RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy140
(184 letters)
>gnl|CDD|239679 cd03708, GTPBP_III, Domain III of the GP-1 family of GTPase. This
group includes proteins similar to GTPBP1 and GTPBP2.
GTPB1 is structurally, related to elongation factor 1
alpha, a key component of protein biosynthesis
machinery. Immunohistochemical analyses on mouse
tissues revealed that GTPBP1 is expressed in some
neurons and smooth muscle cells of various organs as
well as macrophages. Immunofluorescence analyses
revealed that GTPBP1 is localized exclusively in
cytoplasm and shows a diffuse granular network forming
a gradient from the nucleus to the periphery of the
cells in smooth muscle cell lines and macrophages. No
significant difference was observed in the immune
response to protein antigen between mutant mice and
wild-type mice, suggesting normal function of
antigen-presenting cells of the mutant mice. The
absence of an eminent phenotype in GTPBP1-deficient
mice may be due to functional compensation by GTPBP2,
which is similar to GTPBP1 in structure and tissue
distribution.
Length = 87
Score = 162 bits (413), Expect = 9e-53
Identities = 63/87 (72%), Positives = 70/87 (80%)
Query: 11 VAVWEFEGEILVLHHPTTISSRYQAMVHCGSIRQTASILSMSAECLRTGDKAAVHFRFIK 70
A WEFE EILVLHHPTTIS YQA VH GSIRQTA I+S+ + LRTGD+A V FRF+
Sbjct: 1 KACWEFEAEILVLHHPTTISPGYQATVHIGSIRQTARIVSIDKDVLRTGDRALVRFRFLY 60
Query: 71 HPEYLRAGQRMVFREGRTKAVGNVTKV 97
HPEYLR GQR++FREGRTK VG VTKV
Sbjct: 61 HPEYLREGQRLIFREGRTKGVGEVTKV 87
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 108 bits (272), Expect = 6e-28
Identities = 41/98 (41%), Positives = 58/98 (59%), Gaps = 1/98 (1%)
Query: 1 MVMVSPALNPVAVWEFEGEILVLHHPTTISSRYQAMVHCGSIRQTASILSMSAECLRTGD 60
MV+ + A +P AV EF+ E+LVL HPTTI + Y+ + H +IR+ + L GD
Sbjct: 431 MVLSAGA-DPKAVREFDAEVLVLRHPTTIRAGYEPVFHYETIREAVYFEEIDKGFLMPGD 489
Query: 61 KAAVHFRFIKHPEYLRAGQRMVFREGRTKAVGNVTKVL 98
+ V RF P ++ GQ+ VFREGR+K VG V +V
Sbjct: 490 RGVVRMRFKYRPHHVEEGQKFVFREGRSKGVGRVIRVD 527
>gnl|CDD|217387 pfam03143, GTP_EFTU_D3, Elongation factor Tu C-terminal domain.
Elongation factor Tu consists of three structural
domains, this is the third domain. This domain adopts a
beta barrel structure. This the third domain is
involved in binding to both charged tRNA and binding to
EF-Ts pfam00889.
Length = 91
Score = 92.9 bits (232), Expect = 4e-25
Identities = 34/91 (37%), Positives = 48/91 (52%), Gaps = 3/91 (3%)
Query: 10 PVAVWEFEGEILVLHHPTTISSRYQAMVHCGSIRQTA-SILSMSAECLRTGDKAAVHFRF 68
+F+ ++ +L+HPT I + Y+ + +C + T IL E + GD A V
Sbjct: 2 IKPHTKFKAQVYILNHPTPIFNGYRPVFYCHTADVTGKFILPGKKEFVMPGDNAIVTVEL 61
Query: 69 IKHPEYLRAGQRMVFREG-RTKAVGNVTKVL 98
IK P + GQR REG RT AVG VT+VL
Sbjct: 62 IK-PIAVEKGQRFAIREGGRTVAVGVVTEVL 91
>gnl|CDD|238771 cd01513, Translation_factor_III, Domain III of Elongation factor
(EF) Tu (EF-TU) and EF-G. Elongation factors (EF) EF-Tu
and EF-G participate in the elongation phase during
protein biosynthesis on the ribosome. Their functional
cycles depend on GTP binding and its hydrolysis. The
EF-Tu complexed with GTP and aminoacyl-tRNA delivers
tRNA to the ribosome, whereas EF-G stimulates
translocation, a process in which tRNA and mRNA
movements occur in the ribosome. Experimental data
showed that: (1) intrinsic GTPase activity of EF-G is
influenced by excision of its domain III; (2) that EF-G
lacking domain III has a 1,000-fold decreased GTPase
activity on the ribosome and, a slightly decreased
affinity for GTP; and (3) EF-G lacking domain III does
not stimulate translocation, despite the physical
presence of domain IV which is also very important for
translocation. These findings indicate an essential
contribution of domain III to activation of GTP
hydrolysis. Domains III and V of EF-G have the same fold
(although they are not completely superimposable), the
double split beta-alpha-beta fold. This fold is observed
in a large number of ribonucleotide binding proteins and
is also referred to as the ribonucleoprotein (RNP) or
RNA recognition (RRM) motif. This domain III is found
in several elongation factors, as well as in peptide
chain release factors and in GT-1 family of GTPase
(GTPBP1).
Length = 102
Score = 46.6 bits (111), Expect = 2e-07
Identities = 25/102 (24%), Positives = 40/102 (39%), Gaps = 18/102 (17%)
Query: 11 VAVWEFEGEILVLHHPTTISSRYQAMVHCGSIRQTASILSM------------SAECLRT 58
AV +F EI VL HP +S Y+ +++ G+ I + E L++
Sbjct: 1 QAVDKFVAEIYVLDHPEPLSPGYKPVLNVGTAHVPGRIAKLLSKVDGKTEEKKPPEFLKS 60
Query: 59 GDKAAVHFRFIK-----HPEYLRAGQRMVFRE-GRTKAVGNV 94
G++ V K + G R R+ GRT G +
Sbjct: 61 GERGIVEVELQKPVALETFSENQEGGRFALRDGGRTVGAGLI 102
>gnl|CDD|239675 cd03704, eRF3c_III, This family represents eEF1alpha-like
C-terminal region of eRF3 homologous to the domain III
of EF-Tu. eRF3 is a GTPase, which enhances the
termination efficiency by stimulating the eRF1 activity
in a GTP-dependent manner. The C-terminal region is
responsible for translation termination activity and is
essential for viability. Saccharomyces cerevisiae eRF3
(Sup35p) is a translation termination factor which is
divided into three regions N, M and a C-terminal
eEF1a-like region essential for translation termination.
Sup35NM is a non-pathogenic prion-like protein with
the property of aggregating into polymer-like fibrils.
Length = 108
Score = 38.4 bits (90), Expect = 3e-04
Identities = 29/108 (26%), Positives = 49/108 (45%), Gaps = 23/108 (21%)
Query: 12 AVWEFEGEILVL-HHPTTISSRYQAMVHCGSIRQTASILSMSAEC-LRTGDKAAVHFRFI 69
V EFE +I +L + I++ Y A++H + + +I + A +TG K+ RF+
Sbjct: 2 VVTEFEAQIAILELKRSIITAGYSAVLHIHTAVEEVTIKKLIALIDKKTGKKSKKRPRFV 61
Query: 70 K------------HP-------EYLRAGQRMVFR-EGRTKAVGNVTKV 97
K P ++ + G R R EG+T A+G V K+
Sbjct: 62 KSGMKVIARLETTGPICLEKFEDFPQLG-RFTLRDEGKTIAIGKVLKL 108
>gnl|CDD|129574 TIGR00483, EF-1_alpha, translation elongation factor EF-1 alpha.
This model represents the counterpart of bacterial EF-Tu
for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1
alpha). The trusted cutoff is set fairly high so that
incomplete sequences will score between suggested and
trusted cutoff levels [Protein synthesis, Translation
factors].
Length = 426
Score = 38.3 bits (89), Expect = 0.001
Identities = 30/110 (27%), Positives = 45/110 (40%), Gaps = 20/110 (18%)
Query: 10 PVAVWEFEGEILVLHHPTTISSRYQAMVHCGSI--------------RQTASILSMSAEC 55
P EF +I+VL HP I+ Y + HC + +T +L + +
Sbjct: 315 PKVAKEFTAQIVVLQHPGAITVGYTPVFHCHTAQIACRFDELLKKNDPRTGQVLEENPQF 374
Query: 56 LRTGDKAAVHFRFIKH------PEYLRAGQRMVFREGRTKAVGNVTKVLP 99
L+TGD A V F+ K E G+ + G+T A G + V P
Sbjct: 375 LKTGDAAIVKFKPTKPMVIEAVKEIPPLGRFAIRDMGQTVAAGMIIDVDP 424
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 37.2 bits (87), Expect = 0.003
Identities = 33/123 (26%), Positives = 44/123 (35%), Gaps = 37/123 (30%)
Query: 6 PALNPVAVW-EFEGEILVLHHPTTISSRYQAMVHCGSIRQTASILSMSAEC--------- 55
NP V EF +I+VL HP+ I+ Y + H TA + E
Sbjct: 308 HPDNPPTVAEEFTAQIVVLQHPSAITVGYTPVFHA----HTAQVACTFEELVKKLDPRTG 363
Query: 56 ---------LRTGDKAAVHFRFIKH---------PEYLRAGQR-MVFREGRTKAVGNVTK 96
++TGD A V + K P+ R R M G+T A G V
Sbjct: 364 QVAEENPQFIKTGDAAIVKIKPTKPLVIEKVKEIPQLGRFAIRDM----GQTIAAGMVID 419
Query: 97 VLP 99
V P
Sbjct: 420 VKP 422
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 37.3 bits (87), Expect = 0.003
Identities = 28/111 (25%), Positives = 42/111 (37%), Gaps = 20/111 (18%)
Query: 9 NPVAVWEFEGEILVLHHPTTISSRYQAMVHCGSI--------------RQTASILSMSAE 54
P EF +I+VL HP I+S Y ++H + +T L + +
Sbjct: 318 PPTVSPEFTAQIIVLWHPGIITSGYTPVLHAHTAQVACRIAELLSKLDPRTGKKLEENPQ 377
Query: 55 CLRTGDKAAVHFRFIK-----HPEYLRAGQRMVFRE-GRTKAVGNVTKVLP 99
L+ GD A V K + R R+ G+T A G V +V
Sbjct: 378 FLKRGDAAIVKIEPEKPLCLEKVSEIPQLGRFALRDMGQTIAAGKVLEVKK 428
>gnl|CDD|239676 cd03705, EF1_alpha_III, Domain III of EF-1. Eukaryotic elongation
factor 1 (EF-1) is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to ribosomes. EF-1 is
composed of four subunits: the alpha chain, which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This family is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea (aEF-1
alpha) and eukaryotes (eEF-1 alpha).
Length = 104
Score = 32.9 bits (76), Expect = 0.024
Identities = 28/102 (27%), Positives = 42/102 (41%), Gaps = 24/102 (23%)
Query: 15 EFEGEILVLHHPTTISSRYQAMVHCGSI--------------RQTASILSMSAECLRTGD 60
F +++VL+HP I Y ++ C + +T L + + L++GD
Sbjct: 5 SFTAQVIVLNHPGQIKPGYTPVLDCHTAHVACRFAEILSKIDPRTGKKLEENPKFLKSGD 64
Query: 61 KAAVHFRFIKHP-------EYLRAGQRMVFRE-GRTKAVGNV 94
A V K P EY G R R+ G+T AVG V
Sbjct: 65 AAIVKIVPQK-PLVVETFSEYPPLG-RFAVRDMGQTVAVGIV 104
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 34.0 bits (78), Expect = 0.028
Identities = 31/94 (32%), Positives = 39/94 (41%), Gaps = 12/94 (12%)
Query: 15 EFEGEILVL-------HHPTTISSRYQAMVHCGSIRQTASI-LSMSAECLRTGDKAAVHF 66
+FE EI VL H P + R Q + + T + L + + GD F
Sbjct: 357 KFEAEIYVLTKDEGGRHTPFFSNYRPQFYLRTADV--TGKVELPEGVKMVMPGDNVTAVF 414
Query: 67 RFIKHPEYLRAGQRMVFRE-GRTKAVGNVTKVLP 99
I P L GQR RE GRT G V+KVL
Sbjct: 415 ELI-SPVPLEPGQRFALREGGRTVGAGVVSKVLS 447
>gnl|CDD|165326 PHA03028, PHA03028, hypothetical protein; Provisional.
Length = 185
Score = 32.7 bits (74), Expect = 0.063
Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 6/62 (9%)
Query: 15 EFEGEILVLHHPTTISSRYQAMVHCGSIRQTASILSMSAECLRTGDKAAVHFRFIKHPEY 74
EF+ EIL +HHPT + + + + L SA D + ++ + HPE
Sbjct: 101 EFDMEILCIHHPTMMKQDNKKIEFIPDVNDGIENLKPSA------DSLCIDYKILYHPEI 154
Query: 75 LR 76
+
Sbjct: 155 FK 156
>gnl|CDD|239677 cd03706, mtEFTU_III, Domain III of mitochondrial EF-TU (mtEF-TU).
mtEF-TU is highly conserved and is 55-60% identical to
bacterial EF-TU. The overall structure is similar to
that observed in the Escherichia coli and Thermus
aquaticus EF-TU. However, compared with that observed
in prokaryotic EF-TU the nucleotide-binding domain
(domain I) of EF-TUmt is in a different orientation
relative to the rest of the structure. Furthermore,
domain III is followed by a short 11-amino acid
extension that forms one helical turn. This extension
seems to be specific to the mitochondrial factors and
has not been observed in any of the prokaryotic
factors.
Length = 93
Score = 28.8 bits (65), Expect = 0.51
Identities = 19/71 (26%), Positives = 26/71 (36%), Gaps = 3/71 (4%)
Query: 29 ISSRYQAMVHCGSIRQTASI-LSMSAECLRTGDKAAVHFRFIKHPEYLRAGQRMVFREGR 87
S +Q + + A I L E + G+ V + P L GQR R+G
Sbjct: 24 FVSNFQPQMFSLTWDCAARIDLPPGKEMVMPGEDTKVTLILRR-PMVLEKGQRFTLRDGN 82
Query: 88 -TKAVGNVTKV 97
T G VT
Sbjct: 83 RTIGTGLVTDT 93
>gnl|CDD|237533 PRK13863, PRK13863, type IV secretion system T-DNA border
endonuclease VirD2; Provisional.
Length = 446
Score = 30.3 bits (68), Expect = 0.62
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 2/52 (3%)
Query: 132 SPVTEKPEVKTPRDLDRAGQAGAKRGGVEGAEP-SETKTRQPILEAGPISLL 182
+ + K PRD D +GAKR + G E + PI+
Sbjct: 330 TTSERQQRRKRPRD-DEGEPSGAKRTRLNGIAVGPEANAGEQDGRDDPITSP 380
>gnl|CDD|217923 pfam04140, ICMT, Isoprenylcysteine carboxyl methyltransferase
(ICMT) family. The isoprenylcysteine
o-methyltransferase (EC:2.1.1.100) family carry out
carboxyl methylation of cleaved eukaryotic proteins
that terminate in a CaaX motif. In Saccharomyces
cerevisiae this methylation is carried out by Ste14p,
an integral endoplasmic reticulum membrane protein.
Ste14p is the founding member of the isoprenylcysteine
carboxyl methyltransferase (ICMT) family, whose members
share significant sequence homology.
Length = 94
Score = 26.9 bits (60), Expect = 2.3
Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 5/44 (11%)
Query: 32 RYQAMVHCGSIRQTASILSMSAECLRTGDKAAVHFRFIKHPEYL 75
R MV G I ++ + +G +R+++HP Y
Sbjct: 12 RKWVMVTLGRIWTHRVMILPDHRLVTSGP-----YRYLRHPNYF 50
>gnl|CDD|234666 PRK00147, queA, S-adenosylmethionine:tRNA
ribosyltransferase-isomerase; Provisional.
Length = 342
Score = 27.3 bits (62), Expect = 4.1
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 11/35 (31%)
Query: 65 HFRFIKHPEYLRAGQRMVFREGRTKAVGNVTKVLP 99
HFR + P+YL G +VF N T+V+P
Sbjct: 42 HFRDL--PDYLNPGDLLVF---------NDTRVIP 65
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 27.4 bits (61), Expect = 4.8
Identities = 14/63 (22%), Positives = 30/63 (47%), Gaps = 14/63 (22%)
Query: 16 FEGEILVLHHPTTISSRYQAMVHCGSI--------------RQTASILSMSAECLRTGDK 61
F +++VL+HP I + Y ++ C + R++ +L + + +++GD
Sbjct: 328 FTAQVIVLNHPGQIKNGYTPVLDCHTAHIACKFAEIESKIDRRSGKVLEENPKAIKSGDA 387
Query: 62 AAV 64
A V
Sbjct: 388 AIV 390
>gnl|CDD|151380 pfam10933, DUF2827, Protein of unknown function (DUF2827). This is
a family of uncharacterized proteins found in
Burkholderia.
Length = 364
Score = 27.4 bits (61), Expect = 4.9
Identities = 12/44 (27%), Positives = 18/44 (40%)
Query: 132 SPVTEKPEVKTPRDLDRAGQAGAKRGGVEGAEPSETKTRQPILE 175
+PVT P + P ++R A + G G P R + E
Sbjct: 153 APVTVVPHIWDPMFIERRTAALPEAGLRFGYRPGRPAWRVAVFE 196
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
0.317 0.131 0.388
Gapped
Lambda K H
0.267 0.0688 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,130,698
Number of extensions: 798898
Number of successful extensions: 588
Number of sequences better than 10.0: 1
Number of HSP's gapped: 582
Number of HSP's successfully gapped: 22
Length of query: 184
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 93
Effective length of database: 6,901,388
Effective search space: 641829084
Effective search space used: 641829084
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.4 bits)