RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7063
(188 letters)
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 165 bits (421), Expect = 2e-50
Identities = 69/149 (46%), Positives = 88/149 (59%), Gaps = 24/149 (16%)
Query: 64 NVLFREDCNADELIDVINANRVYLPCIYAYNKIDQISIEEVDRIARQPNSVVVSCNMKLN 123
+VL RED D+LID + NRVY P +Y NKID +EE++R+AR+PNSV +S +N
Sbjct: 217 DVLIREDVTLDDLIDALEGNRVYKPALYVVNKIDLPGLEELERLARKPNSVPISAKKGIN 276
Query: 124 LDYLLDIIWLYLSLIRVYTKKPGAPPDFDDGLILRKG----------------------- 160
LD L + IW L LIRVYTK PG PDFD+ LILR+G
Sbjct: 277 LDELKERIWDVLGLIRVYTKPPGEEPDFDEPLILRRGSTVGDVCRKIHRDLVENFRYARV 336
Query: 161 -GTSTKYSPQRVGLAHVMADEDVIQIVKK 188
G S K+ QRVGL HV+ DED+++I K
Sbjct: 337 WGKSVKHPGQRVGLDHVLEDEDIVEIHAK 365
Score = 40.7 bits (96), Expect = 2e-04
Identities = 15/21 (71%), Positives = 16/21 (76%)
Query: 1 MGILEKISEIEKEIARTQKNK 21
M I EKI IE+EIART KNK
Sbjct: 2 MTIEEKIKAIEEEIARTPKNK 22
>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 = 139 bits (354), Expect = 9e-42
Identities = 54/80 (67%), Positives = 63/80 (78%)
Query: 64 NVLFREDCNADELIDVINANRVYLPCIYAYNKIDQISIEEVDRIARQPNSVVVSCNMKLN 123
+VL RED D+LIDVI NRVY+PC+Y YNKID ISIEE+DR+AR PNSVV+S LN
Sbjct: 154 DVLIREDITVDDLIDVIEGNRVYIPCLYVYNKIDLISIEELDRLARIPNSVVISAEKDLN 213
Query: 124 LDYLLDIIWLYLSLIRVYTK 143
LD LL+ IW YL LIR+YTK
Sbjct: 214 LDELLERIWDYLGLIRIYTK 233
>gnl|CDD|133436 cd01666, TGS_DRG_C, TGS_DRG_C: DRG (developmentally regulated
GTP-binding protein) represents a family of GTP-binding
proteins that includes two members, DRG1 and DRG2. DRG1
and DRG2 have a C-terminal TGS domain (named after the
ThrRS, GTPase, and SpoT proteins where it occurs) with a
predominantly beta-sheet structure. The function of TGS
is unknown but its presence in two types of regulatory
proteins (the DRG GTPases and guanosine polyphosphate
phosphohydrolases/synthetases) suggests a ligand (most
likely nucleotide)-binding, regulatory role.
Length = 75
Score = 89.1 bits (222), Expect = 7e-24
Identities = 36/75 (48%), Positives = 43/75 (57%), Gaps = 24/75 (32%)
Query: 137 LIRVYTKKPGAPPDFDDGLILRKG------------------------GTSTKYSPQRVG 172
LIRVYTK G PDFD+ +ILR+G G+S K+SPQRVG
Sbjct: 1 LIRVYTKPKGQEPDFDEPVILRRGSTVEDVCNKIHKDLVKQFKYALVWGSSVKHSPQRVG 60
Query: 173 LAHVMADEDVIQIVK 187
L HV+ DEDV+QIVK
Sbjct: 61 LDHVLEDEDVVQIVK 75
>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 = 42.1 bits (100), Expect = 7e-05
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 74 DELIDVINANRVYLPCIYAYNKIDQISIEEVDRIARQ-PNSVVVSCNMKLNLDYLLDII 131
+++++ + A + P + YNKID + ++R+ P +V VS LD LL+ I
Sbjct: 291 EKVLEELGAEDI--PQLLVYNKIDLLDEPRIERLEEGYPEAVFVSAKTGEGLDLLLEAI 347
>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 = 39.7 bits (93), Expect = 2e-04
Identities = 14/63 (22%), Positives = 24/63 (38%), Gaps = 5/63 (7%)
Query: 75 ELIDVINANRVYLPCIYAYNKID-----QISIEEVDRIARQPNSVVVSCNMKLNLDYLLD 129
E + P + NKID + ++D++ R V S +L LD ++
Sbjct: 102 EEVSGSFLFLKNKPEMIVANKIDMASENNLKRLKLDKLKRGIPVVPTSALTRLGLDRVIR 161
Query: 130 IIW 132
I
Sbjct: 162 TIR 164
>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 = 39.4 bits (93), Expect = 3e-04
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 80 INANRVYLPCIYAYNKIDQISIEEVDRIAR--QPNSVVVSCNMKLNLDYLLDII 131
+ A+ + P I NKID + EE++ R +P++V +S LD L + I
Sbjct: 149 LGADDI--PIILVLNKIDLLDDEELEERLRAGRPDAVFISAKTGEGLDLLKEAI 200
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 38.0 bits (89), Expect = 0.001
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 88 PCIYAYNKIDQIS-IEEVDRIARQ-PNSVVVSCNMKLNLDYLLDIIWLYLSLIRV 140
P I NKID + E + + R PN V +S LD L + I LS +R
Sbjct: 306 PIILVLNKIDLLEDEEILAELERGSPNPVFISAKTGEGLDLLRERIIELLSGLRT 360
>gnl|CDD|217243 pfam02824, TGS, TGS domain. The TGS domain is named after ThrRS,
GTPase, and SpoT. Interestingly, TGS domain was detected
also at the amino terminus of the uridine kinase from
the spirochaete Treponema pallidum (but not any other
organism, including the related spirochaete Borrelia
burgdorferi). TGS is a small domain that consists of ~50
amino acid residues and is predicted to possess a
predominantly beta-sheet structure. There is no direct
information on the functions of the TGS domain, but its
presence in two types of regulatory proteins (the
GTPases and guanosine polyphosphate
phosphohydrolases/synthetases) suggests a ligand (most
likely nucleotide)-binding, regulatory role.
Length = 60
Score = 32.8 bits (76), Expect = 0.010
Identities = 22/67 (32%), Positives = 27/67 (40%), Gaps = 24/67 (35%)
Query: 138 IRVYTKKPGAPPDFDDGLILRKGGT--------------STKYSP---QRVGLAHVMADE 180
IRVYT G P L +G T + QRVGL HV+ D
Sbjct: 1 IRVYTPD-GKVP------ELPRGSTPEDFAYAIHTDLGKKFIGAKVNGQRVGLDHVLEDG 53
Query: 181 DVIQIVK 187
DV++IV
Sbjct: 54 DVVEIVT 60
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 27.8 bits (63), Expect = 2.3
Identities = 10/44 (22%), Positives = 16/44 (36%)
Query: 88 PCIYAYNKIDQISIEEVDRIARQPNSVVVSCNMKLNLDYLLDII 131
P I NK D +S E + +S +D L + +
Sbjct: 111 PVIVVLNKSDLLSDAEGISELNGKPIIAISAKTGEGIDELKEAL 154
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 27.9 bits (63), Expect = 3.2
Identities = 14/61 (22%), Positives = 22/61 (36%), Gaps = 5/61 (8%)
Query: 74 DELIDVINANRVYLPCIYAYNKIDQISIEEVDRIARQP---NSVVVSCNMKLNLDYLLDI 130
ELI+ + ++ P I NKID + + VS +D L +
Sbjct: 104 LELIEELKERKI--PYIVVINKIDLGEESAELEKLEKKFGLPPIFVSALTGEGIDELKEA 161
Query: 131 I 131
I
Sbjct: 162 I 162
>gnl|CDD|173816 cd07491, Peptidases_S8_7, Peptidase S8 family domain,
uncharacterized subfamily 7. This family is a member of
the Peptidases S8 or Subtilases serine endo- and
exo-peptidase clan. They have an Asp/His/Ser catalytic
triad similar to that found in trypsin-like proteases,
but do not share their three-dimensional structure and
are not homologous to trypsin. The stability of
subtilases may be enhanced by calcium, some members have
been shown to bind up to 4 ions via binding sites with
different affinity. Some members of this clan contain
disulfide bonds. These enzymes can be intra- and
extracellular, some function at extreme temperatures and
pH values.
Length = 247
Score = 27.3 bits (61), Expect = 4.9
Identities = 11/47 (23%), Positives = 18/47 (38%), Gaps = 8/47 (17%)
Query: 5 EKISEIEKEIARTQKNKVLAYCWS--KGTFQSYTSSINRHYYYKSAR 49
I+E+E I +L +C + +G F Y +AR
Sbjct: 120 NDINELENAIKEALDRGILLFCSASDQGAFTGD------TYPPPAAR 160
>gnl|CDD|213292 cd05926, FACL_fum10p_like, Subfamily of fatty acid CoA ligase
(FACL) similar to Fum10p of Gibberella moniliformis.
FACL catalyzes the formation of fatty acyl-CoA in a
two-step reaction: the formation of a fatty acyl-AMP
molecule as an intermediate, followed by the formation
of a fatty acyl-CoA. This is a required step before free
fatty acids can participate in most catabolic and
anabolic reactions. Fum10p is a fatty acid CoA ligase
involved in the synthesis of fumonisin, a polyketide
mycotoxin, in Gibberella moniliformis.
Length = 345
Score = 27.2 bits (61), Expect = 5.1
Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 152 DDGLILRKGGTSTKYSPQRVGLAH 175
D LIL GT+ + P+ V L H
Sbjct: 3 DPALILHTSGTTGR--PKGVPLTH 24
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
0.319 0.136 0.398
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,731,470
Number of extensions: 903923
Number of successful extensions: 904
Number of sequences better than 10.0: 1
Number of HSP's gapped: 899
Number of HSP's successfully gapped: 27
Length of query: 188
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 97
Effective length of database: 6,901,388
Effective search space: 669434636
Effective search space used: 669434636
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: 56 (25.3 bits)