RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11649
(890 letters)
>gnl|CDD|206701 cd04128, Spg1, Septum-promoting GTPase (Spg1). Spg1p. Spg1p
(septum-promoting GTPase) was first identified in the
fission yeast S. pombe, where it regulates septum
formation in the septation initiation network (SIN)
through the cdc7 protein kinase. Spg1p is an essential
gene that localizes to the spindle pole bodies. When
GTP-bound, it binds cdc7 and causes it to translocate to
spindle poles. Sid4p (septation initiation defective) is
required for localization of Spg1p to the spindle pole
body, and the ability of Spg1p to promote septum
formation from any point in the cell cycle depends on
Sid4p. Spg1p is negatively regulated by Byr4 and cdc16,
which form a two-component GTPase activating protein
(GAP) for Spg1p. The existence of a SIN-related pathway
in plants has been proposed. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization.
Length = 182
Score = 39.3 bits (92), Expect = 0.003
Identities = 48/190 (25%), Positives = 79/190 (41%), Gaps = 56/190 (29%)
Query: 40 LIGTKSVGKSTLVFRFLE--KNDTPKPTLALEY----IYARKSGKTVMKDICHLWELGSG 93
L+G +GK++L+ +++E ++ TL + + I R G + I W+LG
Sbjct: 5 LLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIR--GTEITFSI---WDLGGQ 59
Query: 94 TSRLEVASLFSSFSLTAQSGFTLVLMLDLSR---LNSLWTEAETFLAKFRAIFESNESVR 150
+ + L ++ ++ M DL+R LNS+ E R
Sbjct: 60 REFINMLPLVCKDAV------AILFMFDLTRKSTLNSI-----------------KEWYR 96
Query: 151 EKRGSFEHFRTADEHRDKGLIRTFPVPLILIGGKYDLFENLEPNKKR-IAVQCLRYLAHV 209
+ RG +TA P IL+G KYDLF +L P ++ I Q +Y A
Sbjct: 97 QARG---FNKTA-----------IP---ILVGTKYDLFADLPPEEQEEITKQARKY-AKA 138
Query: 210 NGASLLFHSS 219
A L+F S+
Sbjct: 139 MKAPLIFCST 148
Score = 37.4 bits (87), Expect = 0.014
Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 510 ILIGGKYDLFENLEPNKKR-IAVQCLRYLAHVNGASLLFHSS 550
IL+G KYDLF +L P ++ I Q +Y A A L+F S+
Sbjct: 108 ILVGTKYDLFADLPPEEQEEITKQARKY-AKAMKAPLIFCST 148
Score = 37.4 bits (87), Expect = 0.014
Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 723 ILIGGKYDLFENLEPNKKR-IAVQCLRYLAHVNGASLLFHSS 763
IL+G KYDLF +L P ++ I Q +Y A A L+F S+
Sbjct: 108 ILVGTKYDLFADLPPEEQEEITKQARKY-AKAMKAPLIFCST 148
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 36.5 bits (85), Expect = 0.013
Identities = 26/151 (17%), Positives = 49/151 (32%), Gaps = 35/151 (23%)
Query: 32 QSQERTLLLIGTKSVGKSTLVFRFLEKNDTPKPTLALEYIYARKSGKTVMKDICHLWELG 91
+ +L G GK+TL+ R + P + + + K +++ I LG
Sbjct: 1 RRGAGIGVLTGESGSGKTTLLRRLARQL--PNRRVVYVEAPSLGTPKDLLRKILR--ALG 56
Query: 92 SGTSRLEVASLFSSFSLTAQSGFTLVLMLDLSRLNSLWTEAETFLAKFRAIFESNESVRE 151
S A L + + +L++D EA+
Sbjct: 57 LPLSGGTTAELLEAILDALKRRGRPLLIID---------EAQ----------------HL 91
Query: 152 KRGSFEHFRTADEHRDKGLIRTFPVPLILIG 182
+ E R + +KG + +IL+G
Sbjct: 92 SLEALEELRDLYDLSEKG------IQVILVG 116
>gnl|CDD|129583 TIGR00492, alr, alanine racemase. This enzyme interconverts
L-alanine and D-alanine. Its primary function is to
generate D-alanine for cell wall formation. With
D-alanine-D-alanine ligase, it makes up the D-alanine
branch of the peptidoglycan biosynthetic route. It is a
monomer with one pyridoxal phosphate per subunit. In E.
coli, the ortholog is duplicated so that a second
isozyme, DadX, is present. DadX, a paralog of the
biosynthetic Alr, is induced by D- or L-alanine and is
involved in catabolism [Cell envelope, Biosynthesis and
degradation of murein sacculus and peptidoglycan].
Length = 367
Score = 37.7 bits (88), Expect = 0.026
Identities = 29/111 (26%), Positives = 41/111 (36%), Gaps = 12/111 (10%)
Query: 56 LEKNDTPKPTLALEYIYARKSGKTVMKDICHLWELGSGTSRLEVASLFSSFSLTAQSGFT 115
L K P L L +A +K + W+L + +E L
Sbjct: 68 LRKAGITAPILLLGGFFAED-----LKILAA-WDLTTTVHSVEQLQALEEALLKEPKRLK 121
Query: 116 LVLMLD--LSRLNSLWTEAETFLAKFRAIFESNESVREKRGSFEHFRTADE 164
+ L +D ++RL EA F+ K R + E G F HF TADE
Sbjct: 122 VHLKIDTGMNRLGVKPDEAALFVQKLRQ----LKKFLELEGIFSHFATADE 168
Score = 32.3 bits (74), Expect = 1.2
Identities = 22/79 (27%), Positives = 31/79 (39%), Gaps = 6/79 (7%)
Query: 396 WELGSGTSRLEVASLFSSFSLTAQSGFTLVLMLD--LSRLNSLWTEAETFLAKFRAIFES 453
W+L + +E L + L +D ++RL EA F+ K R
Sbjct: 94 WDLTTTVHSVEQLQALEEALLKEPKRLKVHLKIDTGMNRLGVKPDEAALFVQKLRQ---- 149
Query: 454 NESVREKRGSFEHFRTADE 472
+ E G F HF TADE
Sbjct: 150 LKKFLELEGIFSHFATADE 168
>gnl|CDD|206659 cd01867, Rab8_Rab10_Rab13_like, Rab GTPase families 8, 10, 13
(Rab8, Rab10, Rab13). Rab8/Sec4/Ypt2 are known or
suspected to be involved in post-Golgi transport to the
plasma membrane. It is likely that these Rabs have
functions that are specific to the mammalian lineage
and have no orthologs in plants. Rab8 modulates
polarized membrane transport through reorganization of
actin and microtubules, induces the formation of new
surface extensions, and has an important role in
directed membrane transport to cell surfaces. The Ypt2
gene of the fission yeast Schizosaccharomyces pombe
encodes a member of the Ypt/Rab family of small
GTP-binding proteins, related in sequence to Sec4p of
Saccharomyces cerevisiae but closer to mammalian Rab8.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Due to the presence
of truncated sequences in this CD, the lipid
modification site is not available for annotation.
Length = 167
Score = 33.8 bits (78), Expect = 0.17
Identities = 14/25 (56%), Positives = 16/25 (64%)
Query: 38 LLLIGTKSVGKSTLVFRFLEKNDTP 62
LLLIG VGKS L+ RF E + P
Sbjct: 6 LLLIGDSGVGKSCLLLRFSEDSFNP 30
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small
guanosine triphosphatases (GTPases). Rab GTPases form
the largest family within the Ras superfamily. There
are at least 60 Rab genes in the human genome, and a
number of Rab GTPases are conserved from yeast to
humans. Rab GTPases are small, monomeric proteins that
function as molecular switches to regulate vesicle
trafficking pathways. The different Rab GTPases are
localized to the cytosolic face of specific
intracellular membranes, where they regulate distinct
steps in membrane traffic pathways. In the GTP-bound
form, Rab GTPases recruit specific sets of effector
proteins onto membranes. Through their effectors, Rab
GTPases regulate vesicle formation, actin- and
tubulin-dependent vesicle movement, and membrane
fusion. GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular
organisms possess 5-20 Rab members, several have been
found to possess 60 or more Rabs; for many of these Rab
isoforms, homologous proteins are not found in other
organisms. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins. Since crystal structures often lack
C-terminal residues, the lipid modification site is not
available for annotation in many of the CDs in the
hierarchy, but is included where possible.
Length = 159
Score = 33.2 bits (77), Expect = 0.27
Identities = 11/35 (31%), Positives = 24/35 (68%), Gaps = 2/35 (5%)
Query: 38 LLLIGTKSVGKSTLVFRFLEK--NDTPKPTLALEY 70
++LIG VGK++L+ RF++ ++ K T+ +++
Sbjct: 3 IVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDF 37
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 33.8 bits (77), Expect = 0.30
Identities = 31/163 (19%), Positives = 54/163 (33%), Gaps = 48/163 (29%)
Query: 35 ERTLLLIGTKSVGKSTLVFRFLE----KNDTP---KPTLALEYIYARKSGKTVMKDICHL 87
E ++++G VGK+TL+ R + + P A R++ K + D
Sbjct: 5 EFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDT--- 61
Query: 88 WELGSGTSRLEVASLFSSFSLTAQSGFTLVLMLDLSRLNSLWTEAETFLAKFRAIFESNE 147
+G SL + A ++++ D + S S+E
Sbjct: 62 ----AGQEEYR--SLRPEYYRGAN---GILIVYDSTLRES-----------------SDE 95
Query: 148 SVREKRGSFEHFRTADEHRDKGLIRTFPVPLILIGGKYDLFEN 190
E D VP++L+G K DLF+
Sbjct: 96 LTEEWLEELRELAPDD------------VPILLVGNKIDLFDE 126
>gnl|CDD|215692 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac,
Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with
GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025,
pfam00063. As regards Rab GTPases, these are important
regulators of vesicle formation, motility and fusion.
They share a fold in common with all Ras GTPases: this
is a six-stranded beta-sheet surrounded by five
alpha-helices.
Length = 162
Score = 32.9 bits (76), Expect = 0.38
Identities = 41/161 (25%), Positives = 62/161 (38%), Gaps = 57/161 (35%)
Query: 38 LLLIGTKSVGKSTLVFRFLEK--NDTPKPTLALEYIYARKS----GKTVMKDICHLWELG 91
L+L+G VGKS+L+ RF + + PT+ ++ + K+ GKTV I W+
Sbjct: 2 LVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVD--FYTKTIEVDGKTVKLQI---WD-- 54
Query: 92 SGTSRLE-VASLFSSFSLTAQSGFTLVLMLDLSRLNSLWTEAETFLAKFRAIFESNESVR 150
T+ E +L + AQ GF LV +
Sbjct: 55 --TAGQERFRALRPLYYRGAQ-GFLLVYDIT----------------------------- 82
Query: 151 EKRGSFEH----FRTADEHRDKGLIRTFPVPLILIGGKYDL 187
R SFE+ H D+ VP++L+G K DL
Sbjct: 83 -SRDSFENVKKWLEEILRHADEN------VPIVLVGNKCDL 116
>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 = 31.3 bits (71), Expect = 1.1
Identities = 20/117 (17%), Positives = 33/117 (28%), Gaps = 27/117 (23%)
Query: 39 LLIGTKSVGKSTLVFRFLEKN-----DTPKPTLALEYIYARKSGKTV---------MKDI 84
+++G VGKS+L+ L D P T + V + +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEF 60
Query: 85 CHLWELGSGTSRLEVASLFSSFSLTAQSGFTLVLMLDLSRLNSLWTEAETFLAKFRA 141
L L A L +L++D + S L + R
Sbjct: 61 GGLGREELARLLLRGADLI-------------LLVVDSTDRESEEDAKLLILRRLRK 104
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 31.3 bits (72), Expect = 1.2
Identities = 12/35 (34%), Positives = 23/35 (65%), Gaps = 2/35 (5%)
Query: 38 LLLIGTKSVGKSTLVFRFLEK--NDTPKPTLALEY 70
++LIG VGKS+L+ RF + ++ K T+ +++
Sbjct: 3 IILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDF 37
>gnl|CDD|218093 pfam04453, OstA_C, Organic solvent tolerance protein. Family
involved in organic solvent tolerance in bacteria. The
region contains several highly conserved, potentially
catalytic, residues.
Length = 385
Score = 32.0 bits (73), Expect = 1.5
Identities = 14/70 (20%), Positives = 25/70 (35%), Gaps = 4/70 (5%)
Query: 576 VNFDYNKPIFVPFGTDSVASIEGTTQYVTADTEVGRKHLTTKYSSNSALGLMNDNPLWIV 635
++++Y P G D +QY ++ T+ L L P +
Sbjct: 90 LDYNYYLPDLFLGGLD----FSFDSQYRNFARRDDQQPNGTRLHLEPELSLPFSTPWGFL 145
Query: 636 IPKLGLHNTH 645
P+L L T+
Sbjct: 146 TPELSLRGTY 155
>gnl|CDD|206657 cd01865, Rab3, Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C
and Rab3D. The Rab3 subfamily contains Rab3A, Rab3B,
Rab3C, and Rab3D. All four isoforms were found in mouse
brain and endocrine tissues, with varying levels of
expression. Rab3A, Rab3B, and Rab3C localized to
synaptic and secretory vesicles; Rab3D was expressed at
high levels only in adipose tissue, exocrine glands,
and the endocrine pituitary, where it is localized to
cytoplasmic secretory granules. Rab3 appears to control
Ca2+-regulated exocytosis. The appropriate GDP/GTP
exchange cycle of Rab3A is required for Ca2+-regulated
exocytosis to occur, and interaction of the GTP-bound
form of Rab3A with effector molecule(s) is widely
believed to be essential for this process.
Functionally, most studies point toward a role for Rab3
in the secretion of hormones and neurotransmitters.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Due to the presence
of truncated sequences in this CD, the lipid
modification site is not available for annotation.
Length = 165
Score = 30.7 bits (69), Expect = 2.1
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 38 LLLIGTKSVGKSTLVFRFLEKNDTP 62
LL+IG SVGK++ +FR+ + + T
Sbjct: 4 LLIIGNSSVGKTSFLFRYADDSFTS 28
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 29.7 bits (67), Expect = 2.7
Identities = 21/118 (17%), Positives = 44/118 (37%), Gaps = 18/118 (15%)
Query: 38 LLLIGTKSVGKSTLVFRFL------EKNDTPKPTLALEYIYARKSGKTVMKDICHLWELG 91
+++IG K GKS+L+ + + E + TLA++ + + ++W+ G
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVD-----GDTGLLNIWDFG 56
Query: 92 SGTSRLEVASLFSSFSLTAQSGFTLVLMLDLSRLNSLWTEAETFLAKFRAIFESNESV 149
E + +L+ DL+ SL E +A + + +
Sbjct: 57 G----REELKFEHIIFMKWADAI--LLVYDLTDRESL-NEVSRLIAWLPNLRKLGGKI 107
>gnl|CDD|206653 cd01860, Rab5_related, Rab-related GTPase family includes Rab5
and Rab22; regulates early endosome fusion. The
Rab5-related subfamily includes Rab5 and Rab22 of
mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of
plants. The members of this subfamily are involved in
endocytosis and endocytic-sorting pathways. In mammals,
Rab5 GTPases localize to early endosomes and regulate
fusion of clathrin-coated vesicles to early endosomes
and fusion between early endosomes. In yeast, Ypt51p
family members similarly regulate membrane trafficking
through prevacuolar compartments. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 163
Score = 30.2 bits (69), Expect = 3.0
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 38 LLLIGTKSVGKSTLVFRF 55
L+L+G SVGKS++V RF
Sbjct: 4 LVLLGDSSVGKSSIVLRF 21
>gnl|CDD|206656 cd01863, Rab18, Rab GTPase family 18 (Rab18). Rab18 subfamily.
Mammalian Rab18 is implicated in endocytic transport
and is expressed most highly in polarized epithelial
cells. However, trypanosomal Rab, TbRAB18, is
upregulated in the BSF (Blood Stream Form) stage and
localized predominantly to elements of the Golgi
complex. In human and mouse cells, Rab18 has been
identified in lipid droplets, organelles that store
neutral lipids. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins. Due to the presence of truncated sequences in
this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 30.0 bits (68), Expect = 3.1
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 38 LLLIGTKSVGKSTLVFRFLE 57
+LLIG VGKS+L+ RF +
Sbjct: 3 ILLIGDSGVGKSSLLLRFTD 22
>gnl|CDD|206709 cd04137, RheB, Ras Homolog Enriched in Brain (RheB) is a small
GTPase. Rheb (Ras Homolog Enriched in Brain)
subfamily. Rheb was initially identified in rat brain,
where its expression is elevated by seizures or by
long-term potentiation. It is expressed ubiquitously,
with elevated levels in muscle and brain. Rheb
functions as an important mediator between the tuberous
sclerosis complex proteins, TSC1 and TSC2, and the
mammalian target of rapamycin (TOR) kinase to stimulate
cell growth. TOR kinase regulates cell growth by
controlling nutrient availability, growth factors, and
the energy status of the cell. TSC1 and TSC2 form a
dimeric complex that has tumor suppressor activity, and
TSC2 is a GTPase activating protein (GAP) for Rheb. The
TSC1/TSC2 complex inhibits the activation of TOR kinase
through Rheb. Rheb has also been shown to induce the
formation of large cytoplasmic vacuoles in a process
that is dependent on the GTPase cycle of Rheb, but
independent of the TOR kinase, suggesting Rheb plays a
role in endocytic trafficking that leads to cell growth
and cell-cycle progression. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of
most Ras proteins.
Length = 180
Score = 29.9 bits (68), Expect = 3.5
Identities = 10/23 (43%), Positives = 19/23 (82%)
Query: 35 ERTLLLIGTKSVGKSTLVFRFLE 57
+R + ++G++SVGKS+L +F+E
Sbjct: 1 QRKIAVLGSRSVGKSSLTVQFVE 23
>gnl|CDD|133319 cd04119, RJL, Rab GTPase family J-like (RabJ-like). RJLs are found
in many protists and as chimeras with C-terminal DNAJ
domains in deuterostome metazoa. They are not found in
plants, fungi, and protostome metazoa, suggesting a
horizontal gene transfer between protists and
deuterostome metazoa. RJLs lack any known membrane
targeting signal and contain a degenerate
phosphate/magnesium-binding 3 (PM3) motif, suggesting an
impaired ability to hydrolyze GTP. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization.
Length = 168
Score = 29.6 bits (67), Expect = 3.9
Identities = 25/110 (22%), Positives = 46/110 (41%), Gaps = 19/110 (17%)
Query: 38 LLLIGTKSVGKSTLVFRFLEKNDTPK--PTLALEYIYARKS--GKTVMKDICHLWELGSG 93
++ +G VGKS ++ R+ E K PT+ ++Y + S K V + ++L
Sbjct: 3 VISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNF---FDLSGH 59
Query: 94 TSRLEVASLFSSFSLTAQSGFTLVLMLDLSR------LNSLWTEAETFLA 137
LEV + F Q ++L+ D++ L+S E +
Sbjct: 60 PEYLEVRNEFYK---DTQG---VLLVYDVTDRQSFEALDSWLKEMKQEGG 103
>gnl|CDD|206689 cd04102, RabL3, Rab GTPase-like family 3 (Rab-like3). RabL3
(Rab-like3) subfamily. RabL3s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL3 lacks a prenylation site at the
C-terminus. The specific function of RabL3 remains
unknown.
Length = 204
Score = 29.9 bits (67), Expect = 4.0
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 481 TFPVPLILIGGKYDLFEDKGLIRTFPVPLILIGGKYD 517
TFP L++ G YD + G PVPL++IG K D
Sbjct: 112 TFPAGLLVTNGDYDSEQFAGN----PVPLLVIGTKLD 144
Score = 29.9 bits (67), Expect = 4.0
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 694 TFPVPLILIGGKYDLFEDKGLIRTFPVPLILIGGKYD 730
TFP L++ G YD + G PVPL++IG K D
Sbjct: 112 TFPAGLLVTNGDYDSEQFAGN----PVPLLVIGTKLD 144
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 29.8 bits (67), Expect = 4.1
Identities = 33/157 (21%), Positives = 59/157 (37%), Gaps = 47/157 (29%)
Query: 38 LLLIGTKSVGKSTLVFRFLEKNDTPKPTLALEYIYARKSGKTVMKDICHLWELGSGTSRL 97
L+ +G VGK+ L+ RFL DT +P K +TV + +E+ +
Sbjct: 2 LVFMGAAGVGKTALIQRFL--YDTFEP----------KHRRTVEELHSKEYEVAGVKVTI 49
Query: 98 EVASLFSSFS------LTAQSGFTLVLMLDLSRLNSLWTEAETFLAKFRAIFESNESVRE 151
++ S+S L+ Q+G L+ + + E+ FE + +RE
Sbjct: 50 DILDTSGSYSFPAMRKLSIQNGDAFALVYSV-------DDPES--------FEEVKRLRE 94
Query: 152 KRGSFEHFRTADEHRDKGLIRTFPVPLILIGGKYDLF 188
+ K VP++++G K D
Sbjct: 95 -----------EILEVKE---DKFVPIVVVGNKIDSL 117
>gnl|CDD|206661 cd01869, Rab1_Ypt1, Rab GTPase family 1 includes the yeast
homolog Ypt1. Rab1/Ypt1 subfamily. Rab1 is found in
every eukaryote and is a key regulatory component for
the transport of vesicles from the ER to the Golgi
apparatus. Studies on mutations of Ypt1, the yeast
homolog of Rab1, showed that this protein is necessary
for the budding of vesicles of the ER as well as for
their transport to, and fusion with, the Golgi
apparatus. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Due to the presence
of truncated sequences in this CD, the lipid
modification site is not available for annotation.
Length = 166
Score = 29.6 bits (67), Expect = 4.1
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 38 LLLIGTKSVGKSTLVFRF 55
LLLIG VGKS L+ RF
Sbjct: 5 LLLIGDSGVGKSCLLLRF 22
>gnl|CDD|133311 cd04111, Rab39, Rab GTPase family 39 (Rab39). Found in
eukaryotes, Rab39 is mainly found in epithelial cell
lines, but is distributed widely in various human
tissues and cell lines. It is believed to be a novel
Rab protein involved in regulating Golgi-associated
vesicular transport during cellular endocytosis. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins.
Length = 211
Score = 29.7 bits (67), Expect = 4.8
Identities = 14/39 (35%), Positives = 26/39 (66%), Gaps = 3/39 (7%)
Query: 38 LLLIGTKSVGKSTLVFRFLEKN--DTPKPTLALEYIYAR 74
L++IG +VGKS+L+ RF E + PT+ +++ ++R
Sbjct: 5 LIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDF-FSR 42
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 29.4 bits (66), Expect = 5.9
Identities = 41/159 (25%), Positives = 67/159 (42%), Gaps = 39/159 (24%)
Query: 31 IQSQERTLLLIGTKSVGKSTLVFRFLEKN--DTPKPTLALEYIYARKSGKTVMKDICHLW 88
+ S E L+++G VGKS L +F++ + D PT+ Y RK + ++ C L
Sbjct: 1 MASTEYKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSY---RKQ-CVIDEETC-LL 55
Query: 89 ELGSGTSRLEVASLFSSFSLTAQSGFTLVLMLDLSRLNSLWTEAETFLAKFRAIFESNES 148
++ + E +++ + T Q GF V ++ +S FE S
Sbjct: 56 DILDTAGQEEYSAMRDQYMRTGQ-GFLCV--YSITSRSS---------------FEEIAS 97
Query: 149 VREKRGSFEHFRTADEHRDKGLIRTFPVPLILIGGKYDL 187
RE + R D+ R VP+IL+G K DL
Sbjct: 98 FRE-----QILRVKDKDR---------VPMILVGNKCDL 122
>gnl|CDD|179803 PRK04260, PRK04260, acetylornithine aminotransferase; Provisional.
Length = 375
Score = 29.8 bits (67), Expect = 6.4
Identities = 24/103 (23%), Positives = 36/103 (34%), Gaps = 24/103 (23%)
Query: 418 AQSGFTLVLMLDLSRLNSLWTEAETFLAKFRAIFESNESVREKRG---------SFEHFR 468
A + TL +ML L + + + E+V RG + + +
Sbjct: 272 AAASATLDIMLTAGFLEQALENGNYLQEQLQKALQDKETVTTVRGLGYMIGIETTADLSQ 331
Query: 469 TADEHRDKGLIRTFPVPLILIGGKYDLFEDKGLIRTFPVPLIL 511
+ RDKGLI +L G +IR P PL L
Sbjct: 332 LVEAARDKGLI-------VLTAG-------TNVIRLLP-PLTL 359
>gnl|CDD|214541 smart00173, RAS, Ras subfamily of RAS small GTPases. Similar in
fold and function to the bacterial EF-Tu GTPase. p21Ras
couples receptor Tyr kinases and G protein receptors to
protein kinase cascades.
Length = 164
Score = 29.1 bits (66), Expect = 6.8
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 666 ILKWVVSSRGSFEHFRTADEH--RDKGLIRTFPVPLILIGGKYDL 708
+L + ++ R SFE + E R K VP++L+G K DL
Sbjct: 76 LLVYSITDRQSFEEIKKFREQILRVKDRDD---VPIVLVGNKCDL 117
>gnl|CDD|197466 smart00010, small_GTPase, Small GTPase of the Ras superfamily;
ill-defined subfamily. SMART predicts Ras-like small
GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies.
Others that could not be classified in this way are
predicted to be members of the small GTPase superfamily
without predictions of the subfamily.
Length = 166
Score = 28.7 bits (65), Expect = 7.6
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 666 ILKWVVSSRGSFEHFRTADEH--RDKGLIRTFPVPLILIGGKYDL 708
+L + ++ R SFE E R K VP++L+G K DL
Sbjct: 78 LLVYSITDRQSFEEIAKFREQILRVKDRDD---VPIVLVGNKCDL 119
>gnl|CDD|147496 pfam05341, DUF708, Protein of unknown function (DUF708). This
family consists of several uncharacterized
nucleopolyhedrovirus proteins of unknown function.
Length = 105
Score = 28.0 bits (63), Expect = 8.6
Identities = 8/24 (33%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 234 HYAFSSHLASAV--NFDYNKPIFV 255
+ ++L A NFDY +PI+
Sbjct: 36 QSTYRTNLRKANLENFDYKQPIYY 59
Score = 28.0 bits (63), Expect = 8.6
Identities = 8/24 (33%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 350 HYAFSSHLASAV--NFDYNKPIFV 371
+ ++L A NFDY +PI+
Sbjct: 36 QSTYRTNLRKANLENFDYKQPIYY 59
Score = 28.0 bits (63), Expect = 8.6
Identities = 8/24 (33%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 565 HYAFSSHLASAV--NFDYNKPIFV 586
+ ++L A NFDY +PI+
Sbjct: 36 QSTYRTNLRKANLENFDYKQPIYY 59
Score = 28.0 bits (63), Expect = 8.6
Identities = 8/24 (33%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 778 HYAFSSHLASAV--NFDYNKPIFV 799
+ ++L A NFDY +PI+
Sbjct: 36 QSTYRTNLRKANLENFDYKQPIYY 59
>gnl|CDD|206660 cd01868, Rab11_like, Rab GTPase family 11 (Rab11)-like includes
Rab11a, Rab11b, and Rab25. Rab11a, Rab11b, and Rab25
are closely related, evolutionary conserved Rab
proteins that are differentially expressed. Rab11a is
ubiquitously synthesized, Rab11b is enriched in brain
and heart and Rab25 is only found in epithelia.
Rab11/25 proteins seem to regulate recycling pathways
from endosomes to the plasma membrane and to the
trans-Golgi network. Furthermore, Rab11a is thought to
function in the histamine-induced fusion of
tubulovesicles containing H+, K+ ATPase with the plasma
membrane in gastric parietal cells and in
insulin-stimulated insertion of GLUT4 in the plasma
membrane of cardiomyocytes. Overexpression of Rab25 has
recently been observed in ovarian cancer and breast
cancer, and has been correlated with worsened outcomes
in both diseases. In addition, Rab25 overexpression has
also been observed in prostate cancer, transitional
cell carcinoma of the bladder, and invasive breast
tumor cells. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Due to the presence
of truncated sequences in this CD, the lipid
modification site is not available for annotation.
Length = 165
Score = 28.7 bits (65), Expect = 9.4
Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 8/49 (16%)
Query: 38 LLLIGTKSVGKSTLVFRFL--EKNDTPKPTLALEYIYARKS----GKTV 80
++LIG VGKS L+ RF E N K T+ +E +A ++ GKT+
Sbjct: 6 IVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVE--FATRTIQIDGKTI 52
>gnl|CDD|233448 TIGR01526, nadR_NMN_Atrans, nicotinamide-nucleotide
adenylyltransferase, NadR type. The NadR protein of E.
coli and closely related bacteria is both enzyme and
regulatory protein. The first 60 or so amino acids,
N-terminal to the region covered by this model, is a
DNA-binding helix-turn-helix domain (pfam01381)
responsible for repressing the nadAB genes of NAD de
novo biosynthesis. The NadR homologs in Mycobacterium
tuberculosis, Haemophilus influenzae, and others appear
to lack the repressor domain. NadR has recently been
shown to act as an enzyme of the salvage pathway of NAD
biosynthesis, nicotinamide-nucleotide
adenylyltransferase; members of this family are presumed
to share this activity. E. coli NadR has also been found
to regulate the import of its substrate, nicotinamide
ribonucleotide, but it is not known if the other members
of this model share that activity.
Length = 325
Score = 29.0 bits (65), Expect = 9.8
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 36 RTLLLIGTKSVGKSTLVFRFLEKNDTP-KPTLALEYIYARKSGKTVMK 82
+T+ ++G +S GKSTLV + +T A EY+ + G ++
Sbjct: 163 KTVAILGGESTGKSTLVNKLAAVFNTTSAWEYAREYVEEKLGGDEALQ 210
>gnl|CDD|234600 PRK00053, alr, alanine racemase; Reviewed.
Length = 363
Score = 29.4 bits (67), Expect = 9.9
Identities = 21/70 (30%), Positives = 26/70 (37%), Gaps = 9/70 (12%)
Query: 97 LEVASLFSSFSLTAQSGFTLVLMLD--LSRLNSLWTEAETFLAKFRAIFESNESVREKRG 154
LE L + L +D + RL EAE L + A +V G
Sbjct: 105 LEQLEALEKAELG--KPLKVHLKIDTGMHRLGVRPEEAEAALERLLAC----PNV-RLEG 157
Query: 155 SFEHFRTADE 164
F HF TADE
Sbjct: 158 IFSHFATADE 167
Score = 29.4 bits (67), Expect = 9.9
Identities = 21/70 (30%), Positives = 26/70 (37%), Gaps = 9/70 (12%)
Query: 405 LEVASLFSSFSLTAQSGFTLVLMLD--LSRLNSLWTEAETFLAKFRAIFESNESVREKRG 462
LE L + L +D + RL EAE L + A +V G
Sbjct: 105 LEQLEALEKAELG--KPLKVHLKIDTGMHRLGVRPEEAEAALERLLAC----PNV-RLEG 157
Query: 463 SFEHFRTADE 472
F HF TADE
Sbjct: 158 IFSHFATADE 167
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
0.320 0.136 0.404
Gapped
Lambda K H
0.267 0.0830 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 45,148,804
Number of extensions: 4458516
Number of successful extensions: 3987
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3984
Number of HSP's successfully gapped: 52
Length of query: 890
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 784
Effective length of database: 6,236,078
Effective search space: 4889085152
Effective search space used: 4889085152
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 (21.8 bits)
S2: 63 (27.9 bits)