RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15201
(97 letters)
>gnl|CDD|206670 cd01883, EF1_alpha, Elongation Factor 1-alpha (EF1-alpha) protein
family. EF1 is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to the ribosomes. EF1 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 subfamily is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea
(aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha
interacts with the actin of the eukaryotic cytoskeleton
and may thereby play a role in cellular transformation
and apoptosis. EF-Tu can have no such role in bacteria.
In humans, the isoform eEF1A2 is overexpressed in 2/3 of
breast cancers and has been identified as a putative
oncogene. This subfamily also includes Hbs1, a G protein
known to be important for efficient growth and protein
synthesis under conditions of limiting translation
initiation in yeast, and to associate with Dom34. It has
been speculated that yeast Hbs1 and Dom34 proteins may
function as part of a complex with a role in gene
expression.
Length = 219
Score = 116 bits (292), Expect = 4e-34
Identities = 35/80 (43%), Positives = 50/80 (62%), Gaps = 5/80 (6%)
Query: 13 GVNQLGVVINKLDTVS--WSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTT 70
GV QL V +NK+D V+ WSQ+R+ EI K+ FLK+ G+ D+ ++P SG TG+NL
Sbjct: 136 GVKQLIVAVNKMDDVTVNWSQERYDEIKKKVSPFLKKVGYNPKDVPFIPISGFTGDNLIE 195
Query: 71 PSQVPALTSWYSGPCLLDVI 90
S+ WY GP LL+ +
Sbjct: 196 KSE---NMPWYKGPTLLEAL 212
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 99.3 bits (248), Expect = 3e-26
Identities = 33/78 (42%), Positives = 50/78 (64%), Gaps = 3/78 (3%)
Query: 13 GVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTTPS 72
G+ QL V +NK+D VSW ++RF+EIV+++ LK G+ D+ ++P SG G+NLT S
Sbjct: 144 GIKQLIVAVNKMDLVSWDEERFEEIVSEVSKLLKMVGYNPKDVPFIPISGFKGDNLTKKS 203
Query: 73 QVPALTSWYSGPCLLDVI 90
+ WY GP LL+ +
Sbjct: 204 EN---MPWYKGPTLLEAL 218
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 93.8 bits (234), Expect = 3e-24
Identities = 28/78 (35%), Positives = 48/78 (61%), Gaps = 3/78 (3%)
Query: 13 GVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTTPS 72
G+NQL V INK+D V++ + R++E+ ++ LK G++ DI ++P S G+N+ S
Sbjct: 138 GINQLIVAINKMDAVNYDEKRYEEVKEEVSKLLKMVGYKPDDIPFIPVSAFEGDNVVKKS 197
Query: 73 QVPALTSWYSGPCLLDVI 90
+ WY+GP LL+ +
Sbjct: 198 EN---MPWYNGPTLLEAL 212
>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 = 83.4 bits (206), Expect = 2e-20
Identities = 25/78 (32%), Positives = 46/78 (58%), Gaps = 3/78 (3%)
Query: 13 GVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTTPS 72
G+NQL V INK+D+V++ ++ F+ I ++ +K+ G+ + ++P S G+N+ S
Sbjct: 140 GINQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKVGYNPDTVPFIPISAWNGDNVIKKS 199
Query: 73 QVPALTSWYSGPCLLDVI 90
+ T WY G LL+ +
Sbjct: 200 EN---TPWYKGKTLLEAL 214
>gnl|CDD|206729 cd04166, CysN_ATPS, CysN, together with protein CysD, forms the ATP
sulfurylase (ATPS) complex. CysN_ATPS subfamily. CysN,
together with protein CysD, form the ATP sulfurylase
(ATPS) complex in some bacteria and lower eukaryotes.
ATPS catalyzes the production of ATP sulfurylase (APS)
and pyrophosphate (PPi) from ATP and sulfate. CysD,
which catalyzes ATP hydrolysis, is a member of the ATP
pyrophosphatase (ATP PPase) family. CysN hydrolysis of
GTP is required for CysD hydrolysis of ATP; however,
CysN hydrolysis of GTP is not dependent on CysD
hydrolysis of ATP. CysN is an example of lateral gene
transfer followed by acquisition of new function. In
many organisms, an ATPS exists which is not
GTP-dependent and shares no sequence or structural
similarity to CysN.
Length = 209
Score = 77.6 bits (192), Expect = 3e-19
Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 5/77 (6%)
Query: 13 GVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTTPS 72
G+ + V +NK+D V + ++ F+EI AF G DI ++P S L G+N+ + S
Sbjct: 130 GIRHVVVAVNKMDLVDYDEEVFEEIKADYLAFAASLGIE--DITFIPISALEGDNVVSRS 187
Query: 73 QVPALTSWYSGPCLLDV 89
WY GP LL+
Sbjct: 188 ---ENMPWYKGPTLLEH 201
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 75.9 bits (187), Expect = 1e-17
Identities = 31/80 (38%), Positives = 49/80 (61%), Gaps = 5/80 (6%)
Query: 13 GVNQLGVVINKLD--TVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTT 70
GV Q+ V INK+D TV++SQ+R+ EI ++ A+LK+ G+ + ++P SG G+N+
Sbjct: 144 GVKQMIVCINKMDDKTVNYSQERYDEIKKEVSAYLKKVGYNPEKVPFIPISGWQGDNMIE 203
Query: 71 PSQVPALTSWYSGPCLLDVI 90
S WY GP LL+ +
Sbjct: 204 KS---DNMPWYKGPTLLEAL 220
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 75.4 bits (186), Expect = 1e-17
Identities = 27/81 (33%), Positives = 47/81 (58%), Gaps = 5/81 (6%)
Query: 9 SAVSGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 68
+++ G+ + V +NK+D V +S++ F+ IV AF Q G + D+ ++P S L G+N+
Sbjct: 134 ASLLGIRHVVVAVNKMDLVDYSEEVFEAIVADYLAFAAQLGLK--DVRFIPISALLGDNV 191
Query: 69 TTPSQVPALTSWYSGPCLLDV 89
+ S WY GP LL++
Sbjct: 192 VSKS---ENMPWYKGPTLLEI 209
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 72.3 bits (178), Expect = 2e-16
Identities = 29/77 (37%), Positives = 43/77 (55%), Gaps = 4/77 (5%)
Query: 13 GVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTTPS 72
G+ L V +NK+D V +S++ F+ I F +Q + DI +VP S L G+N+ + S
Sbjct: 159 GIKHLVVAVNKMDLVDYSEEVFERIREDYLTFAEQLP-GNLDIRFVPLSALEGDNVVSQS 217
Query: 73 QVPALTSWYSGPCLLDV 89
WYSGP LL+V
Sbjct: 218 ---ESMPWYSGPTLLEV 231
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 71.5 bits (176), Expect = 4e-16
Identities = 28/76 (36%), Positives = 42/76 (55%), Gaps = 5/76 (6%)
Query: 13 GVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTTPS 72
G+ + + +NK+D V + Q+ F EIV AF + G D+ ++P S L G+N+ T S
Sbjct: 156 GIRHVVLAVNKMDLVDYDQEVFDEIVADYRAFAAKLGL--HDVTFIPISALKGDNVVTRS 213
Query: 73 QVPALTSWYSGPCLLD 88
A WY GP LL+
Sbjct: 214 ---ARMPWYEGPSLLE 226
>gnl|CDD|213679 TIGR02034, CysN, sulfate adenylyltransferase, large subunit.
Metabolic assimilation of sulfur from inorganic sulfate,
requires sulfate activation by coupling to a nucleoside,
for the production of high-energy nucleoside
phosphosulfates. This pathway appears to be similar in
all prokaryotic organisms. Activation is first achieved
through sulfation of sulfate with ATP by sulfate
adenylyltransferase (ATP sulfurylase) to produce
5'-phosphosulfate (APS), coupled by GTP hydrolysis.
Subsequently, APS is phosphorylated by an APS kinase to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In
Escherichia coli, ATP sulfurylase is a heterodimer
composed of two subunits encoded by cysD and cysN, with
APS kinase encoded by cysC. These genes are located in a
unidirectionally transcribed gene cluster, and have been
shown to be required for the synthesis of
sulfur-containing amino acids. Homologous to this E.coli
activation pathway are nodPQH gene products found among
members of the Rhizobiaceae family. These gene products
have been shown to exhibit ATP sulfurase and APS kinase
activity, yet are involved in Nod factor sulfation, and
sulfation of other macromolecules. With members of the
Rhizobiaceae family, nodQ often appears as a fusion of
cysN (large subunit of ATP sulfurase) and cysC (APS
kinase) [Central intermediary metabolism, Sulfur
metabolism].
Length = 406
Score = 64.3 bits (157), Expect = 1e-13
Identities = 27/82 (32%), Positives = 49/82 (59%), Gaps = 5/82 (6%)
Query: 9 SAVSGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 68
+++ G+ + + +NK+D V + ++ F+ I AF +Q GFR D+ ++P S L G+N+
Sbjct: 128 ASLLGIRHVVLAVNKMDLVDYDEEVFENIKKDYLAFAEQLGFR--DVTFIPLSALKGDNV 185
Query: 69 TTPSQVPALTSWYSGPCLLDVI 90
+ S WYSGP LL+++
Sbjct: 186 VSRS---ESMPWYSGPTLLEIL 204
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 57.0 bits (137), Expect = 4e-11
Identities = 29/80 (36%), Positives = 45/80 (56%), Gaps = 5/80 (6%)
Query: 13 GVNQLGVVINKLD--TVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTT 70
GV Q+ NK+D T +S+ R+ EIV ++ ++LK+ G+ I +VP SG G+N+
Sbjct: 144 GVKQMICCCNKMDATTPKYSKARYDEIVKEVSSYLKKVGYNPDKIPFVPISGFEGDNMIE 203
Query: 71 PSQVPALTSWYSGPCLLDVI 90
S WY GP LL+ +
Sbjct: 204 RS---TNLDWYKGPTLLEAL 220
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 47.9 bits (115), Expect = 4e-08
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 19 VVINKLDTVSWSQDRFQEIVTKL-GAFLKQAGFRDSDIEYVPCSGLTGENLTT 70
V INK+D V +E+V ++ L++ GF + VP S LTGE +
Sbjct: 123 VFINKIDRVD--DAELEEVVEEISRELLEKYGFGGETVPVVPGSALTGEGIDE 173
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 38.0 bits (89), Expect = 1e-04
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 5/51 (9%)
Query: 19 VVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFR---DSDIEYVPCSGLTGE 66
V +NK+D V ++ F E++ ++ LK GF D+ +P S LTGE
Sbjct: 119 VAVNKIDRVG--EEDFDEVLREIKELLKLIGFTFLKGKDVPIIPISALTGE 167
>gnl|CDD|206734 cd04171, SelB, SelB, the dedicated elongation factor for delivery
of selenocysteinyl-tRNA to the ribosome. SelB is an
elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 33.0 bits (76), Expect = 0.010
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 13 GVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 68
G+ + VV+ K D V +DR + + ++ L D+ I P S +TGE +
Sbjct: 102 GIKKGLVVLTKADLV--DEDRLELVEEEILELLAGTFLADAPI--FPVSSVTGEGI 153
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 32.4 bits (75), Expect = 0.014
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 6/53 (11%)
Query: 19 VVINKLDTVSWSQ---DRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 68
V INK+D ++ +R + +++LG ++ G D+ VP S TGE +
Sbjct: 106 VAINKIDKPYGTEADPERVKNELSELGLVGEEWG---GDVSIVPISAKTGEGI 155
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 31.9 bits (74), Expect = 0.024
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 8/50 (16%)
Query: 19 VVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 68
+V+NK+D V ++ ++ +L + A E VP S L G+N+
Sbjct: 118 LVLNKIDLVK-DKEELLPLLEELSELMDFA-------EIVPISALKGDNV 159
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 30.9 bits (71), Expect = 0.055
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 12/52 (23%)
Query: 19 VVINKLDTVSWSQD--RFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 68
+V+NK+D V +D E + +L F E P S L GEN+
Sbjct: 116 LVLNKIDLVKDKEDLLPLLEKLKELHPF----------AEIFPISALKGENV 157
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 30.5 bits (70), Expect = 0.068
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 9/50 (18%)
Query: 19 VVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 68
VV+NK+D + ++RF+++ L + P S LTGE L
Sbjct: 119 VVLNKIDLLDA-EERFEKLKELLKEL--------KGKKVFPISALTGEGL 159
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 30.9 bits (71), Expect = 0.076
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 10/50 (20%)
Query: 19 VVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 68
VV+NK+D + ++ +E++ +L L P S LTGE L
Sbjct: 278 VVLNKIDLLD--EEELEELLKELKEAL--------GKPVFPISALTGEGL 317
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 30.5 bits (70), Expect = 0.079
Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 17/65 (26%)
Query: 7 GKSAVSGVNQLGVVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPC---SGL 63
GK+ + +V+NK D V + +E +L L ++Y P S L
Sbjct: 113 GKALI-------IVVNKWDLVEKDEKTMKEFEKELRRKLPF-------LDYAPIVFISAL 158
Query: 64 TGENL 68
TG+ +
Sbjct: 159 TGQGV 163
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 29.5 bits (67), Expect = 0.21
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 4/50 (8%)
Query: 19 VVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 68
+V+NK D V + +E KL L F V S LTG+ L
Sbjct: 294 IVVNKWDLVEEDEATMEEFKKKLRRKLPFLDF----APIVFISALTGQGL 339
>gnl|CDD|236388 PRK09133, PRK09133, hypothetical protein; Provisional.
Length = 472
Score = 29.2 bits (66), Expect = 0.28
Identities = 14/40 (35%), Positives = 16/40 (40%), Gaps = 1/40 (2%)
Query: 30 SQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLT 69
S + A LK AGF D+DIE G NL
Sbjct: 54 STGSTTPAAEAMAARLKAAGFADADIEVTGPYPRKG-NLV 92
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 28.5 bits (65), Expect = 0.38
Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 9/51 (17%)
Query: 19 VVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLT 69
+V+NK+D + ++R + +L A S +TGE L
Sbjct: 276 LVLNKIDLLDEEEEREKRAALELAALGG---------PVFLISAVTGEGLD 317
>gnl|CDD|235738 PRK06199, PRK06199, ornithine cyclodeaminase; Validated.
Length = 379
Score = 28.5 bits (64), Expect = 0.43
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 4/49 (8%)
Query: 27 VSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENLTTPSQVP 75
+W + + +I + R SDI SG TG+ PS P
Sbjct: 198 ATWVAETYPQITNVEVVDSIEEVVRGSDIVTYCNSGETGD----PSTYP 242
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 27.8 bits (62), Expect = 0.93
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 19 VVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 68
V INK+D + DR ++ +++ G + G D +VP S LTG+ +
Sbjct: 192 VAINKIDKPEANPDRVKQELSEYGLVPEDWG---GDTIFVPVSALTGDGI 238
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 27.0 bits (61), Expect = 1.4
Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 13/50 (26%)
Query: 19 VVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 68
VV NK+D +E L F ++ G + P S LTG+ L
Sbjct: 279 VVANKMD-----LPEAEE---NLEEFKEKLG-----PKVFPISALTGQGL 315
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 26.8 bits (60), Expect = 1.5
Identities = 8/31 (25%), Positives = 13/31 (41%)
Query: 38 VTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 68
++L L + PCS +TG+ L
Sbjct: 118 ESELIELLGLESIKGRRWHIQPCSAVTGDGL 148
>gnl|CDD|218067 pfam04402, SIMPL, Protein of unknown function (DUF541). Members
of this family have so far been found in bacteria and
mouse SwissProt or TrEMBL entries. However possible
family members have also been identified in translated
rat (Genbank:AW144450) and human (Genbank:AI478629)
ESTs. A mouse family member has been named SIMPL
(signalling molecule that associates with mouse
pelle-like kinase). SIMPL appears to facilitate and/or
regulate complex formation between IRAK/mPLK (IL-1
receptor-associated kinase) and IKK (inhibitor of
kappa-B kinase) containing complexes, and thus regulate
NF-kappa-B activity. Separate experiments demonstrate
that a mouse family member (named LaXp180) binds the
Listeria monocytogenes surface protein ActA, which is a
virulence factor that induces actin polymerisation. It
may also bind stathmin, a protein involved in signal
transduction and in the regulation of microtubule
dynamics. In bacteria its function is unknown, but it
is thought to be located in the periplasm or outer
membrane.
Length = 210
Score = 26.2 bits (58), Expect = 2.5
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 31 QDRFQEIVTKLGAFLKQAGFRDSDIE 56
+ E + + A LK+AG D DI+
Sbjct: 33 LEEVNERMNAVLAALKKAGIPDKDIQ 58
>gnl|CDD|147203 pfam04914, DltD_C, DltD C-terminal region. DltD is and integral
membrane protein involved in the biosynthesis of
D-alanyl-lipoteichoic acid. This is important in
controlling the net ionic charge in lipoteichoic acid
(LTA). This family is found in bacteria of the
Bacillus/Clostridium group. DltD binds Dcp and ligates
it with D-alanine. DltD does not ligate acyl carrier
protein (ACP) with D-alanine. It also has thioesterase
activity for mischarged D-alanyl-acyl carrier protein
(ACP). DltD is thought to be responsible for
discriminating between Dcp involved in the D-alanylation
of LTA, and ACP involved in fatty acid biosynthesis.
This family consists of the C-terminal region of DltD.
Length = 130
Score = 26.0 bits (58), Expect = 2.7
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 3/34 (8%)
Query: 29 WSQDRFQEIVTKLGAFLKQAGFR--D-SDIEYVP 59
S++ Q+ K+ LK GF D SD Y P
Sbjct: 69 LSKEMRQQYYKKIKYQLKSQGFNIADLSDDGYEP 102
>gnl|CDD|187861 cd09730, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1.
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;
Large proteins, some contain Zn-finger domain; signature
gene for I-A subtype; also known as TM1802 family.
Length = 579
Score = 26.2 bits (58), Expect = 3.1
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 17 LGVVINKLDTVSWSQDRFQEIVTKL 41
LGV++ KL + +S+D + + KL
Sbjct: 490 LGVLVGKLLNIQYSKDENKPFLNKL 514
>gnl|CDD|129923 TIGR00843, benE, benzoate transporter. The benzoate transporter
family contains only a single characterised member, the
benzoate transporter of Acinetobacter calcoaceticus,
which functions as a benzoate/proton symporter
[Transport and binding proteins, Carbohydrates, organic
alcohols, and acids].
Length = 395
Score = 26.1 bits (57), Expect = 3.3
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 62 GLTGENLTTPSQVPALTSWYSGPCLLDVIGLSGLSL 97
++G L+ + P LT+W + L V G G+SL
Sbjct: 68 AVSGIFLSIRFKTPVLTAWSAPGAALLVTGFPGISL 103
>gnl|CDD|147983 pfam06113, BRE, Brain and reproductive organ-expressed protein
(BRE). This family consists of several eukaryotic brain
and reproductive organ-expressed (BRE) proteins. BRE is
a putative stress-modulating gene, found able to
down-regulate TNF-alpha-induced-NF-kappaB activation
upon over expression. A total of six isoforms are
produced by alternative splicing predominantly at either
end of the gene.Compared to normal cells, immortalised
human cell lines uniformly express higher levels of BRE.
Peripheral blood monocytes respond to LPS by
down-regulating the expression of all the BRE
isoforms.It is thought that the function of BRE and its
isoforms is to regulate peroxisomal activities.
Length = 238
Score = 25.8 bits (56), Expect = 3.7
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 5/64 (7%)
Query: 32 DRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGEN---LTTPSQVPALTSWYSG--PCL 86
DRF+ + G LK ++ +P + GE+ L PS + L W +G CL
Sbjct: 54 DRFKLHIPYAGETLKWDIIFNAQYPELPPDFIFGEDADFLPDPSALHHLAQWDAGNPECL 113
Query: 87 LDVI 90
L ++
Sbjct: 114 LLLV 117
>gnl|CDD|215409 PLN02765, PLN02765, pyruvate kinase.
Length = 526
Score = 25.8 bits (57), Expect = 4.7
Identities = 13/36 (36%), Positives = 17/36 (47%)
Query: 20 VINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDI 55
V NK+D +S S R E V + FL G + I
Sbjct: 217 VPNKIDFLSLSYTRHAEDVREAREFLSSLGLSQTQI 252
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 25.3 bits (56), Expect = 5.6
Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 8/50 (16%)
Query: 19 VVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 68
+V+NK+D V S++ KL D+ + S L GE +
Sbjct: 109 LVLNKIDLVPESEEEELLRERKLELLP--------DLPVIAVSALPGEGI 150
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 25.2 bits (56), Expect = 5.8
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 13 GVNQLGVVINKLDTVSWSQ--DRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 68
G+ + +V NK+D VS + + +++I F+K G + +P S L N+
Sbjct: 138 GIKNIVIVQNKIDLVSKERALENYEQIK----EFVK--GTVAENAPIIPVSALHKVNI 189
>gnl|CDD|216094 pfam00747, Viral_DNA_bp, ssDNA binding protein. This protein is
found in herpesviruses and is needed for replication.
Length = 1111
Score = 25.4 bits (56), Expect = 6.2
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 6/54 (11%)
Query: 35 QEIVTKLGAFLKQAGFRDSDIEYVPC-SGLTGENLTTPSQVPALTSWYSGPCLL 87
E + L DSD+ +P GLT E+ + + V T+ Y G +L
Sbjct: 29 LEELALLSL-----RSVDSDVVILPLLRGLTVESDFSTNVVKTPTTGYGGTGVL 77
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 25.1 bits (55), Expect = 6.2
Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 8/50 (16%)
Query: 19 VVINKLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGENL 68
+V NK+D + + V +L + A + S TGE +
Sbjct: 111 LVGNKIDLLE------EREVEELLRLEELAKI--LGVPVFEVSAKTGEGV 152
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 24.9 bits (55), Expect = 6.6
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 19 VVINKLDTVSWSQDRFQEIVTKLG 42
V +NK+D + + EI +LG
Sbjct: 135 VAVNKMDKIKNRDEVLDEIAERLG 158
>gnl|CDD|236328 PRK08662, PRK08662, nicotinate phosphoribosyltransferase; Reviewed.
Length = 343
Score = 24.8 bits (55), Expect = 7.5
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 23 KLDTVSWSQDRFQEIVTKLGAFLKQAGFRDSDI 55
+LDT S + F++IV ++ L G+ I
Sbjct: 232 RLDTPSSRRGNFRKIVREVRWTLDIRGYEHVKI 264
>gnl|CDD|220105 pfam09084, NMT1, NMT1/THI5 like. This family contains the NMT1 and
THI5 proteins. These proteins are proposed to be
required for the biosynthesis of the pyrimidine moiety
of thiamine. They are regulated by thiamine.
Length = 216
Score = 24.8 bits (55), Expect = 8.2
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 6/46 (13%)
Query: 41 LGAFLKQAGFRDSDIEYVPCSGLTGENLTTP---SQVPALTSWYSG 83
L A L +AG SD+ V G +L+ +V A+ Y
Sbjct: 108 LKAMLAKAGGDPSDVTLVNVGGT---SLSPALLTGKVDAVIGGYYN 150
>gnl|CDD|133123 cd06592, GH31_glucosidase_KIAA1161, KIAA1161 is an uncharacterized
Homo sapiens protein with a glycosyl hydrolase family 31
(GH31) domain that is homologous to the Escherichia coli
YihQ glucosidase. Orthologs of KIA1161 are found in
eukaryotes and prokaryotes. In bacteria, YihQ (along
with YihO) is important for bacterial O-antigen capsule
assembly and translocation. Enzymes of the GH31 family
possess a wide range of different hydrolytic activities
including alpha-glucosidase (glucoamylase and
sucrase-isomaltase), alpha-xylosidase,
6-alpha-glucosyltransferase,
3-alpha-isomaltosyltransferase and alpha-1,4-glucan
lyase. All GH31 enzymes cleave a terminal carbohydrate
moiety from a substrate that varies considerably in
size, depending on the enzyme, and may be either a
starch or a glycoprotein.
Length = 303
Score = 24.9 bits (55), Expect = 8.6
Identities = 8/21 (38%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 70 TPSQVPALTSWYSGPC-LLDV 89
+PALT W++G +LD
Sbjct: 114 PSGDIPALTRWWNGTAAVLDF 134
>gnl|CDD|206725 cd04160, Arfrp1, Arf-related protein 1 (Arfrp1). Arfrp1
(Arf-related protein 1), formerly known as ARP, is a
membrane-associated Arf family member that lacks the
N-terminal myristoylation motif. Arfrp1 is mainly
associated with the trans-Golgi compartment and the
trans-Golgi network, where it regulates the targeting of
Arl1 and the GRIP domain-containing proteins, golgin-97
and golgin-245, onto Golgi membranes. It is also
involved in the anterograde transport of the vesicular
stomatitis virus G protein from the Golgi to the plasma
membrane, and in the retrograde transport of TGN38 and
Shiga toxin from endosomes to the trans-Golgi network.
Arfrp1 also inhibits Arf/Sec7-dependent activation of
phospholipase D. Deletion of Arfrp1 in mice causes
embryonic lethality at the gastrulation stage and
apoptosis of mesodermal cells, indicating its importance
in development.
Length = 168
Score = 24.6 bits (54), Expect = 8.6
Identities = 19/62 (30%), Positives = 25/62 (40%), Gaps = 9/62 (14%)
Query: 9 SAVSGVNQLGVVINKLDTVSWSQDRF--QEIVTKLGAFLKQAGFRDSDIEYVPCSGLTGE 66
A+ GV L V+ NK D D EI + G RD ++ P S L GE
Sbjct: 104 EALEGVPLL-VLANKQD----LPDALSVAEIKEVFDDCIALIGRRDCLVQ--PVSALEGE 156
Query: 67 NL 68
+
Sbjct: 157 GV 158
>gnl|CDD|234446 TIGR04043, rSAM_MSMEG_0568, radical SAM protein, MSMEG_0568 family.
Members of this protein family are radical SAM proteins
related to MSMEG_0568 from Mycobacterium smegmatis.
Members occur within 8-gene operons in species as
diverse as M. smegmatis, Rhizobium leguminosarum,
Synechococcus elongatus, and Sorangium cellulosum. The
function of the operon is unknown, but similarity of
MSMEG_0568 to some cofactor biosynthesis radical SAM
proteins suggests a similar biosynthetic function
[Unknown function, Enzymes of unknown specificity].
Length = 354
Score = 24.6 bits (54), Expect = 9.3
Identities = 6/26 (23%), Positives = 11/26 (42%)
Query: 30 SQDRFQEIVTKLGAFLKQAGFRDSDI 55
S ++ + L+ AG +DI
Sbjct: 312 SPAFMADVYQPVAKMLRAAGMSSADI 337
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 0.136 0.417
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,885,708
Number of extensions: 389883
Number of successful extensions: 422
Number of sequences better than 10.0: 1
Number of HSP's gapped: 399
Number of HSP's successfully gapped: 48
Length of query: 97
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 33
Effective length of database: 8,098,946
Effective search space: 267265218
Effective search space used: 267265218
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: 53 (24.1 bits)