RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy104
(86 letters)
>gnl|CDD|201420 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are polypeptides
of 30-65kDa with three characteristic GTPase motifs
(G-1, G-3 and G-4) that are similar to those of the Ras
family. The G-4 motif is strictly conserved with a
unique septin consensus of AKAD. Most septins are
thought to have at least one coiled-coil region, which
in some cases is necessary for intermolecular
interactions that allow septins to polymerise to form
rod-shaped complexes. In turn, these are arranged into
tandem arrays to form filaments. They are
multifunctional proteins, with roles in cytokinesis,
sporulation, germ cell development, exocytosis and
apoptosis.
Length = 280
Score = 105 bits (265), Expect = 1e-29
Identities = 40/72 (55%), Positives = 52/72 (72%)
Query: 8 RQGKTTTIEKKSMDIEERGVKLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDE 67
+ KT I+ +++IEE GVKL LTV+DTPGFGD+I++ W+ YID+QF QY DE
Sbjct: 41 KIKKTVEIKATTVEIEEDGVKLNLTVIDTPGFGDAIDNSNCWKPIVEYIDEQFEQYLRDE 100
Query: 68 SGLNRKNIVDNR 79
S LNR +IVDNR
Sbjct: 101 SRLNRTSIVDNR 112
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated with
diverse processes in dividing and non-dividing cells.
They were first discovered in the budding yeast S.
cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of the
cell cortex and exocytosis. In humans, 12 septin genes
generate dozens of polypeptides, many of which comprise
heterooligomeric complexes. Since septin mutants are
commonly defective in cytokinesis and formation of the
neck formation of the neck filaments/septin rings,
septins have been considered to be the primary
constituents of the neck filaments. Septins belong to
the GTPase superfamily for their conserved GTPase motifs
and enzymatic activities.
Length = 275
Score = 101 bits (253), Expect = 6e-28
Identities = 36/70 (51%), Positives = 48/70 (68%), Gaps = 1/70 (1%)
Query: 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDESGL 70
KT I+ ++EE GVKL+LTV+DTPGFGD+IN+ + W+ YIDDQF Y +ES +
Sbjct: 44 KTVEIKISKAELEENGVKLKLTVIDTPGFGDNINNSDCWKPIVDYIDDQFESYLREESRI 103
Query: 71 NR-KNIVDNR 79
NR + I D R
Sbjct: 104 NRNRRIPDTR 113
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 75.4 bits (186), Expect = 8e-18
Identities = 30/70 (42%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDESGL 70
T I+ ++EE G L LTV+DTPGFGD I++ + W YIDDQF QY ++E +
Sbjct: 64 PTLEIKITKAELEEDGFHLNLTVIDTPGFGDFIDNSKCWEPIVDYIDDQFDQYLDEEQKI 123
Query: 71 NR-KNIVDNR 79
R D R
Sbjct: 124 KRNPKFKDTR 133
>gnl|CDD|206651 cd01852, AIG1, AvrRpt2-Induced Gene 1 (AIG1). This group
represents Arabidoposis protein AIG1 (avrRpt2-induced
gene 1) that appears to be involved in plant resistance
to bacteria. The Arabidopsis disease resistance gene
RPS2 is involved in recognition of bacterial pathogens
carrying the avirulence gene avrRpt2. AIG1 exhibits
RPS2- and avrRpt1-dependent induction early after
infection with Pseudomonas syringae carrying avrRpt2.
This subfamily also includes IAN-4 protein, which has
GTP-binding activity and shares sequence homology with
a novel family of putative GTP-binding proteins: the
immuno-associated nucleotide (IAN) family. The
evolutionary conservation of the IAN family provides a
unique example of a plant pathogen response gene
conserved in animals. The IAN/IMAP subfamily has been
proposed to regulate apoptosis in vertebrates and
angiosperm plants, particularly in relation to cancer,
diabetes, and infections. The human IAN genes were
renamed GIMAP (GTPase of the immunity associated
proteins).
Length = 201
Score = 34.0 bits (79), Expect = 0.003
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 9 QGKTTTIEKKSMDIEERGVKLRLTVVDTPGFGDSINSEESWR 50
G T T +K+S + R R+ V+DTPG D+ S E
Sbjct: 33 SGVTKTCQKESAVWDGR----RVNVIDTPGLFDTSVSPEQLS 70
>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 = 30.1 bits (68), Expect = 0.080
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 2/42 (4%)
Query: 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPGFGDSINSEESWRA 51
G T + ++++ VKL L VDTPG + A
Sbjct: 30 GTTRDPDVYVKELDKGKVKLVL--VDTPGLDEFGGLGREELA 69
>gnl|CDD|185337 PRK15440, PRK15440, L-rhamnonate dehydratase; Provisional.
Length = 394
Score = 28.2 bits (63), Expect = 0.51
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 28 KLRLTVVDTPGFGDSINSE 46
++ +V+D PGFG +N +
Sbjct: 367 RIHKSVLDKPGFGVELNRD 385
>gnl|CDD|237727 PRK14489, PRK14489, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobA/MobB;
Provisional.
Length = 366
Score = 27.0 bits (60), Expect = 1.2
Identities = 12/46 (26%), Positives = 20/46 (43%)
Query: 5 GNNRQGKTTTIEKKSMDIEERGVKLRLTVVDTPGFGDSINSEESWR 50
G + GKTT +EK ++ RG ++ L ++S R
Sbjct: 212 GYSGTGKTTLLEKLIPELIARGYRIGLIKHSHHRVDIDKPGKDSHR 257
>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 = 26.4 bits (59), Expect = 1.6
Identities = 8/38 (21%), Positives = 15/38 (39%), Gaps = 3/38 (7%)
Query: 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPGFGDSINSEE 47
G T +K ++ G + ++DTPG +
Sbjct: 30 GTTRDPVRKEWELLPLG---PVVLIDTPGLDEEGGLGR 64
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 26.1 bits (58), Expect = 2.2
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 5 GNNRQGKTTTIEKKSMDIEERGVKLRLTVVDT 36
G N GKTTTI K + +++ G + + DT
Sbjct: 147 GVNGTGKTTTIAKLAYYLKKNGFSVVIAAGDT 178
>gnl|CDD|218178 pfam04616, Glyco_hydro_43, Glycosyl hydrolases family 43. The
glycosyl hydrolase family 43 contains members that are
arabinanase. Rabinanases hydrolyses the
alpha-1,5-linked L-arabinofuranoside backbone of plant
cell wall arabinans. The structure of arabinanase
Arb43A from Cellvibrio japonicus reveals a five-bladed
beta-propeller fold. A long V-shaped groove, partially
enclosed at one end, forms a single extended
substrate-binding surface across the face of the
propeller.
Length = 284
Score = 26.1 bits (58), Expect = 2.6
Identities = 10/41 (24%), Positives = 15/41 (36%)
Query: 32 TVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDESGLNR 72
V+D D + SW SY D +F Y+ +
Sbjct: 51 HVLDRRSQLDGRGNPNSWAPDISYHDGKFYLYYTAVKVTHG 91
>gnl|CDD|213286 cd05919, BCL_like, Benzoate CoA ligase (BCL) and similar adenylate
forming enzymes. This family contains benzoate CoA
ligase (BCL) and related ligases that catalyze the
acylation of benzoate derivatives, 2-aminobenzoate and
4-hydroxybenzoate. Aromatic compounds represent the
second most abundant class of organic carbon compounds
after carbohydrates. Xenobiotic aromatic compounds are
also a major class of man-made pollutants. Some bacteria
use benzoate as the sole source of carbon and energy
through benzoate degradation. Benzoate degradation
starts with its activation to benzoyl-CoA by benzoate
CoA ligase. The reaction catalyzed by benzoate CoA
ligase proceeds via a two-step process; the first
ATP-dependent step forms an acyl-AMP intermediate, and
the second step forms the acyl-CoA ester with release of
the AMP.
Length = 436
Score = 25.8 bits (57), Expect = 3.5
Identities = 8/29 (27%), Positives = 11/29 (37%)
Query: 23 EERGVKLRLTVVDTPGFGDSINSEESWRA 51
E+ V+L+ VV PG E
Sbjct: 373 EDGLVRLKAFVVPRPGEAIQQLLERDLHR 401
>gnl|CDD|193570 cd08659, M20_ArgE_DapE_like, Peptidase M20 acetylornithine
deacetylase/succinyl-diaminopimelate desuccinylase
(ArgE/DapE)-like. Peptidase M20 acetylornithine
deacetylase/succinyl-diaminopimelate desuccinylase
(ArgE/DapE) like family of enzymes catalyze analogous
reactions and share a common activator, the metal ion
(usually Co2+ or Zn2+). ArgE catalyzes a broad range of
substrates, including N-acetylornithine,
alpha-N-acetylmethionine and alpha-N-formylmethionine,
while DapE catalyzes the hydrolysis of
N-succinyl-L,L-diaminopimelate (L,L-SDAP) to
L,L-diaminopimelate and succinate. Proteins in this
family are mostly bacterial and have been inferred by
homology as being related to both, ArgE and DapE. This
family also includes N-acetyl-L-citrulline deacetylase
(ACDase; acetylcitrulline deacetylase), a unique, novel
enzyme found in Xanthomonas campestris, a plant
pathogen, in which N-acetyl-L-ornithine is the
substrate for transcarbamoylation reaction, and the
product is N-acetyl-L-citrulline. Thus, in the arginine
biosynthesis pathway, ACDase subsequently catalyzes the
hydrolysis of N-acetyl-L-citrulline to acetate and
L-citrulline.
Length = 365
Score = 25.3 bits (56), Expect = 4.4
Identities = 8/40 (20%), Positives = 12/40 (30%), Gaps = 4/40 (10%)
Query: 41 DSINSEESWRACCSYIDDQFRQY-FN---DESGLNRKNIV 76
S+N Y+ + DE R N+V
Sbjct: 10 PSVNPPGGEAEVADYLAELLEDLGIPVEVDEVAPGRPNLV 49
>gnl|CDD|206738 cd08771, DLP_1, Dynamin_like protein family includes dynamins and
Mx proteins. The dynamin family of large
mechanochemical GTPases includes the classical dynamins
and dynamin-like proteins (DLPs) that are found
throughout the Eukarya. These proteins catalyze membrane
fission during clathrin-mediated endocytosis. Dynamin
consists of five domains; an N-terminal G domain that
binds and hydrolyzes GTP, a middle domain (MD) involved
in self-assembly and oligomerization, a pleckstrin
homology (PH) domain responsible for interactions with
the plasma membrane, GED, which is also involved in
self-assembly, and a proline arginine rich domain (PRD)
that interacts with SH3 domains on accessory proteins.
To date, three vertebrate dynamin genes have been
identified; dynamin 1, which is brain specific, mediates
uptake of synaptic vesicles in presynaptic terminals;
dynamin-2 is expressed ubiquitously and similarly
participates in membrane fission; mutations in the MD,
PH and GED domains of dynamin 2 have been linked to
human diseases such as Charcot-Marie-Tooth peripheral
neuropathy and rare forms of centronuclear myopathy.
Dynamin 3 participates in megakaryocyte progenitor
amplification, and is also involved in cytoplasmic
enlargement and the formation of the demarcation
membrane system. This family also includes
interferon-induced Mx proteins that inhibit a wide range
of viruses by blocking an early stage of the replication
cycle. Dynamin oligomerizes into helical structures
around the neck of budding vesicles in a GTP
hydrolysis-dependent manner.
Length = 278
Score = 25.3 bits (56), Expect = 4.6
Identities = 9/21 (42%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 19 SMDIEERGVKLRLTVVDTPGF 39
++IE V LT+VD PG
Sbjct: 101 RLEIESPDV-PNLTLVDLPGL 120
>gnl|CDD|224017 COG1092, COG1092, Predicted SAM-dependent methyltransferases
[General function prediction only].
Length = 393
Score = 25.0 bits (55), Expect = 5.3
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 9 QGKTTTIEKKSMDIEERGVKLRLTVVD 35
Q + + IEE GVK + +VD
Sbjct: 169 QYLKGEEAPEEVVIEENGVKFLVDLVD 195
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The
dynamin family of large mechanochemical GTPases
includes the classical dynamins and dynamin-like
proteins (DLPs) that are found throughout the Eukarya.
This family also includes bacterial DLPs. These
proteins catalyze membrane fission during
clathrin-mediated endocytosis. Dynamin consists of five
domains; an N-terminal G domain that binds and
hydrolyzes GTP, a middle domain (MD) involved in
self-assembly and oligomerization, a pleckstrin
homology (PH) domain responsible for interactions with
the plasma membrane, GED, which is also involved in
self-assembly, and a proline arginine rich domain (PRD)
that interacts with SH3 domains on accessory proteins.
To date, three vertebrate dynamin genes have been
identified; dynamin 1, which is brain specific,
mediates uptake of synaptic vesicles in presynaptic
terminals; dynamin-2 is expressed ubiquitously and
similarly participates in membrane fission; mutations
in the MD, PH and GED domains of dynamin 2 have been
linked to human diseases such as Charcot-Marie-Tooth
peripheral neuropathy and rare forms of centronuclear
myopathy. Dynamin 3 participates in megakaryocyte
progenitor amplification, and is also involved in
cytoplasmic enlargement and the formation of the
demarcation membrane system. This family also includes
mitofusins (MFN1 and MFN2 in mammals) that are involved
in mitochondrial fusion. Dynamin oligomerizes into
helical structures around the neck of budding vesicles
in a GTP hydrolysis-dependent manner.
Length = 180
Score = 24.4 bits (54), Expect = 7.4
Identities = 6/19 (31%), Positives = 9/19 (47%)
Query: 31 LTVVDTPGFGDSINSEESW 49
+ +VDTPG +I
Sbjct: 48 VVLVDTPGLNSTIEHHTEI 66
>gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an
ATPase enzyme and as a kinase, and phosphorylates
periplasmic binding proteins involved in the LAO
(lysine, arginine, ornithine)/AO transport systems.
Length = 267
Score = 24.6 bits (54), Expect = 8.3
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 10 GKTTTIEKKSMDIEERGVKLRLTVVD--TPGFGDSI 43
GK+T IE M++ RG ++ + VD +P G SI
Sbjct: 41 GKSTLIEALGMELRRRGHRVAVLAVDPSSPFTGGSI 76
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 24.6 bits (54), Expect = 9.5
Identities = 7/29 (24%), Positives = 12/29 (41%), Gaps = 4/29 (13%)
Query: 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPG 38
G T + + + K T++D PG
Sbjct: 70 GVTIDVAHSKFETD----KYNFTIIDAPG 94
>gnl|CDD|129833 TIGR00750, lao, LAO/AO transport system ATPase. In E. coli,
mutation of this kinase blocks phosphorylation of two
transporter system periplasmic binding proteins and
consequently inhibits those transporters. This kinase
is also found in Gram-positive bacteria, archaea, and
the roundworm C. elegans. It may have a more general,
but still unknown function. Mutations have also been
found that do not phosphorylate the periplasmic binding
proteins, yet still allow transport. The ATPase
activity of this protein seems to be necessary, however
[Transport and binding proteins, Amino acids, peptides
and amines, Regulatory functions, Protein
interactions].
Length = 300
Score = 24.3 bits (53), Expect = 9.8
Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 10 GKTTTIEKKSMDIEERGVKLRLTVVD--TPGFGDSI 43
GK+T +E M++ RG+++ + VD +P G SI
Sbjct: 46 GKSTLLEALGMELRRRGLRVAVIAVDPSSPFTGGSI 81
>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 = 24.0 bits (53), Expect = 9.9
Identities = 13/61 (21%), Positives = 19/61 (31%), Gaps = 32/61 (52%)
Query: 10 GKTTTIEK-------------------KSMDIE-ERGV------------KLRLTVVDTP 37
GKTT + + E ERG+ K + ++DTP
Sbjct: 15 GKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVSFETKKRLINIIDTP 74
Query: 38 G 38
G
Sbjct: 75 G 75
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
0.313 0.131 0.375
Gapped
Lambda K H
0.267 0.0725 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,250,057
Number of extensions: 330727
Number of successful extensions: 342
Number of sequences better than 10.0: 1
Number of HSP's gapped: 342
Number of HSP's successfully gapped: 30
Length of query: 86
Length of database: 10,937,602
Length adjustment: 54
Effective length of query: 32
Effective length of database: 8,542,486
Effective search space: 273359552
Effective search space used: 273359552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.2 bits)