RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2429
(108 letters)
>gnl|CDD|238181 cd00292, EF1B, Elongation factor 1 beta (EF1B) guanine nucleotide
exchange domain. EF1B catalyzes the exchange of GDP
bound to the G-protein, EF1A, for GTP, an important
step in the elongation cycle of the protein
biosynthesis. EF1A binds to and delivers the aminoacyl
tRNA to the ribosome. The guanine nucleotide exchange
domain of EF1B, which is the alpha subunit in yeast, is
responsible for the catalysis of this exchange
reaction.
Length = 88
Score = 113 bits (284), Expect = 3e-34
Identities = 44/79 (55%), Positives = 59/79 (74%), Gaps = 1/79 (1%)
Query: 21 IAKSNIILDVKPWGDDTDMKEMEKQVRAIQMDGLLWGASKLAPLAYGINKLQISCVVEDD 80
+AKS ++L VKPW D+ D+ E+E+++RAI MDGLLWG SKL P+A+G+ LQI CVVEDD
Sbjct: 1 MAKSLVVLKVKPWDDEVDLDELEEKIRAILMDGLLWGKSKLEPIAFGLKALQIYCVVEDD 60
Query: 81 LVSVDALQESIQDIEDYVS 99
D L+E+I + ED V
Sbjct: 61 EGGTDELEEAISE-EDGVQ 78
>gnl|CDD|201421 pfam00736, EF1_GNE, EF-1 guanine nucleotide exchange domain. This
family is the guanine nucleotide exchange domain of EF-1
beta and EF-1 delta chains.
Length = 87
Score = 99.9 bits (250), Expect = 4e-29
Identities = 48/80 (60%), Positives = 62/80 (77%), Gaps = 3/80 (3%)
Query: 24 SNIILDVKPWGDDTDMKEMEKQV-RAIQMDGLLWG-ASKLAPLAYGINKLQISCVVEDDL 81
S+++L VKPW D+TD++E+EK+V R I MDGL+WG ASKL P+A+G+ KLQISCVVEDD
Sbjct: 1 SSVVLKVKPWDDETDLEELEKKVKRKIPMDGLVWGKASKLEPIAFGLKKLQISCVVEDDK 60
Query: 82 VSVDALQESIQDIEDYVSLV 101
V D L+E+I ED V V
Sbjct: 61 VGTDELEEAI-AFEDGVQSV 79
>gnl|CDD|214886 smart00888, EF1_GNE, EF-1 guanine nucleotide exchange domain.
Translation elongation factors are responsible for two
main processes during protein synthesis on the
ribosome. EF1A (or EF-Tu) is responsible for the
selection and binding of the cognate aminoacyl-tRNA to
the A-site (acceptor site) of the ribosome. EF2 (or
EF-G) is responsible for the translocation of the
peptidyl-tRNA from the A-site to the P-site
(peptidyl-tRNA site) of the ribosome, thereby freeing
the A-site for the next aminoacyl-tRNA to bind.
Elongation factors are responsible for achieving
accuracy of translation and both EF1A and EF2 are
remarkably conserved throughout evolution. Elongation
factor EF1B (also known as EF-Ts or
EF-1beta/gamma/delta) is a nucleotide exchange factor
that is required to regenerate EF1A from its inactive
form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is
then ready to interact with a new aminoacyl-tRNA to
begin the cycle again. EF1B is more complex in
eukaryotes than in bacteria, and can consist of three
subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or
EF-1gamma) and EF1B-beta (or EF-1delta). This entry
represents the guanine nucleotide exchange domain of
the beta (EF-1beta, also known as EF1B-alpha) and delta
(EF-1delta, also known as EF1B-beta) chains of EF1B
proteins from eukaryotes and archaea. The beta and
delta chains have exchange activity, which mainly
resides in their homologous guanine nucleotide exchange
domains, found in the C-terminal region of the
peptides. Their N-terminal regions may be involved in
interactions with the gamma chain (EF-1gamma).
Length = 88
Score = 95.3 bits (238), Expect = 3e-27
Identities = 35/76 (46%), Positives = 54/76 (71%), Gaps = 2/76 (2%)
Query: 23 KSNIILDVKPWGDDTDMKEMEKQVRAI-QMDGLLWGAS-KLAPLAYGINKLQISCVVEDD 80
K ++L V P D+ D++E+E++V++I MDGLLWGA +L P+A+G+ LQI VVEDD
Sbjct: 1 KVLVVLKVMPESDEVDLEELEEKVKSILPMDGLLWGAGIELEPIAFGLKALQIYVVVEDD 60
Query: 81 LVSVDALQESIQDIED 96
D L+E+I+++E
Sbjct: 61 EGGTDELEEAIEEVEG 76
>gnl|CDD|225003 COG2092, EFB1, Translation elongation factor EF-1beta
[Translation, ribosomal structure and biogenesis].
Length = 88
Score = 77.0 bits (190), Expect = 4e-20
Identities = 21/75 (28%), Positives = 44/75 (58%)
Query: 22 AKSNIILDVKPWGDDTDMKEMEKQVRAIQMDGLLWGASKLAPLAYGINKLQISCVVEDDL 81
A ++L V P + D++E+E++++ +G + P+A+G+ L++ VVED
Sbjct: 2 ADVLVVLKVMPDDPEVDLEELEEKIKEKLPEGYELIKIEEEPIAFGLKALKLYVVVEDKE 61
Query: 82 VSVDALQESIQDIED 96
DAL+E+++++E
Sbjct: 62 GGTDALEEALEEVEG 76
>gnl|CDD|129580 TIGR00489, aEF-1_beta, translation elongation factor aEF-1 beta.
This model describes the archaeal translation
elongation factor aEF-1 beta. The member from
Sulfolobus solfataricus was demonstrated
experimentally. It is a dimer that catalyzes the
exchange of GDP for GTP on aEF-1 alpha [Protein
synthesis, Translation factors].
Length = 88
Score = 32.9 bits (75), Expect = 0.006
Identities = 15/66 (22%), Positives = 34/66 (51%)
Query: 30 VKPWGDDTDMKEMEKQVRAIQMDGLLWGASKLAPLAYGINKLQISCVVEDDLVSVDALQE 89
V P D D++ ++++++ +G+ P+A+G+ + + V+ D +A +E
Sbjct: 10 VMPESPDVDLEALKEKIKERIPEGVEIRKIDEEPIAFGLVAINVMVVMGDAEGGTEAAEE 69
Query: 90 SIQDIE 95
S+ IE
Sbjct: 70 SLSGIE 75
>gnl|CDD|187838 cd09707, Csf3_U, CRISPR/Cas system-associated RAMP superfamily
protein Csf3. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
RAMP superfamily protein.
Length = 214
Score = 31.5 bits (71), Expect = 0.052
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 29 DVKPWGDDTDMKEMEKQVRAIQMDGLLWGASKLAPLAYG 67
PWGD D+ E + + D +W AS+L LA+
Sbjct: 38 SADPWGDARDLSEDLPLGKEEEGDSWVWKASRLEVLAFL 76
>gnl|CDD|132160 TIGR03116, cas_csf3, CRISPR type AFERR-associated protein Csf3.
Members of this family show up near CRISPR repeats in
Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp.
EbN1, and Rhodoferax ferrireducens DSM 15236. In the
latter two species, the CRISPR/cas locus is found on a
plasmid. This family is one of several characteristic
of a type of CRISPR-associated (cas) gene cluster we
designate Aferr after A. ferrooxidans, where it is both
chromosomal and the only type of cas gene cluster
found. The gene is designated csf3 (CRISPR/cas Subtype
as in A. ferrooxidans protein 3), as it lies third
closest to the repeats [Mobile and extrachromosomal
element functions, Other].
Length = 214
Score = 31.5 bits (71), Expect = 0.052
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 29 DVKPWGDDTDMKEMEKQVRAIQMDGLLWGASKLAPLAYG 67
PWGD D+ E + + D +W AS+L LA+
Sbjct: 38 SADPWGDARDLSEDLPLGKEEEGDSWVWKASRLEVLAFL 76
>gnl|CDD|179023 PRK00435, ef1B, elongation factor 1-beta; Validated.
Length = 88
Score = 29.4 bits (67), Expect = 0.12
Identities = 14/75 (18%), Positives = 39/75 (52%), Gaps = 10/75 (13%)
Query: 27 ILDVKPWGDDTDMKEMEKQVRAIQMDGLLWGASKLA-----PLAYGINKLQISCVVEDDL 81
+L V P + D+ E++++++ +L K+ P+A+G+ L++ ++ D+
Sbjct: 7 VLKVMPESPEVDLDELKEKIKE-----VLPEGYKINGIEEEPIAFGLKALKLYVIMPDEE 61
Query: 82 VSVDALQESIQDIED 96
+ ++E+ ++E
Sbjct: 62 GGTEPVEEAFANVEG 76
>gnl|CDD|145929 pfam03043, Herpes_UL87, Herpesvirus UL87 family. Members of this
family are functionally uncharacterized. This family
groups together EBV BcRF1, HSV-6 U58, HVS-1 24 and HCMV
UL87. The proteins range from 575 to 950 amino acids in
length.
Length = 533
Score = 28.4 bits (64), Expect = 0.80
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 6 TYKLFLLPSHVEPALIAKSNIILDV 30
K FL + PA + N LD+
Sbjct: 306 VLKCFLPIKTIFPASVCNWNSTLDL 330
>gnl|CDD|224390 COG1473, AbgB, Metal-dependent
amidase/aminoacylase/carboxypeptidase [General function
prediction only].
Length = 392
Score = 27.6 bits (62), Expect = 1.3
Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 11/78 (14%)
Query: 24 SNIILD-VKPWG-----DDTDMKEMEKQVRAIQMDGLLWGASKLAPLAYGINKLQISCVV 77
+N+I D + G D +++E ++ I G + I+ + V
Sbjct: 245 ANVIPDSAELEGTIRTFSDEVREKLEARIERI-----AKGIAAAYGAEAEIDYERGYPPV 299
Query: 78 EDDLVSVDALQESIQDIE 95
+D D L E+ +++
Sbjct: 300 VNDPALTDLLAEAAEEVG 317
>gnl|CDD|215226 PLN02405, PLN02405, hexokinase.
Length = 497
Score = 27.5 bits (61), Expect = 1.6
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 19 ALIAKSNIILDVKPWGDDTDMKEMEKQVRAIQMDGLLW 56
A ++ + I +K G DT +K+ EKQ I MDG L+
Sbjct: 407 ARLSAAGIYGILKKLGRDT-VKDGEKQKSVIAMDGGLF 443
>gnl|CDD|163191 TIGR03235, DNA_S_dndA, cysteine desulfurase DndA. This model
describes DndA, a protein related to IscS and part of a
larger family of cysteine desulfurases. It is encoded,
typically, divergently from a conserved, sparsely
distributed operon for sulfur modification of DNA. This
modification system is designated dnd, after the
phenotype of DNA degradation during electrophoresis. The
system is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndB is described
as a putative ATPase [DNA metabolism,
Restriction/modification].
Length = 353
Score = 25.9 bits (57), Expect = 5.4
Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 5/75 (6%)
Query: 26 IILDVKPWGDDTDMKEMEKQVRAIQMDGLLWGASKLAPLAYGINKLQISCVVEDDLVSVD 85
IL + G+ K + AI+ +L L + + L + E + VD
Sbjct: 75 AILGLARAGEQKGKKHI--ITSAIEHPAVLEPIRALERNGFTVTYLPVD---ESGRIDVD 129
Query: 86 ALQESIQDIEDYVSL 100
L ++I+ VS+
Sbjct: 130 ELADAIRPDTLLVSI 144
>gnl|CDD|206779 cd11386, MCP_signal, Methyl-accepting chemotaxis protein (MCP),
signaling domain. Methyl-accepting chemotaxis proteins
(MCPs or chemotaxis receptors) are an integral part of
the transmembrane protein complex that controls
bacterial chemotaxis, together with the histidine kinase
CheA, the receptor-coupling protein CheW,
receptor-modification enzymes, and localized
phosphatases. MCPs contain a four helix trans membrane
region, an N-terminal periplasmic ligand binding domain,
and a C-terminal HAMP domain followed by a cytoplasmic
signaling domain. This C-terminal signaling domain
dimerizes into a four-helix bundle and interacts with
CheA through the adaptor protein CheW.
Length = 200
Score = 24.9 bits (55), Expect = 8.5
Identities = 9/30 (30%), Positives = 19/30 (63%)
Query: 72 QISCVVEDDLVSVDALQESIQDIEDYVSLV 101
QI V++ + +V+ L+ES +I + V ++
Sbjct: 44 QIDESVDEAVSAVEELEESSAEIGEIVEVI 73
>gnl|CDD|176549 cd08607, GDPD_GDE5, Glycerophosphodiester phosphodiesterase domain
of putative mammalian glycerophosphodiester
phosphodiesterase GDE5 and similar proteins. This
subfamily corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in putative
mammalian GDE5 and similar proteins. Mammalian GDE5 is
widely expressed in mammalian tissues, with highest
expression in the spinal chord. Although its biological
function remains unclear, mammalian GDE5 shows higher
sequence homology to fungal and plant
glycerophosphodiester phosphodiesterases (GP-GDEs, EC
3.1.4.46) than to other bacterial and mammalian GP-GDEs.
It may also hydrolyze glycerophosphodiesters to
sn-glycerol-3-phosphate (G3P) and the corresponding
alcohols. In addition to C-terminal GDPD domain, all
members in this subfamily have a starch binding domain
(CBM20) in the N-terminus, which suggests these proteins
may play a distinct role in glycerol metabolism.
Length = 290
Score = 24.9 bits (55), Expect = 8.9
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 33 WGDDTDMKEMEKQVRAIQMDGLLW 56
WGDD + E K+++ + +DGL++
Sbjct: 264 WGDDLNDPENRKKLKELGVDGLIY 287
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 0.401
Gapped
Lambda K H
0.267 0.0827 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,379,618
Number of extensions: 440232
Number of successful extensions: 406
Number of sequences better than 10.0: 1
Number of HSP's gapped: 402
Number of HSP's successfully gapped: 20
Length of query: 108
Length of database: 10,937,602
Length adjustment: 73
Effective length of query: 35
Effective length of database: 7,699,760
Effective search space: 269491600
Effective search space used: 269491600
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 (24.0 bits)