RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7060
(160 letters)
>gnl|CDD|206683 cd01896, DRG, Developmentally Regulated GTP-binding protein (DRG).
The developmentally regulated GTP-binding protein (DRG)
subfamily is an uncharacterized member of the Obg
family, an evolutionary branch of GTPase superfamily
proteins. GTPases act as molecular switches regulating
diverse cellular processes. DRG2 and DRG1 comprise the
DRG subfamily in eukaryotes. In view of their widespread
expression in various tissues and high conservation
among distantly related species in eukaryotes and
archaea, DRG proteins may regulate fundamental cellular
processes. It is proposed that the DRG subfamily
proteins play their physiological roles through RNA
binding.
Length = 233
Score = 186 bits (476), Expect = 1e-60
Identities = 81/159 (50%), Positives = 98/159 (61%), Gaps = 36/159 (22%)
Query: 1 MLDATKQDVQRGLLEKELESVGIRLNKKKPNIYFKQKKAGGIAFNSTCPLTQVNEKLVQL 60
+LDATK + QR +LE+ELE VGIRLNKK PN+ K+KK GGI ST PLT+++EK V+
Sbjct: 84 VLDATKPEGQREILERELEGVGIRLNKKPPNVTIKKKKKGGINITSTVPLTKLDEKTVKA 143
Query: 61 ILHEYKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELI 120
IL EYKI NA+ VL RED D+LI
Sbjct: 144 ILREYKIHNAD------------------------------------VLIREDITVDDLI 167
Query: 121 DVINANRVYLPCIYAYNKIDQISIEEVDRIARQPNSVVV 159
DVI NRVY+PC+Y YNKID ISIEE+DR+AR PNSVV+
Sbjct: 168 DVIEGNRVYIPCLYVYNKIDLISIEELDRLARIPNSVVI 206
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 135 bits (341), Expect = 6e-39
Identities = 63/158 (39%), Positives = 87/158 (55%), Gaps = 36/158 (22%)
Query: 2 LDATKQDVQRGLLEKELESVGIRLNKKKPNIYFKQKKAGGIAFNSTCPLTQVNEKLVQLI 61
LD + R ++E+ELE VGIRLNK+ P++ K+K++GGI N T PLT ++E V
Sbjct: 148 LDVFEDPHHRDIIERELEDVGIRLNKRPPDVTIKKKESGGIRINGTGPLTHLDEDTV--- 204
Query: 62 LHEYKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELID 121
+A IL EY+I NA+VL RED D+LID
Sbjct: 205 ------------RA---------------------ILREYRIHNADVLIREDVTLDDLID 231
Query: 122 VINANRVYLPCIYAYNKIDQISIEEVDRIARQPNSVVV 159
+ NRVY P +Y NKID +EE++R+AR+PNSV +
Sbjct: 232 ALEGNRVYKPALYVVNKIDLPGLEELERLARKPNSVPI 269
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 38.6 bits (91), Expect = 5e-04
Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 21/87 (24%)
Query: 79 AFNSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDV-------INANRVYLP 131
AF +T L +V E L+LH V+ D + +E I+ + A + P
Sbjct: 258 AFRAT--LEEVRE--ADLLLH--------VVDASDPDREEQIEAVEKVLEELGAEDI--P 303
Query: 132 CIYAYNKIDQISIEEVDRIARQPNSVV 158
+ YNKID + ++R+ V
Sbjct: 304 QLLVYNKIDLLDEPRIERLEEGYPEAV 330
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 33.1 bits (76), Expect = 0.030
Identities = 14/59 (23%), Positives = 17/59 (28%), Gaps = 12/59 (20%)
Query: 91 EKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAYNKIDQISIEEVDR 149
E V L + K N EV P + NKID S + R
Sbjct: 87 EDCVGDPLEDQKTLNEEV------------SGSFLFLKNKPEMIVANKIDMASENNLKR 133
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 31.3 bits (72), Expect = 0.16
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 123 INANRVYLPCIYAYNKIDQISIEEVDRIAR--QPNSVVV 159
+ A+ + P I NKID + EE++ R +P++V +
Sbjct: 149 LGADDI--PIILVLNKIDLLDDEELEERLRAGRPDAVFI 185
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 30.3 bits (69), Expect = 0.39
Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 1/30 (3%)
Query: 131 PCIYAYNKIDQIS-IEEVDRIARQPNSVVV 159
P I NKID + E + + R + V
Sbjct: 306 PIILVLNKIDLLEDEEILAELERGSPNPVF 335
>gnl|CDD|241451 cd13297, PH3_MyoX-like, Myosin X-like Pleckstrin homology (PH)
domain, repeat 3. MyoX, a MyTH-FERM myosin, is a
molecular motor that has crucial functions in the
transport and/or tethering of integrins in the
actin-based extensions known as filopodia, microtubule
binding, and in netrin-mediated axon guidance. It
functions as a dimer. MyoX walks on bundles of actin,
rather than single filaments, unlike the other
unconventional myosins. MyoX is present in organisms
ranging from humans to choanoflagellates, but not in
Drosophila and Caenorhabditis elegans.MyoX consists of
a N-terminal motor/head region, a neck made of 3 IQ
motifs, and a tail consisting of a coiled-coil domain,
a PEST region, 3 PH domains, a myosin tail homology 4
(MyTH4), and a FERM domain at its very C-terminus. The
first PH domain in the MyoX tail is a split-PH domain,
interupted by the second PH domain such that PH 1a and
PH 1b flanks PH 2. The third PH domain (PH 3) follows
the PH 1b domain. This cd contains the third MyoX PH
repeat. PLEKHH3/Pleckstrin homology (PH) domain
containing, family H (with MyTH4 domain) member 3 is
also part of this CD and like MyoX contains a FERM
domain, a MyTH4 domain, and a single PH domain. Not
much is known about the function of PLEKHH3. 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 = 123
Score = 27.3 bits (61), Expect = 1.9
Identities = 23/71 (32%), Positives = 31/71 (43%), Gaps = 15/71 (21%)
Query: 1 MLDATKQDV-QRGLLEKELESVGIRLNKKK------PNI--YFK-----QKKAGGIAFNS 46
D Q+V ++G L KE G L KKK PN Y+K K G + NS
Sbjct: 5 QTDEGDQEVIEKGWLLKEGGKGG-NLTKKKRWFVLTPNSLDYYKSSERNALKLGSLVLNS 63
Query: 47 TCPLTQVNEKL 57
C + +EK+
Sbjct: 64 LCSVVPPDEKV 74
>gnl|CDD|169553 PRK08690, PRK08690, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 261
Score = 26.9 bits (59), Expect = 5.7
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 6/57 (10%)
Query: 65 YKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELID 121
Y I A +++ +AF T V +KL + + ++E++FR D +D+ I+
Sbjct: 22 YGIAKACREQGAELAF------TYVVDKLEERVRKMAAELDSELVFRCDVASDDEIN 72
>gnl|CDD|161785 TIGR00239, 2oxo_dh_E1, 2-oxoglutarate dehydrogenase, E1 component.
The 2-oxoglutarate dehydrogenase complex consists of
this thiamine pyrophosphate-binding subunit (E1),
dihydrolipoamide succinyltransferase (E2), and lipoamide
dehydrogenase (E3). The E1 ortholog from Corynebacterium
glutamicum is unusual in having an N-terminal extension
that resembles the dihydrolipoamide succinyltransferase
(E2) component of 2-oxoglutarate dehydrogenase [Energy
metabolism, TCA cycle].
Length = 929
Score = 26.4 bits (58), Expect = 7.9
Identities = 14/75 (18%), Positives = 27/75 (36%), Gaps = 12/75 (16%)
Query: 85 PLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAYNKIDQISI 144
P+ VN + + V +R D ID++ R + +N+ D+ S
Sbjct: 412 PIFHVNADDPEAVAF---ATRLAVEYRNTFKRDVFIDLVGYRR------HGHNEADEPSA 462
Query: 145 EE---VDRIARQPNS 156
+ +I + P
Sbjct: 463 TQPLMYQKIKKHPTP 477
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 0.137 0.385
Gapped
Lambda K H
0.267 0.0687 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,991,959
Number of extensions: 724945
Number of successful extensions: 662
Number of sequences better than 10.0: 1
Number of HSP's gapped: 662
Number of HSP's successfully gapped: 27
Length of query: 160
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 71
Effective length of database: 6,990,096
Effective search space: 496296816
Effective search space used: 496296816
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: 55 (25.0 bits)