channel
protein. The Transient Receptor Potential Ca2+ Channel
(TRP-CC) Family (TC. 1.A.4)The TRP-CC family has also
been called the store-operated calcium channel (SOC)
family. The prototypical members include the Drosophila
retinal proteinsTRP and TRPL (Montell and Rubin, 1989;
Hardie and Minke, 1993). SOC members of the family
mediate the entry of extracellular Ca2+ into cells in
responseto depletion of intracellular Ca2+ stores
(Clapham, 1996) and agonist stimulated production of
inositol-1,4,5 trisphosphate (IP3). One member of the
TRP-CCfamily, mammalian Htrp3, has been shown to form a
tight complex with the IP3 receptor (TC #1.A.3.2.1).
This interaction is apparently required for IP3
tostimulate Ca2+ release via Htrp3. The vanilloid
receptor subtype 1 (VR1), which is the receptor for
capsaicin (the ?hot? ingredient in chili peppers) and
servesas a heat-activated ion channel in the pain
pathway (Caterina et al., 1997), is also a member of
this family. The stretch-inhibitable non-selective
cation channel(SIC) is identical to the vanilloid
receptor throughout all of its first 700 residues, but
it exhibits a different sequence in its last 100
residues. VR1 and SICtransport monovalent cations as
well as Ca2+. VR1 is about 10x more permeable to Ca2+
than to monovalent ions. Ca2+ overload probably causes
cell deathafter chronic exposure to capsaicin.
(McCleskey and Gold, 1999) [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 743
Score = 30.8 bits (70), Expect = 1.2
Identities = 19/86 (22%), Positives = 29/86 (33%), Gaps = 13/86 (15%)
Query: 10 KIVQQIAILMGCAILPHLKNLVEIIEHGLV-------DEQQKVQENCIDLVGRIADRGPE 62
+ I + K + E G + +E +K+ NC D +G R
Sbjct: 1 RGPLDIVPAEESPLSDEEKAFLPAAERGDLASVYRDLEEPKKLNINCPDRLG----RSAL 56
Query: 63 YVSAREWMRICFELLELLKAHKKAIR 88
+V+A E EL ELL
Sbjct: 57 FVAAIE--NENLELTELLLNLSCRGA 80
>gnl|CDD|241273 cd01240, PH_GRK2_subgroup, G Protein-Coupled Receptor Kinase 2
subgroup pleckstrin homology (PH) domain. GRKs are a
family of serine-threonine kinases which phosphorylates
activated G-protein coupled receptors leading to the
release of the previously bound heterotrimeric G protein
agonist and thus signal termination. There are seven
mammalian GRKs (GRK1-7) grouped into three subfamilies:
GRK1 (GRK1 and 7), GRK2 (GRK2 and 3), and GRK4 (GRK4-6).
GRKs have three functional components: an N-terminal
Regulators of G-protein signaling (RGS) which interacts
with the seven-trans-membrane helical receptor protein
and/or other membrane targets, a central catalytic
protein kinase C (PKc) domain, and a C-terminal section
containing a autophosphorylation region and a variable
region that mediates membrane association. In both GRK2
(also known as beta-adrenergic receptor kinase-1) and
GRK3 (beta-adrenergic receptor kinase-2), the C-terminal
variable region contains a PH domain which gives binding
specificity to Gbetagamma proteins. The GRK2 PH domain
has an extended C-terminal helix, which mediates
interactions with G beta gamma subunits. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 119
Score = 28.8 bits (65), Expect = 1.5
Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 17/71 (23%)
Query: 26 HLKNLVEIIEHGLVDEQQKVQENCIDLV----GRI----ADRGPEYVSAREWMRICFELL 77
KNL+E+ V+E Q E CI L G+ D PE V +W +
Sbjct: 44 SQKNLLELESMDSVEETQIKGEKCILLKLKDGGKQFILRCDSEPELV---QWKK------ 94
Query: 78 ELLKAHKKAIR 88
EL +A ++A R
Sbjct: 95 ELREAFREAQR 105
>gnl|CDD|227484 COG5155, ESP1, Separase, a protease involved in sister chromatid
separation [Cell division and chromosome partitioning /
Posttranslational modification, protein turnover,
chaperones].
Length = 1622
Score = 30.4 bits (68), Expect = 1.5
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 4/60 (6%)
Query: 130 IAIVAETCS--PFTVLPALMNE--YRVPELNVQNGVLKALSFLFEYIGEMGKDYIYAVTP 185
I ++ E+ P+ LP L N+ YRVP L L + + G G+ + Y + P
Sbjct: 1389 ILVLDESTHEFPWESLPVLRNKSVYRVPSLEYLENALSSFHYQLPLQGASGRSFSYILNP 1448
>gnl|CDD|236386 PRK09129, PRK09129, NADH dehydrogenase subunit G; Validated.
Length = 776
Score = 30.3 bits (69), Expect = 1.6
Identities = 27/83 (32%), Positives = 33/83 (39%), Gaps = 31/83 (37%)
Query: 48 NCIDL--VGRIADRGPEYVSAREWMRICFELLELLKAHKKAIRRATVNTFGYIAKAIGPH 105
N IDL VG + + Y SAR W EL RR K++ PH
Sbjct: 191 NMIDLCPVGALTSKPFRY-SARTW--------EL-------SRR----------KSVSPH 224
Query: 106 DVLATLLNNLKVQERQNRVCTTV 128
D L + NL V + NRV V
Sbjct: 225 DSLGS---NLVVHVKNNRVMRVV 244
>gnl|CDD|173778 cd01028, TOPRIM_TopoIA, TOPRIM_TopoIA: topoisomerase-primase
(TOPRIM) nucleotidyl transferase/hydrolase domain of the
type found in the type IA family of DNA topoisomerases
(TopoIA). This subgroup contains proteins similar to
the Type I DNA topoisomerases: E. coli topisomerases I
and III, eukaryotic topoisomerase III and, ATP-dependent
reverse gyrase found in archaea and thermophilic
bacteria. Type IA DNA topoisomerases remove (relax)
negative supercoils in the DNA. These enzymes cleave one
strand of the DNA duplex, covalently link to the 5'
phosphoryl end of the DNA break and allow the other
strand of the duplex to pass through the gap. Reverse
gyrase is also able to insert positive supercoils in the
presence of ATP and negative supercoils in the presence
of AMPPNP. The TOPRIM domain has two conserved motifs,
one of which centers at a conserved glutamate and the
other one at two conserved aspartates (DxD). For
topoisomerases the conserved glutamate is believed to
act as a general base in strand joining and, as a
general acid in strand cleavage. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 142
Score = 28.7 bits (65), Expect = 2.1
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 72 ICFELLELLKAHKKAIRRATVN 93
I +E+LE+LK K ++RA +
Sbjct: 107 IAWEILEVLKCDNKPVKRAWFS 128
>gnl|CDD|205691 pfam13513, HEAT_EZ, HEAT-like repeat. The HEAT repeat family is
related to armadillo/beta-catenin-like repeats (see
pfam00514). These EZ repeats are found in subunits of
cyanobacterial phycocyanin lyase and other proteins and
probably carry out a scaffolding role.
Length = 55
Score = 27.0 bits (60), Expect = 2.3
Identities = 12/53 (22%), Positives = 20/53 (37%)
Query: 157 VQNGVLKALSFLFEYIGEMGKDYIYAVTPLLEDALMDRDLVHRQTACATIKHM 209
V+ AL L E+ + + + P L L D D R+ A + +
Sbjct: 3 VREAAALALGALAGGGPELLRPAVPELLPALLPLLKDDDDEVREAAAWALGRI 55
Score = 26.3 bits (58), Expect = 4.5
Identities = 10/42 (23%), Positives = 19/42 (45%)
Query: 15 IAILMGCAILPHLKNLVEIIEHGLVDEQQKVQENCIDLVGRI 56
+A + P + L+ + L D+ +V+E +GRI
Sbjct: 14 LAGGGPELLRPAVPELLPALLPLLKDDDDEVREAAAWALGRI 55
>gnl|CDD|238678 cd01382, MYSc_type_VI, Myosin motor domain, type VI myosins. Myosin
VI is a monomeric myosin, which moves towards the
minus-end of actin filaments, in contrast to most other
myosins. It has been implicated in endocytosis,
secretion, and cell migration. This catalytic (head)
domain has ATPase activity and belongs to the larger
group of P-loop NTPases. Myosins are actin-dependent
molecular motors that play important roles in muscle
contraction, cell motility, and organelle transport. The
head domain is a molecular motor, which utilizes ATP
hydrolysis to generate directed movement toward the
minus end along actin filaments. A cyclical interaction
between myosin and actin provides the driving force.
Rates of ATP hydrolysis and consequently the speed of
movement along actin filaments vary widely, from about
0.04 micrometer per second for myosin I to 4.5
micrometer per second for myosin II in skeletal muscle.
Myosin II moves in discrete steps about 5-10 nm long and
generates 1-5 piconewtons of force. Upon ATP binding,
the myosin head dissociates from an actin filament. ATP
hydrolysis causes the head to pivot and associate with a
new actin subunit. The release of Pi causes the head to
pivot and move the filament (power stroke). Release of
ADP completes the cycle.
Length = 717
Score = 29.0 bits (65), Expect = 3.5
Identities = 14/38 (36%), Positives = 26/38 (68%), Gaps = 2/38 (5%)
Query: 109 ATLLNNLKVQERQNRVCTTVAIAIVAETCSPFTVLPAL 146
ATLLNN++V+ ++++ T VA ++A +P+ +P L
Sbjct: 18 ATLLNNIRVRYSKDKIYTYVANILIA--VNPYFDIPKL 53
>gnl|CDD|222041 pfam13312, DUF4081, Domain of unknown function (DUF4081). This
domain is often found N-terminal to the GNAT
acetyltransferase domain, pfam00583 and FR47, pfam08445.
Length = 107
Score = 27.6 bits (62), Expect = 4.1
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 10/74 (13%)
Query: 213 VYGFGCEDALTHLLNYVWPNI--FETSPHLVQAFMDAV--EGLRVA--LGP---VRILQY 263
V+G G + LT L + N+ P ++AF D G R + +GP V L
Sbjct: 4 VWGVGDDGRLTALC-WAGANLVPVAADPAALRAFADRARRRGRRCSSIVGPADAVLGLWE 62
Query: 264 VLQGLFHPARKVRD 277
L+ + PAR+VR
Sbjct: 63 RLEPTWGPAREVRA 76
>gnl|CDD|239173 cd02772, MopB_NDH-1_NuoG2, MopB_NDH-1_NuoG2: The second domain of
the NuoG subunit of the NADH-quinone oxidoreductase/NADH
dehydrogenase-1 (NDH-1), found in beta- and
gammaproteobacteria. The NDH-1 is the first
energy-transducting complex in the respiratory chain and
functions as a redox pump that uses the redox energy to
translocate H+ ions across the membrane, resulting in a
significant contribution to energy production. In
Escherichia coli NDH-1, the largest subunit is encoded
by the nuoG gene, and is part of the 14 distinct
subunits constituting the functional enzyme. The NuoG
subunit is made of two domains: the first contains three
binding sites for FeS clusters (the fer2 domain), the
second domain (this CD), is of unknown function or, as
postulated, has lost an ancestral formate dehydrogenase
activity that became redundant during the evolution of
the complex I enzyme. Although only vestigial sequence
evidence remains of a molybdopterin binding site, this
protein domain belongs to the molybdopterin_binding
(MopB) superfamily of proteins.
Length = 414
Score = 28.5 bits (64), Expect = 4.8
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 3/29 (10%)
Query: 100 KAIGPHDVLATLLNNLKVQERQNRVCTTV 128
K++ PHD L + NL V + N+V V
Sbjct: 1 KSVSPHDALGS---NLVVHVKNNKVMRVV 26
>gnl|CDD|217598 pfam03520, KCNQ_channel, KCNQ voltage-gated potassium channel.
This family matches to the C-terminal tail of KCNQ type
potassium channels.
Length = 201
Score = 27.4 bits (61), Expect = 7.2
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 4/48 (8%)
Query: 235 ETSPHLVQAFMDAVEGLRVALGPVRILQY-VLQGLFHPARK---VRDV 278
E + D + A+ +R ++Y V + F A K V+DV
Sbjct: 58 EKELPCITTVEDLTPAHKTAIRAIRRMKYFVAKRKFKEALKPYDVKDV 105
>gnl|CDD|226133 COG3605, PtsP, Signal transduction protein containing GAF and PtsI
domains [Signal transduction mechanisms].
Length = 756
Score = 28.1 bits (63), Expect = 7.4
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 115 LKVQERQNRVCTTVAIAIVAETCS 138
L++QE + + +A+A+V E CS
Sbjct: 16 LELQEALDIIVRDIALAMVTEVCS 39
>gnl|CDD|129937 TIGR00858, bioF, 8-amino-7-oxononanoate synthase.
7-keto-8-aminopelargonic acid synthetase is an alternate
name. This model represents 8-amino-7-oxononanoate
synthase, the BioF protein of biotin biosynthesis. This
model is based on a careful phylogenetic analysis to
separate members of this family from
2-amino-3-ketobutyrate and other related pyridoxal
phosphate-dependent enzymes. In several species,
including Staphylococcus and Coxiella, a candidate
8-amino-7-oxononanoate synthase is confirmed by location
in the midst of a biotin biosynthesis operon but scores
below the trusted cutoff of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Biotin].
Length = 360
Score = 27.6 bits (62), Expect = 9.1
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 210 ALGVYG---FGCEDALTHLLNYVWPNIFETS--PHLVQAFMDAVEGLR 252
ALG YG G + + +L+N IF T+ P + A + A+E ++
Sbjct: 218 ALGSYGAYVAGSQALIDYLINRARTLIFSTALPPAVAAAALAALELIQ 265
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
0.325 0.140 0.421
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,478,305
Number of extensions: 1618433
Number of successful extensions: 1847
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1844
Number of HSP's successfully gapped: 28
Length of query: 318
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 221
Effective length of database: 6,635,264
Effective search space: 1466393344
Effective search space used: 1466393344
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 59 (26.4 bits)