RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9631
(90 letters)
>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 = 87.0 bits (216), Expect = 4e-24
Identities = 31/57 (54%), Positives = 39/57 (68%)
Query: 1 MHDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIIDMGGKDMFMPGEDG 57
HD VEAQ+Y+L+K EGGR +P+ Q ++S TWD AARI GK+M MPGED
Sbjct: 2 PHDKVEAQVYILSKAEGGRHKPFVSNFQPQMFSLTWDCAARIDLPPGKEMVMPGEDT 58
>gnl|CDD|239678 cd03707, EFTU_III, Domain III of elongation factor (EF) Tu. Ef-Tu
consists of three structural domains, designated I, II
and III. Domain III adopts a beta barrel structure.
Domain III is involved in binding to both charged tRNA
and binding to elongation factor Ts (EF-Ts). EF-Ts is
the guanine-nucleotide-exchange factor for EF-Tu.
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.
Crystallographic studies revealed structural
similarities ("molecular mimicry") between tertiary
structures of EF-G and the EF-Tu-aminoacyl-tRNA ternary
complex. Domains III, IV, and V of EF-G mimic the tRNA
structure in the EF-Tu ternary complex; domains III, IV
and V can be related to the acceptor stem, anticodon
helix and T stem of tRNA respectively.
Length = 90
Score = 54.9 bits (133), Expect = 1e-11
Identities = 23/55 (41%), Positives = 31/55 (56%)
Query: 1 MHDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIIDMGGKDMFMPGE 55
H EA++Y+LTKEEGGR P+ + Y +T DV I G +M MPG+
Sbjct: 2 PHTKFEAEVYVLTKEEGGRHTPFFSGYRPQFYIRTTDVTGSITLPEGTEMVMPGD 56
>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 = 52.1 bits (126), Expect = 2e-10
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 5/54 (9%)
Query: 2 HDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIIDMGGKDMFMPGE 55
H +AQ+Y+L Y P Y T DV + I G K+ MPG+
Sbjct: 5 HTKFKAQVYILNHP-TPIFNGYRP----VFYCHTADVTGKFILPGKKEFVMPGD 53
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 52.3 bits (126), Expect = 1e-09
Identities = 25/59 (42%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 2 HDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARII-----DMGGKDMFMPGE 55
H EAQ+Y+LTKEEGGR P+ P + Y +T DV +I D +M MPG+
Sbjct: 312 HTKFEAQVYILTKEEGGRHTPFFPGYRPQFYVRTTDVTGKIESFTADDGSKTEMVMPGD 370
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 49.6 bits (119), Expect = 1e-08
Identities = 22/55 (40%), Positives = 32/55 (58%)
Query: 2 HDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIIDMGGKDMFMPGED 56
H EA++Y+L+KEEGGR P+ + Y +T DV I G +M MPG++
Sbjct: 302 HTKFEAEVYVLSKEEGGRHTPFFHGYRPQFYFRTTDVTGAITLPEGVEMVMPGDN 356
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 47.5 bits (113), Expect = 7e-08
Identities = 21/55 (38%), Positives = 32/55 (58%)
Query: 2 HDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIIDMGGKDMFMPGED 56
+ EA+IY+LTK+EGGR P+ + Y +T DV ++ G M MPG++
Sbjct: 355 YKKFEAEIYVLTKDEGGRHTPFFSNYRPQFYLRTADVTGKVELPEGVKMVMPGDN 409
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 46.9 bits (111), Expect = 1e-07
Identities = 23/59 (38%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 2 HDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIID-MGGKD----MFMPGE 55
H EA +Y+L KEEGGR P+ + Y +T DV ++ M KD M MPG+
Sbjct: 381 HTKFEAIVYVLKKEEGGRHSPFFAGYRPQFYMRTTDVTGKVTSIMNDKDEESKMVMPGD 439
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 46.3 bits (111), Expect = 2e-07
Identities = 22/53 (41%), Positives = 30/53 (56%)
Query: 2 HDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIIDMGGKDMFMPG 54
H EA++Y+L+KEEGGR P+ + Y +T DV I G +M MPG
Sbjct: 304 HTKFEAEVYVLSKEEGGRHTPFFNGYRPQFYFRTTDVTGVIELPEGVEMVMPG 356
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 46.4 bits (111), Expect = 2e-07
Identities = 24/57 (42%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 2 HDHVEAQIYLLTKEEGGRTRP----YTPWGQAHVYSKTWDVAARIIDMGGKDMFMPG 54
H EA++Y+L+KEEGGR P Y P Y +T DV I G +M MPG
Sbjct: 304 HTKFEAEVYVLSKEEGGRHTPFFNGYRP----QFYFRTTDVTGTIELPEGVEMVMPG 356
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 45.3 bits (108), Expect = 5e-07
Identities = 22/54 (40%), Positives = 31/54 (57%)
Query: 2 HDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIIDMGGKDMFMPGE 55
H +A++Y+LTKEEGGR P+ + Y +T DV I G +M MPG+
Sbjct: 302 HTKFKAEVYILTKEEGGRHTPFFNNYRPQFYFRTTDVTGSIELPEGTEMVMPGD 355
>gnl|CDD|129576 TIGR00485, EF-Tu, translation elongation factor TU. This model
models orthologs of translation elongation factor EF-Tu
in bacteria, mitochondria, and chloroplasts, one of
several GTP-binding translation factors found by the
more general pfam model GTP_EFTU. The eukaryotic
conterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this model. EF-Tu is one
of the most abundant proteins in bacteria, as well as
one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation
[Protein synthesis, Translation factors].
Length = 394
Score = 44.8 bits (106), Expect = 7e-07
Identities = 22/55 (40%), Positives = 31/55 (56%)
Query: 2 HDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIIDMGGKDMFMPGED 56
H EA++Y+L KEEGGR P+ + Y +T DV I G +M MPG++
Sbjct: 302 HTKFEAEVYVLKKEEGGRHTPFFSGYRPQFYFRTTDVTGSITLPEGVEMVMPGDN 356
>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 = 33.2 bits (76), Expect = 0.004
Identities = 15/67 (22%), Positives = 22/67 (32%), Gaps = 16/67 (23%)
Query: 2 HDHVEAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIIDM-----------GGKDM 50
D A+IY+L E P +P + + T V RI + +
Sbjct: 3 VDKFVAEIYVLDHPE-----PLSPGYKPVLNVGTAHVPGRIAKLLSKVDGKTEEKKPPEF 57
Query: 51 FMPGEDG 57
GE G
Sbjct: 58 LKSGERG 64
>gnl|CDD|239651 cd03679, MM_CoA_mutase_alpha_like, Coenzyme
B12-dependent-methylmalonyl coenzyme A (CoA) mutase
(MCM) family, Alpha subunit-like subfamily; contains
proteins similar to the alpha subunit of
Propionbacterium shermanni MCM, as well as human and E.
coli MCM. Members of this subfamily contain an
N-terminal MCM domain and a C-terminal coenzyme B12
binding domain. MCM catalyzes the isomerization of
methylmalonyl-CoA to succinyl-CoA. The reaction proceeds
via radical intermediates beginning with a
substrate-induced homolytic cleavage of the Co-C bond of
coenzyme B12 to produce cob(II)alamin and the
deoxyadenosyl radical. MCM plays an important role in
the conversion of propionyl-CoA to succinyl-CoA during
the degradation of propionate for the Krebs cycle. In
higher animals, MCM is involved in the breakdown of
odd-chain fatty acids, several amino acids, and
cholesterol. Methylobacterium extorquens MCM
participates in the glyoxylate regeneration pathway. In
M. extorquens, MCM forms a complex with MeaB; MeaB may
protect MCM from irreversible inactivation. In some
bacteria, MCM is involved in the reverse metabolic
reaction, the rearrangement of succinyl-CoA to
methylmalonyl-CoA. Examples include P. shermanni MCM
during propionic acid fermentation, E.coli MCM in a
pathway for the conversion of succinate to propionate
and Streptomyces MCM in polyketide biosynthesis.
Sinorhizobium meliloti strain SU47 MCM plays a role in
the polyhydroxyalkanoate degradation pathway. P.
shermanni and Streptomyces cinnamonensis MCMs are
alpha/beta heterodimers. It has been shown for P.
shermanni MCM that only the alpha subunit binds coenzyme
B12 and substrates. Human MCM is a homodimer with two
active sites. Mouse and E.coli MCMs are also homodimers.
In humans, impaired activity of MCM results in
methylmalonic aciduria, a disorder of propionic acid
metabolism.
Length = 536
Score = 29.2 bits (66), Expect = 0.21
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 10/48 (20%)
Query: 8 QIYLLTKEEGGRTRPYTPWGQAH--------VYSKTWDVAARIIDMGG 47
Q+ L +EE G T+ PWG ++ + K W + I ++GG
Sbjct: 371 QLIL--QEETGITKVVDPWGGSYYMESLTDDLAEKAWALIQEIEELGG 416
>gnl|CDD|176993 CHL00052, rpl2, ribosomal protein L2.
Length = 273
Score = 29.1 bits (66), Expect = 0.26
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 18 GRTRPYTPWGQA 29
GR +P TPWG+
Sbjct: 240 GRKKPVTPWGKP 251
>gnl|CDD|233067 TIGR00641, acid_CoA_mut_N, methylmalonyl-CoA mutase N-terminal
domain. Methylmalonyl-CoA mutase (EC 5.4.99.2)
catalyzes a reversible isomerization between
L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an
adenosylcobalamin cofactor. It may be a homodimer, as in
mitochondrion, or a heterodimer with partially
homologous beta chain that does not bind the
adenosylcobalamin cofactor, as in Propionibacterium
freudenreichii. The most similar archaeal sequences are
separate chains, such as AF2215 abd AF2219 of
Archaeoglobus fulgidus, that correspond roughly to the
first 500 and last 130 residues, respectively of known
methylmalonyl-CoA mutases. This model describes the
N-terminal domain subfamily. In a neighbor-joining tree,
AF2215 branches with a bacterial isobutyryl-CoA mutase,
which is also the same length. Scoring between the noise
and trusted cutoffs are the non-catalytic, partially
homologous beta chains from certain heterodimeric
examples of 5.4.99.2.
Length = 524
Score = 27.4 bits (61), Expect = 0.97
Identities = 17/57 (29%), Positives = 23/57 (40%), Gaps = 10/57 (17%)
Query: 11 LLTKEEGGRTRPYTPWGQA--------HVYSKTWDVAARIIDMGGKDMFMPGEDGNP 59
+ +EE G TR P G + +Y + W I +MGG M E G P
Sbjct: 352 QIIQEESGVTRVIDPLGGSYYVEWLTDDIYERAWKYIQEIEEMGG--MAKAIERGIP 406
>gnl|CDD|215634 PLN03211, PLN03211, ABC transporter G-25; Provisional.
Length = 659
Score = 27.2 bits (60), Expect = 1.2
Identities = 9/32 (28%), Positives = 12/32 (37%)
Query: 45 MGGKDMFMPGEDGNPDPLRGPMRPHHLLLQSC 76
G + G D + P + LLL SC
Sbjct: 4 FDGVENQNDGPDRSKPPSQDSRDLPSLLLSSC 35
>gnl|CDD|236508 PRK09426, PRK09426, methylmalonyl-CoA mutase; Reviewed.
Length = 714
Score = 27.1 bits (61), Expect = 1.3
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 10/48 (20%)
Query: 8 QIYLLTKEEGGRTRPYTPW-GQAHVYSKTWDVAAR---IID----MGG 47
Q+ L +EE G TR PW G +V S T ++A + I+ +GG
Sbjct: 377 QLIL--QEETGITRVVDPWAGSYYVESLTHELAEKAWAHIEEVEALGG 422
>gnl|CDD|225248 COG2373, COG2373, Large extracellular alpha-helical protein
[General function prediction only].
Length = 1621
Score = 25.8 bits (57), Expect = 3.4
Identities = 12/61 (19%), Positives = 20/61 (32%), Gaps = 9/61 (14%)
Query: 6 EAQIYLLTKEEGGRTRPYTPWGQAHVYSKTWDVAARIID--------MGGKDMFMPGEDG 57
+ LL ++E G G S +DV R + ++ PGE
Sbjct: 353 KPAALLLARKEDGDFLGLDLTGGVFDLSD-FDVEGRAAPGYGLKVYLFTDRGLYRPGETV 411
Query: 58 N 58
+
Sbjct: 412 H 412
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase activity
and may play a role in the transcription of the virus
genome, the unwinding or reannealing of double-stranded
RNA during RNA synthesis. The RTPase activity constitutes
the first step in the capping of RNA, resulting in a
5'-diphosphorylated RNA plus-strand. lambda1 is an
Orthoreovirus core protein, VP3 is the homologous core
protein in Aquareoviruses.
Length = 1166
Score = 25.9 bits (57), Expect = 3.8
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 45 MGGKDMFMPGEDGNPDPLRG 64
M G + + GNP PL G
Sbjct: 982 MNGLEPMVEDAGGNPRPLDG 1001
>gnl|CDD|201900 pfam01642, MM_CoA_mutase, Methylmalonyl-CoA mutase. The enzyme
methylmalonyl-CoA mutase is a member of a class of
enzymes that uses coenzyme B12 (adenosylcobalamin) as a
cofactor. The enzyme induces the formation of an
adenosyl radical from the cofactor. This radical then
initiates a free-radical rearrangement of its substrate,
succinyl-CoA, to methylmalonyl-CoA.
Length = 517
Score = 25.1 bits (55), Expect = 6.8
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 10/48 (20%)
Query: 8 QIYLLTKEEGGRTRPYTPWGQAH--------VYSKTWDVAARIIDMGG 47
Q+ L EE G R PWG ++ + + W + I + GG
Sbjct: 350 QLILQ--EESGVARVIDPWGGSYYVEELTDRIAEEAWKLFQEIEEAGG 395
>gnl|CDD|224043 COG1118, CysA, ABC-type sulfate/molybdate transport systems, ATPase
component [Inorganic ion transport and metabolism].
Length = 345
Score = 24.6 bits (54), Expect = 7.8
Identities = 16/68 (23%), Positives = 22/68 (32%), Gaps = 5/68 (7%)
Query: 20 TRPYTPWGQAHVYSKTWDVAARIIDMGGKDMFMPGEDGNPDPLRGPMRPHHLLLQSCPHK 79
P G+A +Y + DV + G++ P P G L L P
Sbjct: 263 PLQPLPDGKADLYVRPHDVE---LLDHGRNTL-PATVERVSP-LGHTVRVELKLGGDPLA 317
Query: 80 AEYIEELG 87
E EL
Sbjct: 318 VEIEVELA 325
>gnl|CDD|218379 pfam05009, EBV-NA3, Epstein-Barr virus nuclear antigen 3 (EBNA-3).
This family contains EBNA-3A, -3B, and -3C which are
latent infection nuclear proteins important for
Epstein-Barr virus (EBV)-induced B-cell immortalisation
and the immune response to EBV infection.
Length = 254
Score = 24.7 bits (54), Expect = 9.2
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 18 GRTRPYTPWGQAH 30
G T+P TPW AH
Sbjct: 162 GTTKPSTPWLSAH 174
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 0.139 0.455
Gapped
Lambda K H
0.267 0.0670 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,802,353
Number of extensions: 393026
Number of successful extensions: 296
Number of sequences better than 10.0: 1
Number of HSP's gapped: 292
Number of HSP's successfully gapped: 24
Length of query: 90
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 32
Effective length of database: 8,365,070
Effective search space: 267682240
Effective search space used: 267682240
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 (21.7 bits)
S2: 53 (24.3 bits)