RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14042
(238 letters)
>gnl|CDD|206715 cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras
GTPases. RGK subfamily. The RGK (Rem, Rem2, Rad,
Gem/Kir) subfamily of Ras GTPases are expressed in a
tissue-specific manner and are dynamically regulated by
transcriptional and posttranscriptional mechanisms in
response to environmental cues. RGK proteins bind to the
beta subunit of L-type calcium channels, causing
functional down-regulation of these voltage-dependent
calcium channels, and either termination of
calcium-dependent secretion or modulation of electrical
conduction and contractile function. Inhibition of
L-type calcium channels by Rem2 may provide a mechanism
for modulating calcium-triggered exocytosis in
hormone-secreting cells, and has been proposed to
influence the secretion of insulin in pancreatic beta
cells. RGK proteins also interact with and inhibit the
Rho/Rho kinase pathway to modulate remodeling of the
cytoskeleton. Two characteristics of RGK proteins cited
in the literature are N-terminal and C-terminal
extensions beyond the GTPase domain typical of Ras
superfamily members. The N-terminal extension is not
conserved among family members; the C-terminal extension
is reported to be conserved among the family and lack
the CaaX prenylation motif typical of
membrane-associated Ras proteins. However, a putative
CaaX motif has been identified in the alignment of the
C-terminal residues of this CD.
Length = 219
Score = 102 bits (257), Expect = 6e-27
Identities = 35/93 (37%), Positives = 50/93 (53%)
Query: 42 SYHRVEQDVIRLHEEGYLRTRPAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVG 101
S+ + + I+L P I+V NK DL R+R VS Q+ + A F KFIE S
Sbjct: 87 SFEKASELRIQLRRARQAEDIPIILVGNKSDLVRSREVSVQEGRACAVVFDCKFIETSAA 146
Query: 102 IHHNVDELLVGILNQIRLKRSLVQTGGAQAAAP 134
+ HNVDEL GI+ Q+RL+R + + A+
Sbjct: 147 LQHNVDELFEGIVRQVRLRRDSKEKNTRRMASR 179
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. 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.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 160
Score = 63.7 bits (156), Expect = 9e-13
Identities = 30/108 (27%), Positives = 54/108 (50%), Gaps = 21/108 (19%)
Query: 19 EQYEKLTSSDETGLIIVWMLY----KPSYHRVEQDVIRLHEEGYLRTR-----PAIIVAN 69
+QY + + D G I+V Y + S+ ++ + E+ LR + P ++V N
Sbjct: 65 DQY--IRNGD--GFILV---YSITSRESFEEIK----NIREQ-ILRVKDKEDVPIVLVGN 112
Query: 70 KIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQI 117
K DL R VS+++ + LA + F+E S + N+DEL ++ +I
Sbjct: 113 KCDLENERQVSTEEGEALAEEWGCPFLETSAKTNINIDELFNTLVREI 160
>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 = 62.6 bits (153), Expect = 3e-12
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 48 QDVIRLHEEGYLRTR-----PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGI 102
+++ + E+ LR + P ++V NK DL R VS+++ K LA + F+E S
Sbjct: 90 EEIAKFREQ-ILRVKDRDDVPIVLVGNKCDLENERVVSTEEGKELARQWGCPFLETSAKE 148
Query: 103 HHNVDELLVGILNQIRLK 120
NVDE ++ +IR
Sbjct: 149 RINVDEAFYDLVREIRKS 166
>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 = 62.2 bits (152), Expect = 4e-12
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 48 QDVIRLHEEGYLRTR-----PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGI 102
+++ + E+ LR + P ++V NK DL R VS+++ K LA + F+E S
Sbjct: 88 EEIKKFREQ-ILRVKDRDDVPIVLVGNKCDLESERVVSTEEGKELARQWGCPFLETSAKE 146
Query: 103 HHNVDELLVGILNQIR 118
NVDE ++ +IR
Sbjct: 147 RVNVDEAFYDLVREIR 162
>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 = 54.8 bits (133), Expect = 1e-09
Identities = 32/113 (28%), Positives = 50/113 (44%), Gaps = 21/113 (18%)
Query: 11 KVRAIIWN----EQYEKLTSS---DETGLIIVWMLY----KPSYHRVE---QDVIRLHEE 56
KV+ IW+ E++ +TSS G I+V Y + S+ ++ ++
Sbjct: 48 KVKLQIWDTAGQERFRSITSSYYRGAHGAILV---YDVTNRESFENLDKWLNELKEYAPP 104
Query: 57 GYLRTRPAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDEL 109
P I+V NK DL R VS+++A+ A + F E S NVDE
Sbjct: 105 NI----PIILVGNKSDLEDERQVSTEEAQQFAKENGLLFFETSAKTGENVDEA 153
>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 = 54.8 bits (133), Expect = 1e-09
Identities = 29/122 (23%), Positives = 56/122 (45%), Gaps = 15/122 (12%)
Query: 8 HSGKVRAIIWN----EQYEKLTSS---DETGLIIVWMLYKP-SYHRVE---QDVIRLHEE 56
V+ IW+ E++ L G ++V+ + S+ V+ ++++R +E
Sbjct: 44 DGKTVKLQIWDTAGQERFRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADE 103
Query: 57 GYLRTRPAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQ 116
P ++V NK DL R VS+++ + LA + F+E S + NV+E + +
Sbjct: 104 NV----PIVLVGNKCDLEDQRVVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELARE 159
Query: 117 IR 118
I
Sbjct: 160 IL 161
>gnl|CDD|133345 cd04145, M_R_Ras_like, R-Ras2/TC21, M-Ras/R-Ras3. The
M-Ras/R-Ras-like subfamily contains R-Ras2/TC21,
M-Ras/R-Ras3, and related members of the Ras family.
M-Ras is expressed in lympho-hematopoetic cells. It
interacts with some of the known Ras effectors, but
appears to also have its own effectors. Expression of
mutated M-Ras leads to transformation of several types
of cell lines, including hematopoietic cells, mammary
epithelial cells, and fibroblasts. Overexpression of
M-Ras is observed in carcinomas from breast, uterus,
thyroid, stomach, colon, kidney, lung, and rectum. In
addition, expression of a constitutively active M-Ras
mutant in murine bone marrow induces a malignant mast
cell leukemia that is distinct from the monocytic
leukemia induced by H-Ras. TC21, along with H-Ras, has
been shown to regulate the branching morphogenesis of
ureteric bud cell branching in mice. 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. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 54.7 bits (132), Expect = 2e-09
Identities = 31/106 (29%), Positives = 50/106 (47%), Gaps = 15/106 (14%)
Query: 19 EQYEKLTSSDETGLIIVWMLYKP-SYHRVEQDVIRLHEEGYLRTR-----PAIIVANKID 72
EQY + G ++V+ + S+ V+ + H + LR + P I+V NK D
Sbjct: 68 EQYMRTGE----GFLLVFSVTDRGSFEEVD----KFHTQ-ILRVKDRDEFPMILVGNKAD 118
Query: 73 LARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQIR 118
L R VS ++ + LA K+ +IE S NVD+ ++ IR
Sbjct: 119 LEHQRQVSREEGQELARQLKIPYIETSAKDRVNVDKAFHDLVRVIR 164
>gnl|CDD|133338 cd04138, H_N_K_Ras_like, Ras GTPase family containing H-Ras,N-Ras
and K-Ras4A/4B. H-Ras/N-Ras/K-Ras subfamily. H-Ras,
N-Ras, and K-Ras4A/4B are the prototypical members of
the Ras family. These isoforms generate distinct signal
outputs despite interacting with a common set of
activators and effectors, and are strongly associated
with oncogenic progression in tumor initiation. Mutated
versions of Ras that are insensitive to GAP stimulation
(and are therefore constitutively active) are found in a
significant fraction of human cancers. Many Ras guanine
nucleotide exchange factors (GEFs) have been identified.
They are sequestered in the cytosol until activation by
growth factors triggers recruitment to the plasma
membrane or Golgi, where the GEF colocalizes with Ras.
Active (GTP-bound) Ras interacts with several effector
proteins that stimulate a variety of diverse cytoplasmic
signaling activities. Some are known to positively
mediate the oncogenic properties of Ras, including Raf,
phosphatidylinositol 3-kinase (PI3K), RalGEFs, and
Tiam1. Others are proposed to play negative regulatory
roles in oncogenesis, including RASSF and NORE/MST1.
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. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 162
Score = 53.2 bits (128), Expect = 7e-09
Identities = 21/56 (37%), Positives = 34/56 (60%), Gaps = 1/56 (1%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQIR 118
P ++V NK DLA AR VS++ ++LA S+ + +IE S V+E ++ +IR
Sbjct: 108 PMVLVGNKCDLA-ARTVSTRQGQDLAKSYGIPYIETSAKTRQGVEEAFYTLVREIR 162
>gnl|CDD|206654 cd01861, Rab6, Rab GTPase family 6 (Rab6). Rab6 is involved in
microtubule-dependent transport pathways through the
Golgi and from endosomes to the Golgi. Rab6A of mammals
is implicated in retrograde transport through the Golgi
stack, and is also required for a slow,
COPI-independent, retrograde transport pathway from the
Golgi to the endoplasmic reticulum (ER). This pathway
may allow Golgi residents to be recycled through the ER
for scrutiny by ER quality-control systems. Yeast Ypt6p,
the homolog of the mammalian Rab6 GTPase, is not
essential for cell viability. Ypt6p acts in
endosome-to-Golgi, in intra-Golgi retrograde transport,
and possibly also in Golgi-to-ER trafficking. 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 = 51.1 bits (123), Expect = 4e-08
Identities = 17/45 (37%), Positives = 25/45 (55%)
Query: 65 IIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDEL 109
++V NK DL+ R VS+++ + A FIE S HNV +L
Sbjct: 109 VLVGNKTDLSDKRQVSTEEGEKKAKENNAMFIETSAKAGHNVKQL 153
>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 = 50.6 bits (122), Expect = 5e-08
Identities = 35/126 (27%), Positives = 63/126 (50%), Gaps = 13/126 (10%)
Query: 2 NQSLQGHSGKVRAIIWN----EQYEKLTSS---DETGLIIVWMLYKP-SYHRVEQ--DVI 51
+++Q ++A IW+ E+Y +TS+ G ++V+ + K ++ VE+ +
Sbjct: 42 TRTIQIDGKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKEL 101
Query: 52 RLHEEGYLRTRPAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLV 111
R H + + ++V NK DL RAV +++AK A + FIE S NV+E
Sbjct: 102 RDHADSNI---VIMLVGNKSDLRHLRAVPTEEAKAFAEKNGLSFIETSALDGTNVEEAFK 158
Query: 112 GILNQI 117
+L +I
Sbjct: 159 QLLTEI 164
>gnl|CDD|206712 cd04141, Rit_Rin_Ric, Ras-like protein in all tissues (Rit),
Ras-like protein in neurons (Rin) and Ras-related
protein which interacts with calmodulin (Ric). Rit
(Ras-like protein in all tissues), Rin (Ras-like protein
in neurons) and Ric (Ras-related protein which interacts
with calmodulin) form a subfamily with several unique
structural and functional characteristics. These
proteins all lack a the C-terminal CaaX lipid-binding
motif typical of Ras family proteins, and Rin and Ric
contain calmodulin-binding domains. Rin, which is
expressed only in neurons, induces neurite outgrowth in
rat pheochromocytoma cells through its association with
calmodulin and its activation of endogenous Rac/cdc42.
Rit, which is ubiquitously expressed in mammals,
inhibits growth-factor withdrawl-mediated apoptosis and
induces neurite extension in pheochromocytoma cells. Rit
and Rin are both able to form a ternary complex with
PAR6, a cell polarity-regulating protein, and Rac/cdc42.
This ternary complex is proposed to have physiological
function in processes such as tumorigenesis. Activated
Ric is likely to signal in parallel with the Ras pathway
or stimulate the Ras pathway at some upstream point, and
binding of calmodulin to Ric may negatively regulate Ric
activity.
Length = 172
Score = 50.2 bits (120), Expect = 9e-08
Identities = 21/60 (35%), Positives = 36/60 (60%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQIRLKRS 122
P ++V NK+DL + R V++++ +NLA F F E S + +D+ G++ +IR K S
Sbjct: 109 PLVLVGNKVDLEQQRQVTTEEGRNLAREFNCPFFETSAALRFYIDDAFHGLVREIRRKES 168
>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 = 49.9 bits (120), Expect = 1e-07
Identities = 20/55 (36%), Positives = 32/55 (58%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQI 117
P ++V NK DL R VS+++ K LA S+ F+E S + NV+E ++ +I
Sbjct: 108 PIVLVGNKSDLHMERQVSAEEGKKLAESWGAAFLESSAKENENVEEAFELLIEEI 162
>gnl|CDD|133344 cd04144, Ras2, Rat sarcoma (Ras) family 2 of small guanosine
triphosphatases (GTPases). The Ras2 subfamily, found
exclusively in fungi, was first identified in Ustilago
maydis. In U. maydis, Ras2 is regulated by Sql2, a
protein that is homologous to GEFs (guanine nucleotide
exchange factors) of the CDC25 family. Ras2 has been
shown to induce filamentous growth, but the signaling
cascade through which Ras2 and Sql2 regulate cell
morphology is not known. 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 = 190
Score = 49.5 bits (118), Expect = 2e-07
Identities = 34/125 (27%), Positives = 57/125 (45%), Gaps = 11/125 (8%)
Query: 19 EQYEKLTSS---DETGLIIVWMLY-KPSYHRVE---QDVIRLHEEGYLRTRPAIIVANKI 71
E+Y L + G I+V+ + + ++ RVE + + R+ +E P +IV NK
Sbjct: 58 EEYTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADV-PIMIVGNKC 116
Query: 72 DLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQIRLKRSLVQTGGAQA 131
D R VS+++ LA +FIE S + NV+ ++ +R +R Q G
Sbjct: 117 DKVYEREVSTEEGAALARRLGCEFIEASAKTNVNVERAFYTLVRALRQQR---QGGQGPK 173
Query: 132 AAPWK 136
P K
Sbjct: 174 GGPTK 178
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 48.7 bits (117), Expect = 2e-07
Identities = 31/118 (26%), Positives = 53/118 (44%), Gaps = 15/118 (12%)
Query: 11 KVRAIIWN----EQYEKLTSS---DETGLIIVWMLY----KPSYHRVEQDVIRLHEEGYL 59
+V+ IW+ E++ +TSS G ++V Y + S+ +E + L E
Sbjct: 48 RVKLQIWDTAGQERFRSITSSYYRGAVGALLV---YDITNRESFENLENWLKELREYASP 104
Query: 60 RTRPAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQI 117
++V NK DL R VS ++A+ A + F E S + NV+E + +I
Sbjct: 105 NV-VIMLVGNKSDLEEQRQVSREEAEAFAEEHGLPFFETSAKTNTNVEEAFEELAREI 161
>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 = 47.7 bits (114), Expect = 5e-07
Identities = 31/114 (27%), Positives = 56/114 (49%), Gaps = 15/114 (13%)
Query: 16 IWN----EQYEKLTSS---DETGLIIVW-MLYKPSYHRVEQ---DVIRLHEEGYLRTRPA 64
IW+ E++ +TSS G+IIV+ + + S++ V+Q ++ R E +
Sbjct: 55 IWDTAGQERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNK---- 110
Query: 65 IIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQIR 118
++V NK DL + V +AK A + F+E S NV+E + + +I+
Sbjct: 111 LLVGNKCDLTDKKVVDYTEAKEFADELGIPFLETSAKNATNVEEAFMTMAREIK 164
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 47.6 bits (113), Expect = 9e-07
Identities = 23/56 (41%), Positives = 32/56 (57%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQIR 118
P I+V NK DL R VS+ + + LA SF + F+E S NVDE ++ +IR
Sbjct: 112 PMILVGNKCDLDSERQVSTGEGQELAKSFGIPFLETSAKQRVNVDEAFYELVREIR 167
>gnl|CDD|206713 cd04146, RERG_RasL11_like, Ras-related and Estrogen-Regulated
Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like
families. RERG (Ras-related and Estrogen- Regulated
Growth inhibitor) and Ras-like 11 are members of a novel
subfamily of Ras that were identified based on their
behavior in breast and prostate tumors, respectively.
RERG expression was decreased or lost in a significant
fraction of primary human breast tumors that lack
estrogen receptor and are correlated with poor clinical
prognosis. Elevated RERG expression correlated with
favorable patient outcome in a breast tumor subtype that
is positive for estrogen receptor expression. In
contrast to most Ras proteins, RERG overexpression
inhibited the growth of breast tumor cells in vitro and
in vivo. RasL11 was found to be ubiquitously expressed
in human tissue, but down-regulated in prostate tumors.
Both RERG and RasL11 lack the C-terminal CaaX
prenylation motif, where a = an aliphatic amino acid and
X = any amino acid, and are localized primarily in the
cytoplasm. Both are believed to have tumor suppressor
activity.
Length = 166
Score = 46.9 bits (112), Expect = 9e-07
Identities = 16/43 (37%), Positives = 24/43 (55%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHN 105
P I+V NK DL +R VS+++ + LA F EVS ++
Sbjct: 109 PVILVGNKADLLHSRQVSTEEGQKLALELGCLFFEVSAAENYL 151
>gnl|CDD|206710 cd04139, RalA_RalB, Ral (Ras-like) family containing highly
homologous RalA and RalB. The Ral (Ras-like) subfamily
consists of the highly homologous RalA and RalB. Ral
proteins are believed to play a crucial role in
tumorigenesis, metastasis, endocytosis, and actin
cytoskeleton dynamics. Despite their high sequence
similarity (>80% sequence identity), nonoverlapping and
opposing functions have been assigned to RalA and RalBs
in tumor migration. In human bladder and prostate cancer
cells, RalB promotes migration while RalA inhibits it. A
Ral-specific set of GEFs has been identified that are
activated by Ras binding. This RalGEF activity is
enhanced by Ras binding to another of its target
proteins, phosphatidylinositol 3-kinase (PI3K). Ral
effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and
the exocyst (Sec6/8) complex, a heterooctomeric protein
complex that is involved in tethering vesicles to
specific sites on the plasma membrane prior to
exocytosis. In rat kidney cells, RalB is required for
functional assembly of the exocyst and for localizing
the exocyst to the leading edge of migrating cells. In
human cancer cells, RalA is required to support
anchorage-independent proliferation and RalB is required
to suppress apoptosis. RalA has been shown to localize
to the plasma membrane while RalB is localized to the
intracellular vesicles. 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. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 46.7 bits (111), Expect = 1e-06
Identities = 21/56 (37%), Positives = 33/56 (58%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQIR 118
P ++V NK DL R VS ++A NLA + V ++E S NVD++ ++ +IR
Sbjct: 107 PLLLVGNKCDLEDKRQVSVEEAANLAEQWGVNYVETSAKTRANVDKVFFDLVREIR 162
>gnl|CDD|133376 cd04176, Rap2, Rap2 family GTPase consists of Rap2a, Rap2b, and
Rap2c. The Rap2 subgroup is part of the Rap subfamily
of the Ras family. It consists of Rap2a, Rap2b, and
Rap2c. Both isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK) are putative
effectors of Rap2 in mediating the activation of c-Jun
N-terminal kinase (JNK) to regulate the actin
cytoskeleton. In human platelets, Rap2 was shown to
interact with the cytoskeleton by binding the actin
filaments. In embryonic Xenopus development, Rap2 is
necessary for the Wnt/beta-catenin signaling pathway.
The Rap2 interacting protein 9 (RPIP9) is highly
expressed in human breast carcinomas and correlates with
a poor prognosis, suggesting a role for Rap2 in breast
cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a,
or Rap1b, is expressed in human red blood cells, where
it is believed to be involved in vesiculation. A number
of additional effector proteins for Rap2 have been
identified, including the RalGEFs RalGDS, RGL, and Rlf,
which also interact with Rap1 and Ras. 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. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 163
Score = 46.4 bits (110), Expect = 1e-06
Identities = 29/92 (31%), Positives = 45/92 (48%), Gaps = 9/92 (9%)
Query: 31 GLIIVWMLYKPSYHRVEQDVIRLHEEGYLRTR-----PAIIVANKIDLARARAVSSQDAK 85
G I+V+ L + QD I+ + +R + P I+V NK+DL R VSS + +
Sbjct: 75 GFIVVYSL---VNQQTFQD-IKPMRDQIVRVKGYEKVPIILVGNKVDLESEREVSSAEGR 130
Query: 86 NLAASFKVKFIEVSVGIHHNVDELLVGILNQI 117
LA + F+E S V+EL I+ Q+
Sbjct: 131 ALAEEWGCPFMETSAKSKTMVNELFAEIVRQM 162
>gnl|CDD|206711 cd04140, ARHI_like, A Ras homolog member I (ARHI). ARHI (A Ras
homolog member I) is a member of the Ras family with
several unique structural and functional properties.
ARHI is expressed in normal human ovarian and breast
tissue, but its expression is decreased or eliminated in
breast and ovarian cancer. ARHI contains an N-terminal
extension of 34 residues (human) that is required to
retain its tumor suppressive activity. Unlike most other
Ras family members, ARHI is maintained in the
constitutively active (GTP-bound) state in resting cells
and has modest GTPase activity. ARHI inhibits STAT3
(signal transducers and activators of transcription 3),
a latent transcription factor whose abnormal activation
plays a critical role in oncogenesis. 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. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 46.4 bits (110), Expect = 2e-06
Identities = 21/53 (39%), Positives = 31/53 (58%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILN 115
P ++V NK D + +R VSS + LA ++ F+E S +HNV EL +LN
Sbjct: 110 PIMLVGNKCDESPSREVSSSEGAALARTWNCAFMETSAKTNHNVQELFQELLN 162
>gnl|CDD|133375 cd04175, Rap1, Rap1 family GTPase consists of Rap1a and Rap1b
isoforms. The Rap1 subgroup is part of the Rap
subfamily of the Ras family. It can be further divided
into the Rap1a and Rap1b isoforms. In humans, Rap1a and
Rap1b share 95% sequence homology, but are products of
two different genes located on chromosomes 1 and 12,
respectively. Rap1a is sometimes called smg p21 or Krev1
in the older literature. Rap1 proteins are believed to
perform different cellular functions, depending on the
isoform, its subcellular localization, and the effector
proteins it binds. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and the microsomal
membrane of pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. High expression of Rap1 has been observed
in the nucleus of human oropharyngeal squamous cell
carcinomas (SCCs) and cell lines; interestingly, in the
SCCs, the active GTP-bound form localized to the
nucleus, while the inactive GDP-bound form localized to
the cytoplasm. Rap1 plays a role in phagocytosis by
controlling the binding of adhesion receptors (typically
integrins) to their ligands. In yeast, Rap1 has been
implicated in multiple functions, including activation
and silencing of transcription and maintenance of
telomeres. Rap1a, which is stimulated by T-cell receptor
(TCR) activation, is a positive regulator of T cells by
directing integrin activation and augmenting lymphocyte
responses. In murine hippocampal neurons, Rap1b
determines which neurite will become the axon and
directs the recruitment of Cdc42, which is required for
formation of dendrites and axons. In murine platelets,
Rap1b is required for normal homeostasis in vivo and is
involved in integrin activation. 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. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 46.0 bits (109), Expect = 2e-06
Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 49 DVIRLHEEGYLRTR-----PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIH 103
D+ L E+ LR + P I+V NK DL R V + +NLA + F+E S
Sbjct: 90 DLQDLREQ-ILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWGCAFLETSAKAK 148
Query: 104 HNVDELLVGILNQI 117
NV+E+ ++ QI
Sbjct: 149 INVNEIFYDLVRQI 162
>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 = 45.7 bits (109), Expect = 2e-06
Identities = 18/56 (32%), Positives = 31/56 (55%)
Query: 65 IIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQIRLK 120
++V NK D+ R VS ++ + LA + +KF+E S + NV+E + + I K
Sbjct: 112 MLVGNKCDMEEKRVVSKEEGEALAREYGIKFLETSAKANINVEEAFLTLAKDILKK 167
>gnl|CDD|206708 cd04136, Rap_like, Rap-like family consists of Rap1, Rap2 and RSR1.
The Rap subfamily consists of the Rap1, Rap2, and RSR1.
Rap subfamily proteins perform different cellular
functions, depending on the isoform and its subcellular
localization. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and microsomal
membrane of the pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. Rap1 localizes in the nucleus of human
oropharyngeal squamous cell carcinomas (SCCs) and cell
lines. Rap1 plays a role in phagocytosis by controlling
the binding of adhesion receptors (typically integrins)
to their ligands. In yeast, Rap1 has been implicated in
multiple functions, including activation and silencing
of transcription and maintenance of telomeres. Rap2 is
involved in multiple functions, including activation of
c-Jun N-terminal kinase (JNK) to regulate the actin
cytoskeleton and activation of the Wnt/beta-catenin
signaling pathway in embryonic Xenopus. A number of
effector proteins for Rap2 have been identified,
including isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK), and the
RalGEFs RalGDS, RGL, and Rlf, which also interact with
Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and
Rap2. In budding yeasts, it is involved in selecting a
site for bud growth, which directs the establishment of
cell polarization. The Rho family GTPase Cdc42 and its
GEF, Cdc24, then establish an axis of polarized growth.
It is believed that Cdc42 interacts directly with RSR1
in vivo. In filamentous fungi such as Ashbya gossypii,
RSR1 is a key regulator of polar growth in the hypha.
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. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 164
Score = 44.9 bits (106), Expect = 5e-06
Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASF-KVKFIEVSVGIHHNVDELLVGILNQI 117
P I+V NK DL R VS ++ +NLA + F+E S NVDE+ ++ QI
Sbjct: 108 PMILVGNKCDLEDERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLVRQI 163
>gnl|CDD|133323 cd04123, Rab21, Rab GTPase family 21 (Rab21). The localization and
function of Rab21 are not clearly defined, with
conflicting data reported. Rab21 has been reported to
localize in the ER in human intestinal epithelial cells,
with partial colocalization with alpha-glucosidase, a
late endosomal/lysosomal marker. More recently, Rab21
was shown to colocalize with and affect the morphology
of early endosomes. In Dictyostelium, GTP-bound Rab21,
together with two novel LIM domain proteins, LimF and
ChLim, has been shown to regulate phagocytosis. 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 = 162
Score = 44.5 bits (106), Expect = 7e-06
Identities = 19/53 (35%), Positives = 28/53 (52%)
Query: 65 IIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQI 117
+IV NKIDL R R VS +A+ A S K E S ++EL + + ++
Sbjct: 109 VIVGNKIDLERQRVVSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSLAKRM 161
>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 = 44.5 bits (106), Expect = 8e-06
Identities = 17/49 (34%), Positives = 25/49 (51%)
Query: 65 IIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGI 113
+ NK DL R VS+++A+ A + F+E S NV+EL I
Sbjct: 110 ALAGNKADLESKRQVSTEEAQEYADENGLLFMETSAKTGENVNELFTEI 158
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 43.0 bits (101), Expect = 4e-05
Identities = 39/151 (25%), Positives = 66/151 (43%), Gaps = 14/151 (9%)
Query: 3 QSLQGHSGKVRAIIWN----EQYEKLTSSDETGLIIVWMLYKPSYHRVEQDVIRLHEEGY 58
++LQ V+A IW+ E+Y +TS+ G + ++Y + + +V R E
Sbjct: 52 RTLQVEGKTVKAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRE-- 109
Query: 59 LRTRP-----AIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGI 113
LR ++ NK DL R+V+ +D + LA + F+E S NV++ I
Sbjct: 110 LRDHADSNIVIMMAGNKSDLNHLRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFQTI 169
Query: 114 LN---QIRLKRSLVQTGGAQAAAPWKSNTTL 141
L I K++L A + TT+
Sbjct: 170 LLEIYHIISKKALAAQEAAANSGLPGQGTTI 200
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 43.2 bits (103), Expect = 5e-05
Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 10/55 (18%)
Query: 59 LRTRPAIIVANKIDLARARAVSSQDAKNLA---ASFKVKFIEVSVGIHHNVDELL 110
L RP I+VANK+DL A +NL K +S +DELL
Sbjct: 272 LLERPQIVVANKMDLPEA-------EENLEEFKEKLGPKVFPISALTGQGLDELL 319
>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 = 42.0 bits (99), Expect = 6e-05
Identities = 18/53 (33%), Positives = 28/53 (52%)
Query: 65 IIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQI 117
++ ANKIDL + RAVS + + A S K+ E S V+E+ + + I
Sbjct: 114 VVCANKIDLTKHRAVSEDEGRLWAESKGFKYFETSACTGEGVNEMFQTLFSSI 166
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 42.8 bits (102), Expect = 7e-05
Identities = 17/64 (26%), Positives = 25/64 (39%)
Query: 59 LRTRPAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQIR 118
L +P I+V NKIDL + A A+ +S +DELL + +
Sbjct: 269 LADKPRILVLNKIDLLDEEEEREKRAALELAALGGPVFLISAVTGEGLDELLRALWELLE 328
Query: 119 LKRS 122
R
Sbjct: 329 EARR 332
>gnl|CDD|133377 cd04177, RSR1, RSR1/Bud1p family GTPase. RSR1/Bud1p is a member of
the Rap subfamily of the Ras family that is found in
fungi. In budding yeasts, RSR1 is involved in selecting
a site for bud growth on the cell cortex, which directs
the establishment of cell polarization. The Rho family
GTPase cdc42 and its GEF, cdc24, then establish an axis
of polarized growth by organizing the actin cytoskeleton
and secretory apparatus at the bud site. It is believed
that cdc42 interacts directly with RSR1 in vivo. In
filamentous fungi, polar growth occurs at the tips of
hypha and at novel growth sites along the extending
hypha. In Ashbya gossypii, RSR1 is a key regulator of
hyphal growth, localizing at the tip region and
regulating in apical polarization of the actin
cytoskeleton. 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 = 168
Score = 40.5 bits (95), Expect = 2e-04
Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASF-KVKFIEVSVGIHHNVDELLVGILNQIR 118
P ++V NK DL R VS +D +L+ + V F E S NVDE+ + ++ QI
Sbjct: 108 PMVLVGNKADLEDDRQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDLVRQII 164
>gnl|CDD|206700 cd04127, Rab27A, Rab GTPase family 27a (Rab27a). The Rab27a
subfamily consists of Rab27a and its highly homologous
isoform, Rab27b. Unlike most Rab proteins whose
functions remain poorly defined, Rab27a has many known
functions. Rab27a has multiple effector proteins, and
depending on which effector it binds, Rab27a has
different functions as well as tissue distribution
and/or cellular localization. Putative functions have
been assigned to Rab27a when associated with the
effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp,
rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c,
Noc2, JFC1, and Munc13-4. Rab27a has been associated
with several human diseases, including hemophagocytic
syndrome (Griscelli syndrome or GS), Hermansky-Pudlak
syndrome, and choroidermia. In the case of GS, a rare,
autosomal recessive disease, a Rab27a mutation is
directly responsible for the disorder. When Rab27a is
localized to the secretory granules of pancreatic beta
cells, it is believed to mediate glucose-stimulated
insulin secretion, making it a potential target for
diabetes therapy. When bound to JFC1 in prostate cells,
Rab27a is believed to regulate the exocytosis of
prostate- specific markers. 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 = 180
Score = 40.2 bits (94), Expect = 2e-04
Identities = 29/123 (23%), Positives = 58/123 (47%), Gaps = 11/123 (8%)
Query: 5 LQGHSGKVRAIIWN----EQYEKLTSS---DETGLIIVWMLY-KPSYHRVEQDVIRLHEE 56
G + +V +W+ E++ LT++ D G ++++ L + S+ V + +L
Sbjct: 56 TSGKAFRVHLQLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAH 115
Query: 57 GYLRTRPAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVD---ELLVGI 113
Y +++ NK DL R VS + A+ LA + + + E S NV+ E L+ +
Sbjct: 116 AYCENPDIVLIGNKADLPDQREVSERQARELADKYGIPYFETSAATGQNVEKAVETLLDL 175
Query: 114 LNQ 116
+ +
Sbjct: 176 IMK 178
>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 = 39.7 bits (94), Expect = 3e-04
Identities = 20/77 (25%), Positives = 30/77 (38%), Gaps = 5/77 (6%)
Query: 46 VEQDVIRLHEE--GY---LRTRPAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSV 100
+D + E Y L +P I+V NKIDL A + + L K +S
Sbjct: 94 PVEDYETIRNELEAYNPGLAEKPRIVVLNKIDLLDAEERFEKLKELLKELKGKKVFPISA 153
Query: 101 GIHHNVDELLVGILNQI 117
+DELL + +
Sbjct: 154 LTGEGLDELLKKLAKLL 170
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 40.6 bits (96), Expect = 4e-04
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 1/61 (1%)
Query: 58 YLRTRPAIIVANKIDLARARAVSSQDAKNLAASFK-VKFIEVSVGIHHNVDELLVGILNQ 116
L +P I+V NKIDL + K LA + F +S +DELL +
Sbjct: 272 KLAEKPRIVVLNKIDLPLDEEELEELKKALAEALGWEVFYLISALTREGLDELLRALAEL 331
Query: 117 I 117
+
Sbjct: 332 L 332
>gnl|CDD|133306 cd04106, Rab23_like, Rab GTPase family 23 (Rab23)-like. Rab23-like
subfamily. Rab23 is a member of the Rab family of small
GTPases. In mouse, Rab23 has been shown to function as a
negative regulator in the sonic hedgehog (Shh) signaling
pathway. Rab23 mediates the activity of Gli2 and Gli3,
transcription factors that regulate Shh signaling in the
spinal cord, primarily by preventing Gli2 activation in
the absence of Shh ligand. Rab23 also regulates a step
in the cytoplasmic signal transduction pathway that
mediates the effect of Smoothened (one of two integral
membrane proteins that are essential components of the
Shh signaling pathway in vertebrates). In humans, Rab23
is expressed in the retina. Mice contain an isoform that
shares 93% sequence identity with the human Rab23 and an
alternative splicing isoform that is specific to the
brain. This isoform causes the murine open brain
phenotype, indicating it may have a role in the
development of the central nervous system. 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 = 162
Score = 39.3 bits (92), Expect = 4e-04
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDEL 109
P ++V KIDL +++++A+ LA ++ SV NV EL
Sbjct: 108 PMVLVQTKIDLLDQAVITNEEAEALAKRLQLPLFRTSVKDDFNVTEL 154
>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 = 39.0 bits (91), Expect = 6e-04
Identities = 24/87 (27%), Positives = 34/87 (39%), Gaps = 5/87 (5%)
Query: 31 GLIIVWMLYKPSYHRVEQDVIRLHEEGYLRTR-PAIIVANKIDLARARAVSSQD-AKNLA 88
+++V + E+D L + P I+V NKIDL R V + LA
Sbjct: 78 LILLV---VDSTDRESEEDAKLLILRRLRKEGIPIILVGNKIDLLEEREVEELLRLEELA 134
Query: 89 ASFKVKFIEVSVGIHHNVDELLVGILN 115
V EVS VDEL ++
Sbjct: 135 KILGVPVFEVSAKTGEGVDELFEKLIE 161
>gnl|CDD|206688 cd04101, RabL4, Rab GTPase-like family 4 (Rab-like4). RabL4
(Rab-like4) subfamily. RabL4s 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, RabL4 lacks a prenylation site at the
C-terminus. The specific function of RabL4 remains
unknown.
Length = 167
Score = 37.9 bits (88), Expect = 0.001
Identities = 15/38 (39%), Positives = 21/38 (55%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSV 100
P ++V NK DL R V + A+ LA + +KF E S
Sbjct: 112 PGVLVGNKCDLTDRREVDAAQAQALAQANTLKFYETSA 149
>gnl|CDD|206699 cd04120, Rab12, Rab GTPase family 12 (Rab12). Rab12 was first
identified in canine cells, where it was localized to
the Golgi complex. The specific function of Rab12
remains unknown, and inconsistent results about its
cellular localization have been reported. More recent
studies have identified Rab12 associated with post-Golgi
vesicles, or with other small vesicle-like structures
but not with the Golgi complex. 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. 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 = 202
Score = 38.1 bits (88), Expect = 0.001
Identities = 28/121 (23%), Positives = 57/121 (47%), Gaps = 8/121 (6%)
Query: 11 KVRAIIWN----EQYEKLTSS---DETGLIIVWMLYKPSYHRVEQDVIRLHEEGYLRTRP 63
K+R IW+ E++ +TS+ G+I+V+ + K +++ ++
Sbjct: 48 KIRLQIWDTAGQERFNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAE 107
Query: 64 AIIVANKIDLARARAVSSQDAKNLAASFK-VKFIEVSVGIHHNVDELLVGILNQIRLKRS 122
++V NK+D R ++ Q + A ++F E S + NVDE+ + +++ I K
Sbjct: 108 LLLVGNKLDCETDREITRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVDDILKKMP 167
Query: 123 L 123
L
Sbjct: 168 L 168
>gnl|CDD|133314 cd04114, Rab30, Rab GTPase family 30 (Rab30). Rab30 subfamily.
Rab30 appears to be associated with the Golgi stack. It
is expressed in a wide variety of tissue types and in
humans maps to chromosome 11. 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 = 169
Score = 37.6 bits (87), Expect = 0.002
Identities = 30/111 (27%), Positives = 55/111 (49%), Gaps = 9/111 (8%)
Query: 11 KVRAIIWN----EQYEKLTSS---DETGLIIVW-MLYKPSYHRVEQDVIRLHEEGYLRTR 62
K++ IW+ E++ +T S LI+ + + + S+ R + +R E+
Sbjct: 55 KIKLQIWDTAGQERFRSITQSYYRSANALILTYDITCEESF-RCLPEWLREIEQYANNKV 113
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGI 113
I+V NKIDLA R VS Q A+ + + + ++E S NV++L + +
Sbjct: 114 ITILVGNKIDLAERREVSQQRAEEFSDAQDMYYLETSAKESDNVEKLFLDL 164
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 36.8 bits (85), Expect = 0.004
Identities = 16/47 (34%), Positives = 27/47 (57%)
Query: 65 IIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLV 111
+++ NK DLA RAVS+++ + A + F+E S NV+E +
Sbjct: 115 MLIGNKCDLAHRRAVSTEEGEQFAKEHGLIFMEASAKTAQNVEEAFI 161
>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 = 36.7 bits (85), Expect = 0.005
Identities = 26/106 (24%), Positives = 50/106 (47%), Gaps = 8/106 (7%)
Query: 11 KVRAIIWN----EQYEKLTSSDETGLIIVWMLYKPSYHRVEQDVIRLHEEGYLRTRPA-- 64
+++ +W+ E++ +T S + V +++ + + V EE +P
Sbjct: 51 RIKLQLWDTAGQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRP 110
Query: 65 --IIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDE 108
I+V +K DL R V+ ++A+ LA +K+IE S NV+E
Sbjct: 111 VFILVGHKCDLESQRQVTREEAEKLAKDLGMKYIETSARTGDNVEE 156
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7 is
a small Rab GTPase that regulates vesicular traffic from
early to late endosomal stages of the endocytic pathway.
The yeast Ypt7 and mammalian Rab7 are both involved in
transport to the vacuole/lysosome, whereas Ypt7 is also
required for homotypic vacuole fusion. Mammalian Rab7 is
an essential participant in the autophagic pathway for
sequestration and targeting of cytoplasmic components to
the lytic compartment. Mammalian Rab7 is also proposed
to function as a tumor suppressor. 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 = 172
Score = 36.1 bits (84), Expect = 0.006
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 61 TRPAIIVANKIDLARARAVSSQDAKNLAAS-FKVKFIEVSVGIHHNVDE 108
P +++ NKIDL R VS++ A+ S + + E S NVD+
Sbjct: 109 NFPFVVLGNKIDLEEKRQVSTKKAQQWCKSKGNIPYFETSAKEAINVDQ 157
>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 = 35.7 bits (82), Expect = 0.008
Identities = 28/118 (23%), Positives = 55/118 (46%), Gaps = 12/118 (10%)
Query: 8 HSGKVRAIIWN----EQYEKLTSSDETGLIIVWMLY----KPSYHRVEQDVIRLHEEGYL 59
+ +++ IW+ E+Y +T++ G + ++Y + S++ V+ ++ +
Sbjct: 46 NDKRIKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSW- 104
Query: 60 RTRPAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVD---ELLVGIL 114
I+V NK D+ R VS++ + LA +F E S + NV E LV I+
Sbjct: 105 DNAQVILVGNKCDMEDERVVSAERGRQLADQLGFEFFEASAKENINVKQVFERLVDII 162
>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 = 35.4 bits (82), Expect = 0.009
Identities = 32/118 (27%), Positives = 56/118 (47%), Gaps = 19/118 (16%)
Query: 11 KVRAIIWN----EQYEKLTSS---DETGLIIVWMLYKP-SYHRVEQDVIRLHEEGYLRTR 62
KV+ IW+ E++ LTSS G+I+V+ + + ++ ++ L+E T
Sbjct: 48 KVKLAIWDTAGQERFRTLTSSYYRGAQGVILVYDVTRRDTFDNLD---TWLNELDTYSTN 104
Query: 63 PAII---VANKIDLARARAVSSQDAKNLAASFKVKFIEVS----VGIHHNVDELLVGI 113
P + V NKID R V+ ++ + A + FIE S +G+ +EL+ I
Sbjct: 105 PDAVKMLVGNKIDKE-NREVTREEGQKFARKHNMLFIETSAKTRIGVQQAFEELVEKI 161
>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 = 35.9 bits (84), Expect = 0.011
Identities = 16/60 (26%), Positives = 24/60 (40%), Gaps = 1/60 (1%)
Query: 59 LRTRPAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQIR 118
L +P I+V NKIDL + K L + +S +DELL + +
Sbjct: 271 LAEKPRIVVLNKIDLLDEEELEEL-LKELKEALGKPVFPISALTGEGLDELLYALAELLE 329
>gnl|CDD|133267 cd01864, Rab19, Rab GTPase family 19 (Rab19). Rab19 subfamily.
Rab19 proteins are associated with Golgi stacks.
Similarity analysis indicated that Rab41 is closely
related to Rab19. However, the function of these Rabs is
not yet characterized. 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 = 35.1 bits (81), Expect = 0.014
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 65 IIVANKIDLARARAVSSQDAKNLAASFKVKF-IEVSVGIHHNVDE 108
+++ NK DL R V ++A LA + + +E S NV+E
Sbjct: 112 LLIGNKCDLEEQREVLFEEACTLAEHYGILAVLETSAKESSNVEE 156
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 35.2 bits (82), Expect = 0.024
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 47 EQDVIRLHEEGYLRTRPAIIVANKIDLARAR 77
++D++ L E ++P +I ANK DL A
Sbjct: 203 DEDLLELARELRKISKPMVIAANKADLPPAE 233
>gnl|CDD|206658 cd01866, Rab2, Rab GTPase family 2 (Rab2). Rab2 is localized on
cis-Golgi membranes and interacts with Golgi matrix
proteins. Rab2 is also implicated in the maturation of
vesicular tubular clusters (VTCs), which are
microtubule-associated intermediates in transport
between the ER and Golgi apparatus. In plants, Rab2
regulates vesicle trafficking between the ER and the
Golgi bodies and is important to pollen tube growth.
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 = 168
Score = 34.3 bits (79), Expect = 0.024
Identities = 14/44 (31%), Positives = 23/44 (52%)
Query: 65 IIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDE 108
+++ NK DL R VS ++ + A + F+E S NV+E
Sbjct: 113 MLIGNKCDLESRREVSYEEGEAFAREHGLIFMETSAKTASNVEE 156
>gnl|CDD|206695 cd04112, Rab26, Rab GTPase family 26 (Rab26). Rab26 subfamily.
First identified in rat pancreatic acinar cells, Rab26
is believed to play a role in recruiting mature granules
to the plasma membrane upon beta-adrenergic stimulation.
Rab26 belongs to the Rab functional group III, which are
considered key regulators of intracellular vesicle
transport during exocytosis. 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 = 191
Score = 34.5 bits (79), Expect = 0.026
Identities = 25/116 (21%), Positives = 54/116 (46%), Gaps = 9/116 (7%)
Query: 11 KVRAIIWN----EQYEKLTSS---DETGLIIVW-MLYKPSYHRVEQDVIRLHEEGYLRTR 62
KV+ IW+ E++ +T + D L++++ + K S+ + + + E
Sbjct: 49 KVKLQIWDTAGQERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDVV 108
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQIR 118
+++ NK D++ R V +D + LA + V F+E S NV+ + +++
Sbjct: 109 -IMLLGNKADMSGERVVKREDGERLAKEYGVPFMETSAKTGLNVELAFTAVAKELK 163
>gnl|CDD|133321 cd04121, Rab40, Rab GTPase family 40 (Rab40) contains Rab40a,
Rab40b and Rab40c. The Rab40 subfamily contains Rab40a,
Rab40b, and Rab40c, which are all highly homologous. In
rat, Rab40c is localized to the perinuclear recycling
compartment (PRC), and is distributed in a
tissue-specific manor, with high expression in brain,
heart, kidney, and testis, low expression in lung and
liver, and no expression in spleen and skeletal muscle.
Rab40c is highly expressed in differentiated
oligodendrocytes but minimally expressed in
oligodendrocyte progenitors, suggesting a role in the
vesicular transport of myelin components. Unlike most
other Ras-superfamily proteins, Rab40c was shown to have
a much lower affinity for GTP, and an affinity for GDP
that is lower than for 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. 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 = 189
Score = 34.1 bits (78), Expect = 0.027
Identities = 16/46 (34%), Positives = 26/46 (56%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDE 108
P I+V N++ LA R V+++ A+ A + F EVS + N+ E
Sbjct: 112 PKILVGNRLHLAFKRQVATEQAQAYAERNGMTFFEVSPLCNFNITE 157
>gnl|CDD|197651 smart00320, WD40, WD40 repeats. Note that these repeats are
permuted with respect to the structural repeats
(blades) of the beta propeller domain.
Length = 40
Score = 31.5 bits (72), Expect = 0.028
Identities = 10/34 (29%), Positives = 21/34 (61%)
Query: 3 QSLQGHSGKVRAIIWNEQYEKLTSSDETGLIIVW 36
++L+GH+G V ++ ++ + L S + G I +W
Sbjct: 6 KTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 34.3 bits (78), Expect = 0.032
Identities = 32/126 (25%), Positives = 57/126 (45%), Gaps = 9/126 (7%)
Query: 11 KVRAIIWN----EQYEKLTSS---DETGLIIVWMLYKPSYHRVEQDVIRLHEEGYLRTRP 63
+++ IW+ E++ LTSS + G+I+V+ + + DV E Y +
Sbjct: 61 RLKLTIWDTAGQERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQD 120
Query: 64 AI--IVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQIRLKR 121
+ +V NK+D R VS ++ LA F+E S NV++ + +I
Sbjct: 121 CVKMLVGNKVDRESERDVSREEGMALAKEHGCLFLECSAKTRENVEQCFEELALKIMEVP 180
Query: 122 SLVQTG 127
SL++ G
Sbjct: 181 SLLEEG 186
>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 = 33.4 bits (77), Expect = 0.042
Identities = 21/76 (27%), Positives = 29/76 (38%), Gaps = 15/76 (19%)
Query: 47 EQDVIRLHEEGYLRTRPAIIVANKIDLARARAVSSQDAKNLAASFK------VKFIEVSV 100
E + L E R +P ++V NKIDL V + + L K + I VS
Sbjct: 94 EAKLGLLRE----RGKPVLLVLNKIDL-----VPESEEEELLRERKLELLPDLPVIAVSA 144
Query: 101 GIHHNVDELLVGILNQ 116
+DEL I
Sbjct: 145 LPGEGIDELRKKIAEL 160
>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 = 33.7 bits (77), Expect = 0.045
Identities = 26/99 (26%), Positives = 45/99 (45%), Gaps = 2/99 (2%)
Query: 23 KLTSSDETGLIIVWMLYKP-SYHRVEQDVIRLHEEGYLRTRPAIIVANKIDLARARAVSS 81
KL+ + +V+ + P S+ V++ + E + P ++V NKID R V +
Sbjct: 65 KLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNKIDSLAERQVEA 124
Query: 82 QDAKNLAA-SFKVKFIEVSVGIHHNVDELLVGILNQIRL 119
DA + + F+E S + NV E+ +L Q L
Sbjct: 125 ADALSTVELDWNNGFVEASAKDNENVTEVFKELLQQANL 163
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 33.8 bits (78), Expect = 0.064
Identities = 29/109 (26%), Positives = 43/109 (39%), Gaps = 15/109 (13%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQIRLKRS 122
PA+ V NKIDL ++ + LA I GI N+DEL I + + L R
Sbjct: 241 PALYVVNKIDL-----PGLEELERLARKPNSVPISAKKGI--NLDELKERIWDVLGLIRV 293
Query: 123 LVQTGGAQAAAP----WKSNTTLVRASAVIVGSVDGN----RIWGKEFK 163
+ G + + +T+ I + N R+WGK K
Sbjct: 294 YTKPPGEEPDFDEPLILRRGSTVGDVCRKIHRDLVENFRYARVWGKSVK 342
>gnl|CDD|206698 cd04117, Rab15, Rab GTPase family 15 (Rab15). Rab15 colocalizes
with the transferrin receptor in early endosome
compartments, but not with late endosomal markers. It
codistributes with Rab4 and Rab5 on early/sorting
endosomes, and with Rab11 on pericentriolar recycling
endosomes. It is believed to function as an inhibitory
GTPase that regulates distinct steps in early endocytic
trafficking. 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 = 164
Score = 32.6 bits (74), Expect = 0.091
Identities = 26/111 (23%), Positives = 48/111 (43%), Gaps = 9/111 (8%)
Query: 11 KVRAIIWN----EQYEKLTSSDETGLIIVWMLYKPSYHRVEQDVIR----LHEEGYLRTR 62
KVR IW+ E+Y+ +T ++++Y S R Q +++ + E +
Sbjct: 48 KVRIQIWDTAGQERYQTITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQ 107
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGI 113
I++ NK D + R V + LA + + F E S + N+ E +
Sbjct: 108 -KILIGNKADEEQKRQVGDEQGNKLAKEYGMDFFETSACTNKNIKESFTRL 157
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 30.0 bits (68), Expect = 0.097
Identities = 10/34 (29%), Positives = 20/34 (58%)
Query: 3 QSLQGHSGKVRAIIWNEQYEKLTSSDETGLIIVW 36
++L+GH+G V ++ ++ L S + G + VW
Sbjct: 5 RTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVW 38
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 32.1 bits (74), Expect = 0.12
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDEL 109
P I+V NKIDL +S + + + I++S VDEL
Sbjct: 114 PVIVVLNKIDLLTEEDLSEIEKELEKE--GEEVIKISTLTEEGVDEL 158
>gnl|CDD|133322 cd04122, Rab14, Rab GTPase family 14 (Rab14). Rab14 GTPases are
localized to biosynthetic compartments, including the
rough ER, the Golgi complex, and the trans-Golgi
network, and to endosomal compartments, including early
endosomal vacuoles and associated vesicles. Rab14 is
believed to function in both the biosynthetic and
recycling pathways between the Golgi and endosomal
compartments. Rab14 has also been identified on GLUT4
vesicles, and has been suggested to help regulate GLUT4
translocation. In addition, Rab14 is believed to play a
role in the regulation of phagocytosis. 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 = 31.7 bits (72), Expect = 0.15
Identities = 29/121 (23%), Positives = 51/121 (42%), Gaps = 21/121 (17%)
Query: 11 KVRAIIWN----EQYEKLTSSDETGLIIVWMLY----KPSYHRVE---QDVIRLHEEGYL 59
K++ IW+ E++ +T S G M+Y + +Y+ + D L
Sbjct: 50 KIKLQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNL------ 103
Query: 60 RTRPA---IIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQ 116
T P ++ NK DL R V+ ++AK A + F+E S NV++ + +
Sbjct: 104 -TNPNTVIFLIGNKADLEAQRDVTYEEAKQFADENGLLFLECSAKTGENVEDAFLETAKK 162
Query: 117 I 117
I
Sbjct: 163 I 163
>gnl|CDD|206683 cd01896, DRG, Developmentally Regulated GTP-binding protein (DRG).
The developmentally regulated GTP-binding protein (DRG)
subfamily is an uncharacterized member of the Obg
family, an evolutionary branch of GTPase superfamily
proteins. GTPases act as molecular switches regulating
diverse cellular processes. DRG2 and DRG1 comprise the
DRG subfamily in eukaryotes. In view of their widespread
expression in various tissues and high conservation
among distantly related species in eukaryotes and
archaea, DRG proteins may regulate fundamental cellular
processes. It is proposed that the DRG subfamily
proteins play their physiological roles through RNA
binding.
Length = 233
Score = 31.7 bits (73), Expect = 0.21
Identities = 25/74 (33%), Positives = 32/74 (43%), Gaps = 14/74 (18%)
Query: 49 DVIRLHEEGYLRTRPAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDE 108
DVI EG P + V NKIDL +S ++ LA I + N+DE
Sbjct: 168 DVI----EGNRVYIPCLYVYNKIDL-----ISIEELDRLARIPNSVVISAEKDL--NLDE 216
Query: 109 LLVGI---LNQIRL 119
LL I L IR+
Sbjct: 217 LLERIWDYLGLIRI 230
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at
its C-terminus and is 40 residues long, hence the name
WD40; between GH and WD lies a conserved core; serves
as a stable propeller-like platform to which proteins
can bind either stably or reversibly; forms a
propeller-like structure with several blades where each
blade is composed of a four-stranded anti-parallel
b-sheet; instances with few detectable copies are
hypothesized to form larger structures by dimerization;
each WD40 sequence repeat forms the first three strands
of one blade and the last strand in the next blade; the
last C-terminal WD40 repeat completes the blade
structure of the first WD40 repeat to create the closed
ring propeller-structure; residues on the top and
bottom surface of the propeller are proposed to
coordinate interactions with other proteins and/or
small ligands; 7 copies of the repeat are present in
this alignment.
Length = 289
Score = 31.9 bits (73), Expect = 0.22
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 3 QSLQGHSGKVRAIIWNEQYEKLTSSDETGLIIVW 36
++L+GH+G V + ++ + L + G I VW
Sbjct: 3 RTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVW 36
Score = 28.8 bits (65), Expect = 2.0
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 3 QSLQGHSGKVRAIIWNEQYEKLTSSDETGLIIVW 36
+L+GH V ++ ++ L S E G I VW
Sbjct: 213 GTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVW 246
Score = 27.3 bits (61), Expect = 7.0
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 3 QSLQGHSGKVRAIIWNEQYEKLTSSDETGLIIVW 36
+L GH+G+V ++ ++ EKL SS G I +W
Sbjct: 171 ATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLW 204
>gnl|CDD|133310 cd04110, Rab35, Rab GTPase family 35 (Rab35). Rab35 is one of
several Rab proteins to be found to participate in the
regulation of osteoclast cells in rats. In addition,
Rab35 has been identified as a protein that interacts
with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK)
in human cells. Overexpression of NPM-ALK is a key
oncogenic event in some anaplastic large-cell lymphomas;
since Rab35 interacts with N|PM-ALK, it may provide a
target for cancer treatments. 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 = 199
Score = 31.7 bits (72), Expect = 0.22
Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 1/66 (1%)
Query: 65 IIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQIRLKRSLV 124
++V NK D + V ++DA A + E S + NV+E+ I + L+
Sbjct: 114 VLVGNKNDDPERKVVETEDAYKFAGQMGISLFETSAKENINVEEMFNCITELV-LRAKKD 172
Query: 125 QTGGAQ 130
Q
Sbjct: 173 NLAKQQ 178
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 32.1 bits (74), Expect = 0.23
Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 7/63 (11%)
Query: 47 EQDVIRLHEEGYLRTRPAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNV 106
E ++I +E R P I+V NKIDL S + + L F + I VS +
Sbjct: 103 ELELIEELKE---RKIPYIVVINKIDLGEE----SAELEKLEKKFGLPPIFVSALTGEGI 155
Query: 107 DEL 109
DEL
Sbjct: 156 DEL 158
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 31.2 bits (71), Expect = 0.26
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 1/47 (2%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDEL 109
P I+V NKIDL R + + A A I +S N+D
Sbjct: 111 PIILVGNKIDL-RDAKLKTHVAFLFAKLNGEPIIPLSAETGKNIDSA 156
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane protein.
The N terminus contains a P-loop motif suggesting that
iron transport may be ATP dependent.
Length = 159
Score = 30.5 bits (70), Expect = 0.41
Identities = 15/53 (28%), Positives = 21/53 (39%), Gaps = 1/53 (1%)
Query: 62 RPAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGIL 114
P ++ N ID A R + D L+ V + S +DELL I
Sbjct: 103 LPVVVALNMIDEAEKRGIKI-DLDKLSELLGVPVVPTSARKGEGIDELLDAIA 154
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 31.1 bits (71), Expect = 0.45
Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 30 TGLIIVWMLYKP-SYHRVEQDVIRLHEEGYLRTRPAIIVANKIDLARARAVSSQDAKNLA 88
G+I+ + +E+ + L E L P ++V NKID+A + + +
Sbjct: 248 AGVILFLFDPSETCGYSLEEQISLLEEIKELFKAPIVVVINKIDIADEEKL-----EEIE 302
Query: 89 ASFKVKFIEVSVGI 102
AS + E + I
Sbjct: 303 ASVLEEGGEEPLKI 316
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 30.9 bits (71), Expect = 0.49
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 7/51 (13%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFK---VKFIEVSVGIHHNVDELL 110
IIV NKIDL +A+ L A ++ +E+S +DEL
Sbjct: 113 KPIIVLNKIDLLDDLE----EARELLALYRAIGYDVLELSAKEGEGLDELK 159
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 30.5 bits (68), Expect = 0.55
Identities = 31/123 (25%), Positives = 53/123 (43%), Gaps = 13/123 (10%)
Query: 1 MNQSLQGHSGKVRAIIWN----EQYEKLTSS---DETGLIIVW-MLYKPSYHRVEQDVIR 52
++++L G VR +W+ E++ L S D I+V+ + + S+ + +
Sbjct: 18 LSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQD 77
Query: 53 LHEEGYLRTRPAII--VANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELL 110
+ E R + II V NK DL R V+ ++ A + F E S HN+ L
Sbjct: 78 ILNE---RGKDVIIALVGNKTDLGDLRKVTYEEGMQKAQEYNTMFHETSAKAGHNIKVLF 134
Query: 111 VGI 113
I
Sbjct: 135 KKI 137
>gnl|CDD|234724 PRK00315, PRK00315, potassium-transporting ATPase subunit C;
Reviewed.
Length = 193
Score = 30.2 bits (69), Expect = 0.57
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 123 LVQTGGAQAAAPWKSNTTLVRASAVIVGS 151
L+ TG QAA PW++N +L+R +VGS
Sbjct: 25 LLTTGIGQAAFPWQANGSLIRKDGKVVGS 53
>gnl|CDD|206692 cd04107, Rab32_Rab38, Rab GTPase families 18 (Rab18) and 32
(Rab32). Rab38/Rab32 subfamily. Rab32 and Rab38 are
members of the Rab family of small GTPases. Human Rab32
was first identified in platelets but it is expressed in
a variety of cell types, where it functions as an
A-kinase anchoring protein (AKAP). Rab38 has been shown
to be melanocyte-specific. 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 = 201
Score = 30.4 bits (69), Expect = 0.62
Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 63 PAIIVANKIDLARAR-AVSSQDAKNLAASFK-VKFIEVSVGIHHNVDELLVGILNQI 117
PA+++ANK DL + R A + + + E S + N++E + ++ I
Sbjct: 112 PALLLANKCDLKKERLAKDPEQMDQFCKENGFIGWFETSAKENINIEEAMRFLVKNI 168
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 30.6 bits (70), Expect = 0.76
Identities = 17/58 (29%), Positives = 24/58 (41%), Gaps = 15/58 (25%)
Query: 59 LRTRPAIIVANKIDLARARAVSSQDAKNLAASFKVKF-------IEVSVGIHHNVDEL 109
L RP ++V NKID+ DA+ LA + + EVS + EL
Sbjct: 282 LAERPRLVVLNKIDVP--------DARELAEFVRPELEARGWPVFEVSAASREGLREL 331
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 30.2 bits (69), Expect = 0.78
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 1/57 (1%)
Query: 47 EQDVIRLHEEGYLRTRPAIIVANKIDLARARAVSSQDA-KNLAASFKVKFIEVSVGI 102
E+D+ L L +P + VAN + A K LAA + + VS I
Sbjct: 192 EEDLEALASLNLLTAKPMLYVANVSEDDLANLNEYVKRLKELAAKENAEVVPVSAAI 248
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 29.4 bits (67), Expect = 0.88
Identities = 14/57 (24%), Positives = 20/57 (35%), Gaps = 7/57 (12%)
Query: 59 LRTRPAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILN 115
+P I+V NK DL S+ I +S +DEL +L
Sbjct: 107 PAKKPVIVVLNKSDLLSDAEGISELNGK-------PIIAISAKTGEGIDELKEALLE 156
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 29.7 bits (68), Expect = 0.92
Identities = 11/47 (23%), Positives = 18/47 (38%), Gaps = 2/47 (4%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDEL 109
+IV NK DL + ++ + + VS +DEL
Sbjct: 35 EPVIVLNKADLVDDEEL--EELLEIYEKLGYPVLAVSAKTGEGLDEL 79
>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 = 29.4 bits (67), Expect = 1.1
Identities = 16/65 (24%), Positives = 23/65 (35%), Gaps = 13/65 (20%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASF---------KVKFIEVS--VGIHHNVDELLV 111
P I+ NKID + KN + V + +S G +D+LL
Sbjct: 103 PIIVAINKIDKPYGTEADPERVKNELSELGLVGEEWGGDVSIVPISAKTGE--GIDDLLE 160
Query: 112 GILNQ 116
IL
Sbjct: 161 AILLL 165
>gnl|CDD|206696 cd04113, Rab4, Rab GTPase family 4 (Rab4). Rab4 subfamily. Rab4
has been implicated in numerous functions within the
cell. It helps regulate endocytosis through the sorting,
recycling, and degradation of early endosomes. Mammalian
Rab4 is involved in the regulation of many surface
proteins including G-protein-coupled receptors,
transferrin receptor, integrins, and surfactant protein
A. Experimental data implicate Rab4 in regulation of the
recycling of internalized receptors back to the plasma
membrane. It is also believed to influence
receptor-mediated antigen processing in B-lymphocytes,
in calcium-dependent exocytosis in platelets, in
alpha-amylase secretion in pancreatic cells, and in
insulin-induced translocation of Glut4 from internal
vesicles to the cell surface. Rab4 is known to share
effector proteins with Rab5 and Rab11. 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 = 29.3 bits (66), Expect = 1.2
Identities = 16/44 (36%), Positives = 22/44 (50%)
Query: 65 IIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDE 108
I+V NK DL R V+ +A A + F+E S NV+E
Sbjct: 109 ILVGNKKDLEDDREVTFLEASRFAQENGLLFLETSALTGENVEE 152
>gnl|CDD|206686 cd01899, Ygr210, Ygr210 GTPase. Ygr210 is a member of Obg-like
family and present in archaea and fungi. They are
characterized by a distinct glycine-rich motif
immediately following the Walker B motif. The Ygr210 and
YyaF/YchF subfamilies appear to form one major branch of
the Obg-like family. Among eukaryotes, the Ygr210
subfamily is represented only in fungi. These fungal
proteins form a tight cluster with their archaeal
orthologs, which suggests the possibility of horizontal
transfer from archaea to fungi.
Length = 318
Score = 29.5 bits (67), Expect = 1.3
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 47 EQDVIRLHEEGYLRTRPAIIVANKIDLARARAVSSQDAKN 86
++D++RL E R +P +I ANK D+ A S+
Sbjct: 200 DEDLLRLARELRKRRKPMVIAANKADIPDAEENISKLRLK 239
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 29.7 bits (68), Expect = 1.4
Identities = 19/90 (21%), Positives = 33/90 (36%), Gaps = 16/90 (17%)
Query: 21 YEKLTSSDETGLIIVWMLYKPSYHRVEQDVIRLHEEGYLRTRPAIIVANKIDLARARAVS 80
E + +D +++ +L E D I + +P I+V NK DL +
Sbjct: 289 REAIEEAD----LVLLVLDASEPLTEEDDEILEELKD----KPVIVVLNKADLTGEIDLE 340
Query: 81 SQDAKNLAASFKVKFIEVSVGIHHNVDELL 110
++ K I +S +DEL
Sbjct: 341 EENGKP--------VIRISAKTGEGIDELR 362
>gnl|CDD|133315 cd04115, Rab33B_Rab33A, Rab GTPase family 33 includes Rab33A and
Rab33B. Rab33B/Rab33A subfamily. Rab33B is ubiquitously
expressed in mouse tissues and cells, where it is
localized to the medial Golgi cisternae. It colocalizes
with alpha-mannose II. Together with the other cisternal
Rabs, Rab6A and Rab6A', it is believed to regulate the
Golgi response to stress and is likely a molecular
target in stress-activated signaling pathways. Rab33A
(previously known as S10) is expressed primarily in the
brain and immune system cells. In humans, it is located
on the X chromosome at Xq26 and its expression is
down-regulated in tuberculosis patients. Experimental
evidence suggests that Rab33A is a novel CD8+ T cell
factor that likely plays a role in tuberculosis disease
processes. 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 = 170
Score = 28.9 bits (65), Expect = 1.7
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVS 99
P I+V NK DL V + A+ A + + E S
Sbjct: 111 PRILVGNKCDLREQIQVPTDLAQRFADAHSMPLFETS 147
>gnl|CDD|234685 PRK00197, proA, gamma-glutamyl phosphate reductase; Provisional.
Length = 417
Score = 29.3 bits (67), Expect = 1.8
Identities = 11/30 (36%), Positives = 14/30 (46%), Gaps = 6/30 (20%)
Query: 62 RPAIIVANKIDLARARAVSSQDAKNLAASF 91
I+ AN DLA AR A L+A+
Sbjct: 43 AAEILAANAKDLAAAR------ANGLSAAM 66
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 29.2 bits (66), Expect = 2.0
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 7/59 (11%)
Query: 65 IIVANKIDL-ARARAVSSQDA-----KNLAASFKVKFIEVSVGIHHNVDELLVGILNQI 117
IIV NKIDL +R RA+ + + K A I +S N+D L+ I I
Sbjct: 144 IIVQNKIDLVSRERALENYEQIKEFVKGTVAE-NAPIIPISAQHKANIDALIEAIEKYI 201
>gnl|CDD|133343 cd04143, Rhes_like, Ras homolog enriched in striatum (Rhes) and
activator of G-protein signaling 1 (Dexras1/AGS1). This
subfamily includes Rhes (Ras homolog enriched in
striatum) and Dexras1/AGS1 (activator of G-protein
signaling 1). These proteins are homologous, but exhibit
significant differences in tissue distribution and
subcellular localization. Rhes is found primarily in the
striatum of the brain, but is also expressed in other
areas of the brain, such as the cerebral cortex,
hippocampus, inferior colliculus, and cerebellum. Rhes
expression is controlled by thyroid hormones. In rat
PC12 cells, Rhes is farnesylated and localizes to the
plasma membrane. Rhes binds and activates PI3K, and
plays a role in coupling serpentine membrane receptors
with heterotrimeric G-protein signaling. Rhes has
recently been shown to be reduced under conditions of
dopamine supersensitivity and may play a role in
determining dopamine receptor sensitivity. Dexras1/AGS1
is a dexamethasone-induced Ras protein that is expressed
primarily in the brain, with low expression levels in
other tissues. Dexras1 localizes primarily to the
cytoplasm, and is a critical regulator of the circadian
master clock to photic and nonphotic input. 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 = 247
Score = 28.9 bits (65), Expect = 2.1
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNL-AASFKVKFIEVSVGIHHNVDEL 109
P +I NK D R V + + L + EVS + N+DE+
Sbjct: 115 PMVICGNKADRDFPREVQRDEVEQLVGGDENCAYFEVSAKKNSNLDEM 162
>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 = 28.2 bits (64), Expect = 2.7
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 62 RPAIIVANKIDLARARAVSSQDAKNLAASFKVK-FIEVSVGIHHNVDELL 110
P I+V NKIDL + + + L +S NVDELL
Sbjct: 112 TPVILVLNKIDLVKDKEDLLPLLEKLKELHPFAEIFPISALKGENVDELL 161
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 28.8 bits (65), Expect = 2.8
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 1/49 (2%)
Query: 62 RPAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELL 110
P I+ N ID A+ R + D + L+ V + ++EL
Sbjct: 109 IPMILALNMIDEAKKRGIRI-DIEKLSKLLGVPVVPTVAKRGEGLEELK 156
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 28.5 bits (62), Expect = 3.5
Identities = 9/34 (26%), Positives = 18/34 (52%)
Query: 3 QSLQGHSGKVRAIIWNEQYEKLTSSDETGLIIVW 36
++L GHS V ++ ++ + L S G + +W
Sbjct: 278 RTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLW 311
>gnl|CDD|133330 cd04130, Wrch_1, Wnt-1 responsive Cdc42 homolog (Wrch-1) is a Rho
family GTPase similar to Cdc42. Wrch-1 (Wnt-1
responsive Cdc42 homolog) is a Rho family GTPase that
shares significant sequence and functional similarity
with Cdc42. Wrch-1 was first identified in mouse mammary
epithelial cells, where its transcription is upregulated
in Wnt-1 transformation. Wrch-1 contains N- and
C-terminal extensions relative to cdc42, suggesting
potential differences in cellular localization and
function. The Wrch-1 N-terminal extension contains
putative SH3 domain-binding motifs and has been shown to
bind the SH3 domain-containing protein Grb2, which
increases the level of active Wrch-1 in cells. Unlike
Cdc42, which localizes to the cytosol and perinuclear
membranes, Wrch-1 localizes extensively with the plasma
membrane and endosomes. The membrane association,
localization, and biological activity of Wrch-1 indicate
an atypical model of regulation distinct from other Rho
family GTPases. Most Rho 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 Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 173
Score = 27.8 bits (62), Expect = 4.4
Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 3/51 (5%)
Query: 59 LRTRPAIIVANKIDLARARAVSSQDAKNLAASFK-VKFIEVSVGIHHNVDE 108
LRT V ++ + VS AK LA ++IE S N+ E
Sbjct: 116 LRTDVN--VLIQLARYGEKPVSQSRAKALAEKIGACEYIECSALTQKNLKE 164
>gnl|CDD|236931 PRK11563, PRK11563, bifunctional aldehyde dehydrogenase/enoyl-CoA
hydratase; Provisional.
Length = 675
Score = 27.9 bits (63), Expect = 4.8
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 206 GPGSEMGEIAALKYYLNRT 224
G G E+G + +K+Y+ RT
Sbjct: 485 GGGEELGGLRGVKHYMQRT 503
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 27.4 bits (62), Expect = 4.9
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 5/55 (9%)
Query: 63 PAIIVANKIDLARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDELLVGILNQI 117
P I+V NKIDL + ++ + + + + +S +D L I +
Sbjct: 155 PIILVLNKIDL-----LDDEELEERLRAGRPDAVFISAKTGEGLDLLKEAIEELL 204
>gnl|CDD|145774 pfam02796, HTH_7, Helix-turn-helix domain of resolvase.
Length = 45
Score = 25.4 bits (56), Expect = 5.0
Identities = 9/29 (31%), Positives = 13/29 (44%), Gaps = 1/29 (3%)
Query: 40 KPSYHRVEQD-VIRLHEEGYLRTRPAIIV 67
P + + + VI L EEG + A I
Sbjct: 3 PPKLNEEDINEVITLLEEGISIKQIAKIF 31
>gnl|CDD|237407 PRK13516, PRK13516, gamma-glutamyl:cysteine ligase; Provisional.
Length = 373
Score = 28.0 bits (63), Expect = 5.0
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 96 IEVSVGIHHNVDELLVGILNQIRLKRSLVQTG 127
IE++ G+ ++D+ L G L+ +R LVQ
Sbjct: 59 IEIATGVCRDIDQAL-GQLSAMR--DVLVQAA 87
>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 = 27.5 bits (62), Expect = 5.1
Identities = 12/88 (13%), Positives = 27/88 (30%), Gaps = 4/88 (4%)
Query: 18 NEQYEKLTSS--DETGLIIVWMLYKPSYHRVEQDVIRLHEEGYLRTRPAIIVANKIDLAR 75
E + ++T S +I + E++ ++ + + V NKIDL
Sbjct: 60 IEHHTEITESFLPRADAVIFVLSADQPLTESEREFLKEILKWS--GKKIFFVLNKIDLLS 117
Query: 76 ARAVSSQDAKNLAASFKVKFIEVSVGIH 103
+ + ++ I
Sbjct: 118 EEELEEVLEYSREELGVLELGGGEPRIF 145
>gnl|CDD|206675 cd01888, eIF2_gamma, Gamma subunit of initiation factor 2 (eIF2
gamma). eIF2 is a heterotrimeric translation initiation
factor that consists of alpha, beta, and gamma subunits.
The GTP-bound gamma subunit also binds initiator
methionyl-tRNA and delivers it to the 40S ribosomal
subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is
released from the ribosome. The gamma subunit has no
intrinsic GTPase activity, but is stimulated by the
GTPase activating protein (GAP) eIF5, and GDP/GTP
exchange is stimulated by the guanine nucleotide
exchange factor (GEF) eIF2B. eIF2B is a heteropentamer,
and the epsilon chain binds eIF2. Both eIF5 and
eIF2B-epsilon are known to bind strongly to eIF2-beta,
but have also been shown to bind directly to eIF2-gamma.
It is possible that eIF2-beta serves simply as a
high-affinity docking site for eIF5 and eIF2B-epsilon,
or that eIF2-beta serves a regulatory role. eIF2-gamma
is found only in eukaryotes and archaea. It is closely
related to SelB, the selenocysteine-specific elongation
factor from eubacteria. The translational factor
components of the ternary complex, IF2 in eubacteria and
eIF2 in eukaryotes are not the same protein (despite
their unfortunately similar names). Both factors are
GTPases; however, eubacterial IF-2 is a single
polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is
a member of the same family as eubacterial IF2, but the
two proteins are only distantly related. This family
includes translation initiation, elongation, and release
factors.
Length = 197
Score = 27.6 bits (62), Expect = 5.2
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 5/58 (8%)
Query: 65 IIVANKIDL-ARARAVSSQDA-KNLAAS---FKVKFIEVSVGIHHNVDELLVGILNQI 117
II+ NKIDL +A+ + + K I +S + +N+D L I+ +I
Sbjct: 135 IILQNKIDLVKEEQALENYEQIKEFVKGTIAENAPIIPISAQLKYNIDVLCEYIVKKI 192
>gnl|CDD|143398 cd07079, ALDH_F18-19_ProA-GPR, Gamma-glutamyl phosphate reductase
(GPR), aldehyde dehydrogenase families 18 and 19.
Gamma-glutamyl phosphate reductase (GPR), a L-proline
biosynthetic pathway (PBP) enzyme that catalyzes the
NADPH dependent reduction of L-gamma-glutamyl
5-phosphate into L-glutamate 5-semialdehyde and
phosphate. The glutamate route of the PBP involves two
enzymatic steps catalyzed by gamma-glutamyl kinase (GK,
EC 2.7.2.11) and GPR (EC 1.2.1.41). These enzymes are
fused into the bifunctional enzyme, ProA or
delta(1)-pyrroline-5-carboxylate synthetase (P5CS) in
plants and animals, whereas they are separate enzymes
in bacteria and yeast. In humans, the P5CS (ALDH18A1),
an inner mitochondrial membrane enzyme, is essential to
the de novo synthesis of the amino acids proline and
arginine. Tomato (Lycopersicon esculentum) has both the
prokaryotic-like polycistronic operons encoding GK and
GPR (PRO1, ALDH19) and the full-length, bifunctional
P5CS (PRO2, ALDH18B1).
Length = 406
Score = 27.8 bits (63), Expect = 5.8
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 62 RPAIIVANKIDLARARA 78
R I+ AN DLA AR
Sbjct: 37 RDEILEANAKDLAAARE 53
>gnl|CDD|173639 cd05066, PTKc_EphR_A, Catalytic domain of the Protein Tyrosine
Kinases, Class EphA Ephrin Receptors. Protein Tyrosine
Kinase (PTK) family; Ephrin Receptor (EphR) subfamily;
most class EphA receptors including EphA3, EphA4, EphA5,
and EphA7, but excluding EphA1, EphA2 and EphA10;
catalytic (c) domain. The PTKc family is part of a
larger superfamily that includes the catalytic domains
of other kinases such as protein serine/threonine
kinases, RIO kinases, and phosphoinositide 3-kinase
(PI3K). PTKs catalyze the transfer of the
gamma-phosphoryl group from ATP to tyrosine (tyr)
residues in protein substrates. EphRs comprise the
largest subfamily of receptor tyr kinases (RTKs). In
general, class EphA receptors bind GPI-anchored ephrin-A
ligands. There are ten vertebrate EphA receptors
(EphA1-10), which display promiscuous interactions with
six ephrin-A ligands. One exception is EphA4, which also
binds ephrins-B2/B3. EphRs contain an ephrin-binding
domain and two fibronectin repeats extracellularly, a
transmembrane segment, and a cytoplasmic tyr kinase
domain. Binding of the ephrin ligand to EphR requires
cell-cell contact since both are anchored to the plasma
membrane. The resulting downstream signals occur
bidirectionally in both EphR-expressing cells (forward
signaling) and ephrin-expressing cells (reverse
signaling). Ephrin/EphR interaction mainly results in
cell-cell repulsion or adhesion, making it important in
neural development and plasticity, cell morphogenesis,
cell-fate determination, embryonic development, tissue
patterning, and angiogenesis. EphARs and ephrin-A
ligands are expressed in multiple areas of the
developing brain, especially in the retina and tectum.
They are part of a system controlling retinotectal
mapping.
Length = 267
Score = 27.6 bits (61), Expect = 6.0
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 20 QYEKLTSSDETGL--IIVW--MLY--KPSYHRVEQDVIRLHEEGY 58
Y K TS+ + I++W M Y +P + QDVI+ EEGY
Sbjct: 182 AYRKFTSASDVWSYGIVMWEVMSYGERPYWEMSNQDVIKAIEEGY 226
>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 = 27.2 bits (61), Expect = 6.2
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 54 HEEGYLRTRPAIIVANKIDLARARAVS 80
EE L+ P +I+ANK DL A S
Sbjct: 95 EEE--LKGAPLLILANKQDLPGALTES 119
>gnl|CDD|206694 cd04109, Rab28, Rab GTPase family 28 (Rab28). Rab28 subfamily.
First identified in maize, Rab28 has been shown to be a
late embryogenesis-abundant (Lea) protein that is
regulated by the plant hormone abcisic acid (ABA). In
Arabidopsis, Rab28 is expressed during embryo
development and is generally restricted to provascular
tissues in mature embryos. Unlike maize Rab28, it is not
ABA-inducible. Characterization of the human Rab28
homolog revealed two isoforms, which differ by a 95-base
pair insertion, producing an alternative sequence for
the 30 amino acids at the C-terminus. The two human
isoforms are presumably the result of alternative
splicing. Since they differ at the C-terminus but not in
the GTP-binding region, they are predicted to be
targeted to different cellular locations. 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 = 213
Score = 27.5 bits (61), Expect = 6.4
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 61 TRPAI-IVANKIDLARARAVSSQDAKNLAASFKVKFIEVS 99
T+P + +V NK DL R V+++ A ++ I VS
Sbjct: 108 TKPKMVLVGNKTDLEHNRQVTAEKHARFAQENDMESIFVS 147
>gnl|CDD|218287 pfam04841, Vps16_N, Vps16, N-terminal region. This protein forms
part of the Class C vacuolar protein sorting (Vps)
complex. Vps16 is essential for vacuolar protein
sorting, which is essential for viability in plants, but
not yeast. The Class C Vps complex is required for
SNARE-mediated membrane fusion at the lysosome-like
yeast vacuole. It is thought to play essential roles in
membrane docking and fusion at the Golgi-to-endosome and
endosome-to-vacuole stages of transport. The role of
VPS16 in this complex is not known.
Length = 408
Score = 27.5 bits (61), Expect = 6.5
Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 5/79 (6%)
Query: 122 SLVQTGGAQAAA--PWKSNTTLVRASAVIVGSVDGNRIWGK-EFKKTSMLGVQWTSDSQN 178
+ GG A P+ + + + + G ++ GK + ++ + W S +
Sbjct: 35 AAAPYGGPIAVTRSPFNLRPAYDQRPMIQIYNYSG-QLLGKILWNHEPLVKMGW-SKDEE 92
Query: 179 LLFAIKGGQVHLYDYEGNF 197
L+ K G V +Y G F
Sbjct: 93 LIVVQKSGIVIVYGLLGEF 111
>gnl|CDD|133318 cd04118, Rab24, Rab GTPase family 24 (Rab24). Rab24 is distinct
from other Rabs in several ways. It exists primarily in
the GTP-bound state, having a low intrinsic GTPase
activity; it is not efficiently geranyl-geranylated at
the C-terminus; it does not form a detectable complex
with Rab GDP-dissociation inhibitors (GDIs); and it has
recently been shown to undergo tyrosine phosphorylation
when overexpressed in vitro. The specific function of
Rab24 still remains unknown. It is found in a transport
route between ER-cis-Golgi and late endocytic
compartments. It is putatively involved in an autophagic
pathway, possibly directing misfolded proteins in the ER
to degradative pathways. 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 = 193
Score = 27.1 bits (60), Expect = 6.7
Identities = 15/48 (31%), Positives = 19/48 (39%), Gaps = 4/48 (8%)
Query: 66 IVANKIDL----ARARAVSSQDAKNLAASFKVKFIEVSVGIHHNVDEL 109
+ K DL R V D ++ A K + E S NVDEL
Sbjct: 110 LCGTKSDLIEQDRSLRQVDFHDVQDFADEIKAQHFETSSKTGQNVDEL 157
>gnl|CDD|184420 PRK13960, PRK13960,
phosphoribosylaminoimidazole-succinocarboxamide
synthase; Provisional.
Length = 367
Score = 27.4 bits (61), Expect = 6.9
Identities = 12/26 (46%), Positives = 14/26 (53%), Gaps = 6/26 (23%)
Query: 8 HSGKVRAIIWNEQYEKLTSSDETGLI 33
HSGKVR++ W LT D LI
Sbjct: 23 HSGKVRSVYW------LTEEDSRRLI 42
>gnl|CDD|143446 cd07128, ALDH_MaoC-N, N-terminal domain of the monoamine oxidase C
dehydratase. The N-terminal domain of the MaoC
dehydratase, a monoamine oxidase regulatory protein.
Orthologs of MaoC include PaaZ (Escherichia coli) and
PaaN (Pseudomonas putida), which are putative
ring-opening enzymes of the aerobic phenylacetic acid
(PA) catabolic pathway. The C-terminal domain of MaoC
has sequence similarity to enoyl-CoA hydratase. Also
included in this CD is a novel Burkholderia xenovorans
LB400 ALDH of the aerobic benzoate oxidation (box)
pathway. This pathway involves first the synthesis of a
CoA thio-esterified aromatic acid, with subsequent
dihydroxylation and cleavage steps, yielding the CoA
thio-esterified aliphatic aldehyde,
3,4-dehydroadipyl-CoA semialdehyde, which is further
converted into its corresponding CoA acid by the
Burkholderia LB400 ALDH.
Length = 513
Score = 27.6 bits (62), Expect = 7.5
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 206 GPGSEMGEIAALKYYLNRT 224
G G E+G + +K+Y+ RT
Sbjct: 481 GGGEELGGLRGVKHYMQRT 499
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 26.8 bits (59), Expect = 8.2
Identities = 25/136 (18%), Positives = 47/136 (34%), Gaps = 25/136 (18%)
Query: 7 GHSGKVRAIIWN----EQYEKLTSSDETGLIIVWMLYKPSYHRVEQDVIR--LHEEGYLR 60
+ ++ +W+ E+Y L G + ++Y + ++ L E L
Sbjct: 49 PYRRNIKLQLWDTAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELA 108
Query: 61 TR--PAIIVANKIDLARARAVSSQDAKNLA---------------ASFKVKFIEVSVGIH 103
P ++V NKIDL ++ S + L +E S
Sbjct: 109 PDDVPILLVGNKIDLFDEQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSL 168
Query: 104 H--NVDELLVGILNQI 117
NV+EL +L ++
Sbjct: 169 TGPNVNELFKELLRKL 184
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 27.2 bits (61), Expect = 8.3
Identities = 11/34 (32%), Positives = 14/34 (41%)
Query: 41 PSYHRVEQDVIRLHEEGYLRTRPAIIVANKIDLA 74
P + V + E P I+V NKIDL
Sbjct: 284 PEILEKLEAVEDVLAEIGADEIPIILVLNKIDLL 317
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 26.8 bits (60), Expect = 8.6
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 45 RVEQDVIRLHEEGYLRTRPAIIVANKIDLARA 76
+ E + EE L P +I+ANK DL A
Sbjct: 101 KEELHALLNEEE--LADAPLLILANKQDLPGA 130
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 27.1 bits (61), Expect = 9.9
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 10/60 (16%)
Query: 63 PAIIVANKIDLARARA--VSSQDAKN--LAASF--KVKFIEVS--VGIHHNVDELLVGIL 114
P ++ NKID A V + + + + V F+ VS G +DELL IL
Sbjct: 109 PIVVAINKIDKPEANPDKVKQELQEYGLVPEEWGGDVIFVPVSAKTGE--GIDELLELIL 166
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 0.132 0.386
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,874,821
Number of extensions: 1103285
Number of successful extensions: 1056
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1047
Number of HSP's successfully gapped: 125
Length of query: 238
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 144
Effective length of database: 6,768,326
Effective search space: 974638944
Effective search space used: 974638944
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: 57 (25.7 bits)