RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11135
(191 letters)
>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 = 328 bits (844), Expect = e-117
Identities = 134/162 (82%), Positives = 148/162 (91%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQE 62
EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGET LLDILDTAGQE
Sbjct: 1 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQE 60
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLST 122
EYSAMRDQYMRTGEGFL VFA+NS KSFEDI +YREQIKRVKD+++VPMVLVGNKCDL+
Sbjct: 61 EYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDLAA 120
Query: 123 WAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIK 164
V Q Q+LA+ + IP+I+TSAKTR GV++AFYTLVREI+
Sbjct: 121 RTVSTRQGQDLAKSYGIPYIETSAKTRQGVEEAFYTLVREIR 162
>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 = 301 bits (772), Expect = e-106
Identities = 115/164 (70%), Positives = 136/164 (82%), Gaps = 1/164 (0%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQE 62
EYKLVV+G GGVGKSALTIQ +Q HFVDEYDPTIEDSYRKQ+ IDGE LLDILDTAGQE
Sbjct: 2 EYKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIEDSYRKQIEIDGEVCLLDILDTAGQE 61
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLST 122
E+SAMRDQYMRTGEGFLLV+++ +SFE+I +REQI RVKD ++VP+VLVGNKCDL
Sbjct: 62 EFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDRDDVPIVLVGNKCDLEN 121
Query: 123 W-AVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
V + +ELA Q+ PF++TSAK R+ VD+AFY LVREI+K
Sbjct: 122 ERVVSTEEGKELARQWGCPFLETSAKERINVDEAFYDLVREIRK 165
>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 = 298 bits (766), Expect = e-105
Identities = 114/163 (69%), Positives = 137/163 (84%), Gaps = 1/163 (0%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEE 63
YKLVV+G+GGVGKSALTIQ IQ HFVD+YDPTIEDSYRKQ+ IDGE LLDILDTAGQEE
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIEDSYRKQIEIDGEVCLLDILDTAGQEE 60
Query: 64 YSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLSTW 123
+SAMRDQYMRTGEGFLLV+++ +SFE+I +REQI RVKD ++VP+VLVGNKCDL +
Sbjct: 61 FSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVGNKCDLESE 120
Query: 124 -AVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
V + +ELA Q+ PF++TSAK R+ VD+AFY LVREI+K
Sbjct: 121 RVVSTEEGKELARQWGCPFLETSAKERVNVDEAFYDLVREIRK 163
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 271 bits (695), Expect = 4e-94
Identities = 128/183 (69%), Positives = 146/183 (79%), Gaps = 4/183 (2%)
Query: 1 MAEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAG 60
EYKLVVVG GGVGKSALTIQ IQNHF+DEYDPTIEDSYRKQ VID ET LLDILDTAG
Sbjct: 3 STEYKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEETCLLDILDTAG 62
Query: 61 QEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL 120
QEEYSAMRDQYMRTG+GFL V+++ S SFE+I S+REQI RVKD + VPM+LVGNKCDL
Sbjct: 63 QEEYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDL 122
Query: 121 -STWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKKD---KMLRGKEKKK 176
S V + QELA+ F IPF++TSAK R+ VD+AFY LVREI+K M K+KKK
Sbjct: 123 DSERQVSTGEGQELAKSFGIPFLETSAKQRVNVDEAFYELVREIRKYLKEDMPSQKQKKK 182
Query: 177 RGI 179
G+
Sbjct: 183 GGL 185
>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 = 259 bits (664), Expect = 1e-89
Identities = 104/160 (65%), Positives = 131/160 (81%), Gaps = 1/160 (0%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
KLVV+GAGGVGKSALTI+ + FV+EYDPTIEDSYRKQ+V+DGET LDILDTAGQEE+
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYTLDILDTAGQEEF 60
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLSTW- 123
SAMRDQY+R G+GF+LV+++ S +SFE+I + REQI RVKD E+VP+VLVGNKCDL
Sbjct: 61 SAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIVLVGNKCDLENER 120
Query: 124 AVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREI 163
V + + LAE++ PF++TSAKT + +D+ F TLVREI
Sbjct: 121 QVSTEEGEALAEEWGCPFLETSAKTNINIDELFNTLVREI 160
>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 = 244 bits (625), Expect = 8e-84
Identities = 107/162 (66%), Positives = 125/162 (77%), Gaps = 1/162 (0%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEE 63
YKLVVVG GGVGKSALTIQ IQ++FV +YDPTIEDSY KQ IDG+ A LDILDTAGQEE
Sbjct: 3 YKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIEDSYTKQCEIDGQWARLDILDTAGQEE 62
Query: 64 YSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL-ST 122
+SAMR+QYMRTGEGFLLVF+V SFE++ + QI RVKD +E PM+LVGNK DL
Sbjct: 63 FSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADLEHQ 122
Query: 123 WAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIK 164
V + QELA Q IP+I+TSAK R+ VD AF+ LVR I+
Sbjct: 123 RQVSREEGQELARQLKIPYIETSAKDRVNVDKAFHDLVRVIR 164
>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 = 234 bits (599), Expect = 7e-80
Identities = 82/163 (50%), Positives = 108/163 (66%), Gaps = 3/163 (1%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTI-EDSYRKQVVIDGETALLDILDTAGQEE 63
KLV+VG GGVGKS+L I+ QN F +EY PTI D Y K + +DG+T L I DTAGQE
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQER 60
Query: 64 YSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLSTW 123
+ A+R Y R +GFLLV+ + S SFE++ + E+I R D E VP+VLVGNKCDL
Sbjct: 61 FRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHAD-ENVPIVLVGNKCDLEDQ 119
Query: 124 -AVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
V + + LA++ +PF++TSAKT V++AF L REI K
Sbjct: 120 RVVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELAREILK 162
>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 = 228 bits (582), Expect = 3e-77
Identities = 91/163 (55%), Positives = 128/163 (78%), Gaps = 1/163 (0%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEE 63
+K+++VG+GGVGKSALT+Q + + FV++Y+PT DSYRK+VV+DGE L+ILDTAGQE+
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQLNILDTAGQED 60
Query: 64 YSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLSTW 123
Y+A+RD Y R+GEGFLLVF++ M+SF + +REQI RVK+ + VP++LVGNKCDL
Sbjct: 61 YAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLLLVGNKCDLEDK 120
Query: 124 A-VDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
V + +A LAEQ+ + +++TSAKTR VD F+ LVREI++
Sbjct: 121 RQVSVEEAANLAEQWGVNYVETSAKTRANVDKVFFDLVREIRQ 163
>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 = 217 bits (555), Expect = 8e-73
Identities = 99/190 (52%), Positives = 135/190 (71%), Gaps = 3/190 (1%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
KLVV+G GGVGK+ALTIQL NHFV+ YDPTIEDSYRKQVV+DG+ +L++LDTAGQEEY
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYRKQVVVDGQPCMLEVLDTAGQEEY 60
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKD--AEEVPMVLVGNKCDLST 122
+A+RDQ++R GEGF+LV+++ S +FE + +REQI+RVKD A +VP+++VGNKCD
Sbjct: 61 TALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKVY 120
Query: 123 -WAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKKDKMLRGKEKKKRGISG 181
V + LA + FI+ SAKT + V+ AFYTLVR +++ + K
Sbjct: 121 EREVSTEEGAALARRLGCEFIEASAKTNVNVERAFYTLVRALRQQRQGGQGPKGGPTKKK 180
Query: 182 NKLKQCCVLL 191
K K+ CV++
Sbjct: 181 EKKKRKCVIM 190
>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 = 212 bits (541), Expect = 4e-71
Identities = 94/164 (57%), Positives = 127/164 (77%), Gaps = 1/164 (0%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQE 62
EYKLVV+G+GGVGKSALT+Q +Q FV++YDPTIEDSYRKQV +DG+ +L+ILDTAG E
Sbjct: 1 EYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDGQQCMLEILDTAGTE 60
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL-S 121
+++AMRD YM+ G+GF+LV+++ + +F D+ REQI RVKD E+VPM+LVGNKCDL
Sbjct: 61 QFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLED 120
Query: 122 TWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
V Q Q LA Q+ F++TSAK ++ V++ FY LVR+I +
Sbjct: 121 ERVVGKEQGQNLARQWGCAFLETSAKAKINVNEIFYDLVRQINR 164
>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 = 205 bits (522), Expect = 4e-68
Identities = 90/163 (55%), Positives = 122/163 (74%), Gaps = 2/163 (1%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQE 62
+YK+VV+GAGGVGKSALT+Q +QN F++ YDPTIEDSYRKQV IDG L+ILDTAG E
Sbjct: 1 DYKIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQVEIDGRQCDLEILDTAGTE 60
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL-S 121
+++AMR+ Y+++G+GFLLV++V S S ++G REQ+ R+KD++ VPMVLVGNK DL
Sbjct: 61 QFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLED 120
Query: 122 TWAVDMNQAQELAEQFN-IPFIKTSAKTRMGVDDAFYTLVREI 163
V L++Q+ +PF +TSA+ R VD+ F LVR+I
Sbjct: 121 DRQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDLVRQI 163
>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 = 204 bits (521), Expect = 7e-68
Identities = 90/167 (53%), Positives = 122/167 (73%), Gaps = 1/167 (0%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQE 62
EYK+V++GAGGVGKSA+T+Q I + F D +DPTIED+Y+ Q ID E ALLDILDTAGQ
Sbjct: 2 EYKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQARIDNEPALLDILDTAGQA 61
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL-S 121
E++AMRDQYMR GEGF++ ++V SF++ ++E I RV+ E++P+VLVGNK DL
Sbjct: 62 EFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLTEDIPLVLVGNKVDLEQ 121
Query: 122 TWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKKDKM 168
V + + LA +FN PF +TSA R +DDAF+ LVREI++ +
Sbjct: 122 QRQVTTEEGRNLAREFNCPFFETSAALRFYIDDAFHGLVREIRRKES 168
>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 = 200 bits (511), Expect = 2e-66
Identities = 95/163 (58%), Positives = 128/163 (78%), Gaps = 2/163 (1%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQE 62
EYKLVV+G+GGVGKSALT+Q +Q FVD+YDPTIEDSYRKQ+ +D + +L+ILDTAG E
Sbjct: 1 EYKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIEDSYRKQIEVDCQQCMLEILDTAGTE 60
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL-S 121
+++AMRD Y++ G+GF LV+++ + +SF D+ REQI RVKD E+VPM+LVGNKCDL
Sbjct: 61 QFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVGNKCDLED 120
Query: 122 TWAVDMNQAQELAEQF-NIPFIKTSAKTRMGVDDAFYTLVREI 163
V + Q LA Q+ N PF++TSAK+++ VD+ FY LVR+I
Sbjct: 121 ERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLVRQI 163
>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 = 192 bits (490), Expect = 3e-63
Identities = 77/162 (47%), Positives = 125/162 (77%), Gaps = 1/162 (0%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQE 62
EYK+VV+G+GGVGKSALT+Q + F+++YDPTIED YRK++ +D ++L+ILDTAG E
Sbjct: 1 EYKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIEDFYRKEIEVDSSPSVLEILDTAGTE 60
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLST 122
++++MRD Y++ G+GF++V+++ + ++F+DI R+QI RVK E+VP++LVGNK DL +
Sbjct: 61 QFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLES 120
Query: 123 W-AVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREI 163
V + + LAE++ PF++TSAK++ V++ F +VR++
Sbjct: 121 EREVSSAEGRALAEEWGCPFMETSAKSKTMVNELFAEIVRQM 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 = 162 bits (413), Expect = 1e-51
Identities = 59/160 (36%), Positives = 95/160 (59%), Gaps = 3/160 (1%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTI-EDSYRKQVVIDGETALLDILDTAGQE 62
+K+V++G GVGK++L ++ + N F + Y TI D K + +DG+ L I DTAGQE
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQE 60
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL-S 121
+ ++ Y R G +LV+ V + +SFE++ + ++K +P++LVGNK DL
Sbjct: 61 RFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAP-PNIPIILVGNKSDLED 119
Query: 122 TWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVR 161
V +AQ+ A++ + F +TSAKT VD+AF +L R
Sbjct: 120 ERQVSTEEAQQFAKENGLLFFETSAKTGENVDEAFESLAR 159
>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 = 157 bits (399), Expect = 4e-49
Identities = 67/162 (41%), Positives = 105/162 (64%), Gaps = 1/162 (0%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
K+ V+G+ VGKS+LT+Q ++ HFV+ Y PTIE+++ K + G+ L+I+DTAGQ+EY
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTFSKIITYKGQEYHLEIVDTAGQDEY 62
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLSTW- 123
S + +Y G++LV++V S KSFE + ++I + E VP+VLVGNK DL
Sbjct: 63 SILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDLHMER 122
Query: 124 AVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
V + ++LAE + F+++SAK V++AF L+ EI+K
Sbjct: 123 QVSAEEGKKLAESWGAAFLESSAKENENVEEAFELLIEEIEK 164
>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 = 149 bits (379), Expect = 2e-46
Identities = 59/163 (36%), Positives = 85/163 (52%), Gaps = 5/163 (3%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNH-FVDEYDPTIEDSYRKQVV-IDGETALLDILDTAG 60
E K+V+VG VGKS L +L+ N + EY P +Y V+ DG+T ++LDTAG
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG 60
Query: 61 QEEYSAMRDQYMRTGEGFLLVFA-VNSMKSFEDI-GSYREQIKRVKDAEEVPMVLVGNKC 118
QE+Y A+R Y R E L VF V + E+I ++I ++ VP++LVGNK
Sbjct: 61 QEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAES-GVPIILVGNKI 119
Query: 119 DLSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVR 161
DL + + A A+ P I SA+T +D AF +
Sbjct: 120 DLRDAKLKTHVAFLFAKLNGEPIIPLSAETGKNIDSAFKIVEA 162
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 145 bits (369), Expect = 8e-45
Identities = 59/164 (35%), Positives = 97/164 (59%), Gaps = 3/164 (1%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYR-KQVVIDGETALLDILDTAGQE 62
+K++++G GVGKS+L + F ++Y TI ++ K + +DG+ L I DTAGQE
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQE 60
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLST 122
+ ++ Y R G LLV+ + + +SFE++ ++ ++++ V ++LVGNK DL
Sbjct: 61 RFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYAS-PNVVIMLVGNKSDLEE 119
Query: 123 W-AVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
V +A+ AE+ +PF +TSAKT V++AF L REI K
Sbjct: 120 QRQVSREEAEAFAEEHGLPFFETSAKTNTNVEEAFEELAREILK 163
>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 = 132 bits (334), Expect = 1e-39
Identities = 63/165 (38%), Positives = 100/165 (60%), Gaps = 3/165 (1%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYR-KQVVIDGETALLDILDTAGQE 62
+KL+++G GVGKS L ++ + + + Y TI ++ + + +DG+T L I DTAGQE
Sbjct: 3 FKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQE 62
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL-S 121
+ + Y R G ++V+ V +SF ++ + ++I R +E V +LVGNKCDL
Sbjct: 63 RFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYA-SENVNKLLVGNKCDLTD 121
Query: 122 TWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKKD 166
VD +A+E A++ IPF++TSAK V++AF T+ REIKK
Sbjct: 122 KKVVDYTEAKEFADELGIPFLETSAKNATNVEEAFMTMAREIKKR 166
>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 = 129 bits (326), Expect = 2e-38
Identities = 60/166 (36%), Positives = 99/166 (59%), Gaps = 5/166 (3%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
K+ V+GA GVGKSALT++ + F+ EY+P +E Y +QV IDGE L+I DT GQ++
Sbjct: 1 KIAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYSRQVTIDGEQVSLEIQDTPGQQQN 60
Query: 65 SA--MRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVK-DAEEVPMVLVGNKCDLS 121
++ +R +GF+LV+++ SF+ + + I+ +K E+P++LVGNK DL
Sbjct: 61 EDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVILVGNKADLL 120
Query: 122 TW-AVDMNQAQELAEQFNIPFIKTSA-KTRMGVDDAFYTLVREIKK 165
V + Q+LA + F + SA + + V + F+ L RE+++
Sbjct: 121 HSRQVSTEEGQKLALELGCLFFEVSAAENYLEVQNVFHELCREVRR 166
>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 = 131 bits (331), Expect = 3e-38
Identities = 61/166 (36%), Positives = 96/166 (57%), Gaps = 10/166 (6%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEE 63
Y++VV+GA VGK+A+ + + F ++Y PTIED +RK I GE LDILDT+G
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIEDFHRKLYSIRGEVYQLDILDTSGNHP 60
Query: 64 YSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQI--------KRVKDAEEVPMVLVG 115
+ AMR + TG+ F+LVF++++ +SFE++ REQI + K+ ++PMV+ G
Sbjct: 61 FPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICG 120
Query: 116 NKCDLSTW-AVDMNQAQEL-AEQFNIPFIKTSAKTRMGVDDAFYTL 159
NK D V ++ ++L N + + SAK +D+ F L
Sbjct: 121 NKADRDFPREVQRDEVEQLVGGDENCAYFEVSAKKNSNLDEMFRAL 166
>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 = 126 bits (318), Expect = 3e-37
Identities = 61/161 (37%), Positives = 97/161 (60%), Gaps = 3/161 (1%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQE 62
+Y++VV GAGGVGKS+L ++ ++ F + Y PTIED+YR+ + L I DT G
Sbjct: 1 DYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCSKSICTLQITDTTGSH 60
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVK--DAEEVPMVLVGNKCDL 120
++ AM+ + G F+LV+++ S +S E++ E I +K + E++P++LVGNKCD
Sbjct: 61 QFPAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNNLEKIPIMLVGNKCDE 120
Query: 121 STW-AVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLV 160
S V ++ LA +N F++TSAKT V + F L+
Sbjct: 121 SPSREVSSSEGAALARTWNCAFMETSAKTNHNVQELFQELL 161
>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 = 120 bits (302), Expect = 1e-34
Identities = 58/164 (35%), Positives = 96/164 (58%), Gaps = 3/164 (1%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYR-KQVVIDGETALLDILDTAGQE 62
+KL+++G GVGKS L ++ ++ F + TI ++ + + +DG+ L I DTAGQE
Sbjct: 4 FKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAGQE 63
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLS- 121
+ + Y R G +LV+ + KSFE+I ++ I +E+V +LVGNKCD+
Sbjct: 64 RFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHA-SEDVERMLVGNKCDMEE 122
Query: 122 TWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
V + + LA ++ I F++TSAK + V++AF TL ++I K
Sbjct: 123 KRVVSKEEGEALAREYGIKFLETSAKANINVEEAFLTLAKDILK 166
>gnl|CDD|206641 cd00157, Rho, Ras homology family (Rho) of small guanosine
triphosphatases (GTPases). Members of the Rho (Ras
homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1,
RhoBTB, and Rop. There are 22 human Rho family members
identified currently. These proteins are all involved in
the reorganization of the actin cytoskeleton in response
to external stimuli. They also have roles in cell
transformation by Ras in cytokinesis, in focal adhesion
formation and in the stimulation of stress-activated
kinase. These various functions are controlled through
distinct effector proteins and mediated through a
GTP-binding/GTPase cycle involving three classes of
regulating proteins: GAPs (GTPase-activating proteins),
GEFs (guanine nucleotide exchange factors), and GDIs
(guanine nucleotide dissociation inhibitors). 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. Since crystal structures
often lack C-terminal residues, this feature is not
available for annotation in many of the CDs in the
hierarchy.
Length = 171
Score = 119 bits (302), Expect = 1e-34
Identities = 63/173 (36%), Positives = 94/173 (54%), Gaps = 20/173 (11%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
K+VVVG G VGK+ L I N F EY PT+ D+Y V +DG+ L + DTAGQEEY
Sbjct: 2 KIVVVGDGAVGKTCLLISYTTNKFPTEYVPTVFDNYSANVTVDGKQVNLGLWDTAGQEEY 61
Query: 65 SAMRD-QYMRTGEGFLLVFAVNSMKSFEDIGS--YREQIKRVKDAEEVPMVLVGNKCDL- 120
+R Y +T + FLL F+V+S SFE++ + Y E IK VP++LVG K DL
Sbjct: 62 DRLRPLSYPQT-DVFLLCFSVDSPSSFENVKTKWYPE-IK--HYCPNVPIILVGTKIDLR 117
Query: 121 -----------STWAVDMNQAQELAEQFN-IPFIKTSAKTRMGVDDAFYTLVR 161
+ + ++LA++ + +++ SA T+ G+ + F +R
Sbjct: 118 DDGNTLKKLEKKQKPITPEEGEKLAKEIGAVKYMECSALTQEGLKEVFDEAIR 170
>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 = 118 bits (297), Expect = 4e-34
Identities = 55/161 (34%), Positives = 91/161 (56%), Gaps = 1/161 (0%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYR-KQVVIDGETALLDILDTAGQE 62
K++++G GVGKS+L ++ + F ++ TI ++ K V +DG+ L I DTAGQE
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE 60
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLST 122
+ + Y R +G +LV+ V +F+++ ++ ++ + +LVGNK D
Sbjct: 61 RFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVGNKIDKEN 120
Query: 123 WAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREI 163
V + Q+ A + N+ FI+TSAKTR+GV AF LV +I
Sbjct: 121 REVTREEGQKFARKHNMLFIETSAKTRIGVQQAFEELVEKI 161
>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 = 118 bits (297), Expect = 5e-34
Identities = 53/162 (32%), Positives = 99/162 (61%), Gaps = 3/162 (1%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDS-YRKQVVIDGETALLDILDTAGQE 62
+K+V++G G VGK++L ++ ++N F ++++ T + S ++K V I G+ L I DTAGQE
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQE 60
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL-S 121
Y A+ Y R +G +LV+ + SF+ + + +++K+++ + +V+VGNK DL
Sbjct: 61 RYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMR-GNNISLVIVGNKIDLER 119
Query: 122 TWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREI 163
V ++A+E A+ +TSAKT G+++ F +L + +
Sbjct: 120 QRVVSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSLAKRM 161
>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 = 117 bits (294), Expect = 3e-33
Identities = 57/162 (35%), Positives = 96/162 (59%), Gaps = 2/162 (1%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
+LV +GA GVGK+AL + + + F ++ T+E+ + K+ + G +DILDT+G +
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVEELHSKEYEVAGVKVTIDILDTSGSYSF 60
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCD-LSTW 123
AMR ++ G+ F LV++V+ +SFE++ RE+I VK+ + VP+V+VGNK D L+
Sbjct: 61 PAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNKIDSLAER 120
Query: 124 AVDMNQAQELAE-QFNIPFIKTSAKTRMGVDDAFYTLVREIK 164
V+ A E +N F++ SAK V + F L+++
Sbjct: 121 QVEAADALSTVELDWNNGFVEASAKDNENVTEVFKELLQQAN 162
>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 = 115 bits (291), Expect = 3e-33
Identities = 60/163 (36%), Positives = 93/163 (57%), Gaps = 5/163 (3%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTI--EDSYRKQVVIDGETALLDILDTAGQ 61
+K+V++G GVGKS L + +N F + TI E + R + IDG+T I DTAGQ
Sbjct: 4 FKIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATR-TIQIDGKTIKAQIWDTAGQ 62
Query: 62 EEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL- 120
E Y A+ Y R G LLV+ + +FE++ + ++++ D+ + ++LVGNK DL
Sbjct: 63 ERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKELRDHADS-NIVIMLVGNKSDLR 121
Query: 121 STWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREI 163
AV +A+ AE+ + FI+TSA V++AF L+ EI
Sbjct: 122 HLRAVPTEEAKAFAEKNGLSFIETSALDGTNVEEAFKQLLTEI 164
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 116 bits (292), Expect = 9e-33
Identities = 64/217 (29%), Positives = 104/217 (47%), Gaps = 27/217 (12%)
Query: 1 MAEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQ-VVIDGETALLDILDTA 59
M E+K+VV+G GGVGK+ L +L+ + F + Y PTI + + + L + DTA
Sbjct: 3 MKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTA 62
Query: 60 GQEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCD 119
GQEEY ++R +Y R G L+V+ +S +++ + R ++VP++LVGNK D
Sbjct: 63 GQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKID 122
Query: 120 LSTW----AVDMNQ------------AQELAEQFNIPFIKTSAK--TRMGVDDAFYTLVR 161
L +NQ L E N ++TSAK T V++ F L+R
Sbjct: 123 LFDEQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELFKELLR 182
Query: 162 EI--KKDKMLRGKEKKKRGISGN------KLKQCCVL 190
++ + +K++ E ++ N CVL
Sbjct: 183 KLLEEIEKLVLKNELRQLDRLNNPIEQAALASFNCVL 219
>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 = 111 bits (279), Expect = 2e-31
Identities = 53/163 (32%), Positives = 94/163 (57%), Gaps = 3/163 (1%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSY-RKQVVIDGETALLDILDTAGQ 61
++KLV++G VGKS++ ++ ++N F + + TI ++ + V +D T +I DTAGQ
Sbjct: 1 QFKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQ 60
Query: 62 EEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL- 120
E Y ++ Y R ++V+ + S +SFE S+ ++++ V + L GNK DL
Sbjct: 61 ERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQEHGPPNIV-IALAGNKADLE 119
Query: 121 STWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREI 163
S V +AQE A++ + F++TSAKT V++ F + R++
Sbjct: 120 SKRQVSTEEAQEYADENGLLFMETSAKTGENVNELFTEIARKL 162
>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 = 112 bits (283), Expect = 2e-31
Identities = 60/182 (32%), Positives = 104/182 (57%), Gaps = 4/182 (2%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQN-HFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQE 62
Y++V++G GVGKS+L + Y+ + +D+Y + V +DGE A L + D QE
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVVYDHWEQE 60
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLS- 121
+ + D M+ G+ +++V++V SFE R Q++R + AE++P++LVGNK DL
Sbjct: 61 DGMWLEDSCMQVGDAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPIILVGNKSDLVR 120
Query: 122 TWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKKDKMLRGKEKKKRGISG 181
+ V + + + A F+ FI+TSA + VD+ F +VR+++ + KEK R ++
Sbjct: 121 SREVSVQEGRACAVVFDCKFIETSAALQHNVDELFEGIVRQVRLRR--DSKEKNTRRMAS 178
Query: 182 NK 183
K
Sbjct: 179 RK 180
>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 = 110 bits (277), Expect = 6e-31
Identities = 59/164 (35%), Positives = 93/164 (56%), Gaps = 6/164 (3%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTI-EDSYRKQVVIDGETALLDILDTAGQE 62
K++++G GVGK++L Q + F ++Y TI D K+V +D L I DTAGQE
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQE 60
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIK---RVKDAEEVPMVLVGNKCD 119
+ ++ + R + +LV+ V + KSFE + S+R++ +D E P V++GNK D
Sbjct: 61 RFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPENFPFVVLGNKID 120
Query: 120 LSTW-AVDMNQAQELAE-QFNIPFIKTSAKTRMGVDDAFYTLVR 161
L V +AQ+ + + NIP+ +TSAK + VD AF T+ R
Sbjct: 121 LEEKRQVSTKKAQQWCKSKGNIPYFETSAKEAINVDQAFETIAR 164
>gnl|CDD|206704 cd04132, Rho4_like, Ras homology family 4 (Rho4) of small guanosine
triphosphatases (GTPases)-like. Rho4 is a GTPase that
controls septum degradation by regulating secretion of
Eng1 or Agn1 during cytokinesis. Rho4 also plays a role
in cell morphogenesis. Rho4 regulates septation and cell
morphology by controlling the actin cytoskeleton and
cytoplasmic microtubules. The localization of Rho4 is
modulated by Rdi1, which may function as a GDI, and by
Rga9, which is believed to function as a GAP. In S.
pombe, both Rho4 deletion and Rho4 overexpression result
in a defective cell wall, suggesting a role for Rho4 in
maintaining cell wall integrity. 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.
Length = 197
Score = 109 bits (275), Expect = 2e-30
Identities = 56/207 (27%), Positives = 95/207 (45%), Gaps = 31/207 (14%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVI-DGETALLDILDTAGQ 61
+ K+VVVG GG GK+ L + Q F +EY PT+ ++Y + + +G+ L + DTAGQ
Sbjct: 3 KVKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPNGKIIELALWDTAGQ 62
Query: 62 EEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIK---RVKD-AEEVPMVLVGNK 117
E+Y +R + L+ ++V++ S +++ + K V P+VLVG K
Sbjct: 63 EDYDRLRPLSYPDVDVILICYSVDNPTSLDNV-----EDKWYPEVNHFCPGTPIVLVGLK 117
Query: 118 CDLS-------------TWAVDMNQAQELAEQFN-IPFIKTSAKTRMGVDDAFYTLVREI 163
DL V Q + +A+ + +I+ SAK VD+ F +
Sbjct: 118 TDLRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVFDAAINVA 177
Query: 164 KKDKMLRGKEKKKRGISGNKLKQCCVL 190
++KKK+ K+C +L
Sbjct: 178 LSKSGRAARKKKKK-------KKCVIL 197
>gnl|CDD|206697 cd04116, Rab9, Rab GTPase family 9 (Rab9). Rab9 is found in late
endosomes, together with mannose 6-phosphate receptors
(MPRs) and the tail-interacting protein of 47 kD
(TIP47). Rab9 is a key mediator of vesicular transport
from late endosomes to the trans-Golgi network (TGN) by
redirecting the MPRs. Rab9 has been identified as a key
component for the replication of several viruses,
including HIV1, Ebola, Marburg, and measles, making it a
potential target for inhibiting a variety of viruses.
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 = 108 bits (270), Expect = 5e-30
Identities = 54/164 (32%), Positives = 91/164 (55%), Gaps = 5/164 (3%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSY-RKQVVIDGETALLDILDTAGQEE 63
K++++G GGVGKS+L + + N F + TI + K + +DG L I DTAGQE
Sbjct: 7 KVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQER 66
Query: 64 YSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQI---KRVKDAEEVPMVLVGNKCDL 120
+ ++R + R + LL F+V+ +SF+++ +++++ VK+ E P V++GNK D+
Sbjct: 67 FRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKIDI 126
Query: 121 STWAVDMNQAQE-LAEQFNIPFIKTSAKTRMGVDDAFYTLVREI 163
V +AQ + + P+ +TSAK V AF VR +
Sbjct: 127 PERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRRV 170
>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 = 107 bits (268), Expect = 8e-30
Identities = 53/166 (31%), Positives = 78/166 (46%), Gaps = 16/166 (9%)
Query: 7 VVVGAGGVGKSALTIQLIQNHFV---DEYDPTI-EDSYRKQVVIDGETALLDILDTAGQE 62
VVVG GGVGKS+L L+ D T D Y K++ L ++DT G +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVK--LVLVDTPGLD 58
Query: 63 EYSAMRD-----QYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNK 117
E+ + +R + LLV +S ED + I R E +P++LVGNK
Sbjct: 59 EFGGLGREELARLLLRGADLILLVVDSTDRESEEDA---KLLILRRLRKEGIPIILVGNK 115
Query: 118 CDL--STWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVR 161
DL ++ + +ELA+ +P + SAKT GVD+ F L+
Sbjct: 116 IDLLEEREVEELLRLEELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
>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 = 104 bits (260), Expect = 2e-28
Identities = 58/167 (34%), Positives = 89/167 (53%), Gaps = 6/167 (3%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYR-KQVVIDGETALLDILDTAGQE 62
+K++V+G VGK+ LT + F + + TI +R + V IDGE + + DTAGQE
Sbjct: 3 FKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQE 62
Query: 63 EY-SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL- 120
+ +M Y R + V+ V +M SF + S+ E+ ++ EVP +LVGNKCDL
Sbjct: 63 RFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLR 122
Query: 121 STWAVDMNQAQELAEQFNIPFIKTSAK---TRMGVDDAFYTLVREIK 164
V + AQ A+ ++P +TSAK V+ F TL ++K
Sbjct: 123 EQIQVPTDLAQRFADAHSMPLFETSAKDPSENDHVEAIFMTLAHKLK 169
>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 = 104 bits (260), Expect = 2e-28
Identities = 57/156 (36%), Positives = 88/156 (56%), Gaps = 6/156 (3%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTI-EDSYRKQVVID--GETALLDILDTAGQ 61
K++VVG G VGKS++ + ++ F +Y TI D KQ+ + E L + DTAGQ
Sbjct: 2 KVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQ 61
Query: 62 EEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLS 121
EE+ A+ Y R + +LVF+ +SFE I S++E+++ ++PMVLV K DL
Sbjct: 62 EEFDAITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEAE--CGDIPMVLVQTKIDLL 119
Query: 122 TWAVDMNQ-AQELAEQFNIPFIKTSAKTRMGVDDAF 156
AV N+ A+ LA++ +P +TS K V + F
Sbjct: 120 DQAVITNEEAEALAKRLQLPLFRTSVKDDFNVTELF 155
>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 = 103 bits (259), Expect = 2e-28
Identities = 51/157 (32%), Positives = 87/157 (55%), Gaps = 7/157 (4%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTI-EDSYRKQVVIDGETALLDILDTAGQE 62
+KLV +G VGK+++ + + + F ++Y TI D K + +D +T L + DTAGQE
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQE 60
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAE--EVPMVLVGNKCDL 120
+ ++ Y+R ++V+ + + +SF++ + I V+D +V +VLVGNK DL
Sbjct: 61 RFRSLIPSYIRDSSVAVVVYDITNRQSFDNT---DKWIDDVRDERGNDVIIVLVGNKTDL 117
Query: 121 ST-WAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAF 156
S V + ++ A++ N FI+TSAK V F
Sbjct: 118 SDKRQVSTEEGEKKAKENNAMFIETSAKAGHNVKQLF 154
>gnl|CDD|197554 smart00174, RHO, Rho (Ras homology) subfamily of Ras-like small
GTPases. Members of this subfamily of Ras-like small
GTPases include Cdc42 and Rac, as well as Rho isoforms.
Length = 174
Score = 103 bits (258), Expect = 4e-28
Identities = 59/172 (34%), Positives = 91/172 (52%), Gaps = 19/172 (11%)
Query: 6 LVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEYS 65
LVVVG G VGK+ L I N F ++Y PT+ ++Y V +DG+ L + DTAGQE+Y
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTVFENYSADVEVDGKPVELGLWDTAGQEDYD 60
Query: 66 AMRD-QYMRTGEGFLLVFAVNSMKSFEDIGS-YREQIKRVKDAEEVPMVLVGNKCDLSTW 123
+R Y T + FL+ F+V+S SFE++ + ++K VP++LVG K DL
Sbjct: 61 RLRPLSYPDT-DVFLICFSVDSPASFENVKEKWYPEVK--HFCPNVPIILVGTKLDLRND 117
Query: 124 AVDMN-------------QAQELAEQFN-IPFIKTSAKTRMGVDDAFYTLVR 161
+ Q Q LA++ + +++ SA T+ GV + F +R
Sbjct: 118 KSTLEELSKKKQEPVTYEQGQALAKRIGAVKYLECSALTQEGVREVFEEAIR 169
>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 = 100 bits (251), Expect = 7e-27
Identities = 59/194 (30%), Positives = 105/194 (54%), Gaps = 11/194 (5%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYR-KQVVIDGETALLDILDTAGQE 62
+KL+++G GVGKS+L ++ N F Y TI ++ + V I+GE L I DTAGQE
Sbjct: 7 FKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQE 66
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKC-DLS 121
+ + Y R G ++V+ V + +SF ++ + ++I+ ++ ++V VLVGNK D
Sbjct: 67 RFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIE--QNCDDVCKVLVGNKNDDPE 124
Query: 122 TWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREI---KKDKMLRGKEKKKRG 178
V+ A + A Q I +TSAK + V++ F + + KKD + + +++++
Sbjct: 125 RKVVETEDAYKFAGQMGISLFETSAKENINVEEMFNCITELVLRAKKDNLAKQQQQQQND 184
Query: 179 I----SGNKLKQCC 188
+ +K K+ C
Sbjct: 185 VVKLPKNSKRKKRC 198
>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 = 98.6 bits (246), Expect = 2e-26
Identities = 55/164 (33%), Positives = 89/164 (54%), Gaps = 3/164 (1%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVV-IDGETALLDILDTAGQE 62
+K +++G GVGKS L +Q F +D TI + +++ IDG+ L I DTAGQE
Sbjct: 5 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQE 64
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL-S 121
+ ++ Y R G LLV+ + ++F + S+ E ++ ++ M L+GNKCDL S
Sbjct: 65 SFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIM-LIGNKCDLES 123
Query: 122 TWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
V + + A + + F++TSAKT V++AF +EI
Sbjct: 124 RREVSYEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEIYD 167
>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 = 96.8 bits (241), Expect = 1e-25
Identities = 57/173 (32%), Positives = 91/173 (52%), Gaps = 12/173 (6%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYR-KQVVID----------GETALL 53
KL+ +G GVGK+ + N F ++ T+ +R K+VV + L
Sbjct: 6 KLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVHL 65
Query: 54 DILDTAGQEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVL 113
+ DTAGQE + ++ + R GFLL+F + S +SF ++ ++ Q++ E +VL
Sbjct: 66 QLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCENPDIVL 125
Query: 114 VGNKCDLSTW-AVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
+GNK DL V QA+ELA+++ IP+ +TSA T V+ A TL+ I K
Sbjct: 126 IGNKADLPDQREVSERQARELADKYGIPYFETSAATGQNVEKAVETLLDLIMK 178
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 94.6 bits (235), Expect = 2e-24
Identities = 54/164 (32%), Positives = 89/164 (54%), Gaps = 3/164 (1%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSY-RKQVVIDGETALLDILDTAGQE 62
+K +++G GVGKS L +Q F +D TI + + + ID + L I DTAGQE
Sbjct: 7 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDTAGQE 66
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLS- 121
+ ++ Y R G LLV+ + ++F + S+ E ++ +A M L+GNKCDL+
Sbjct: 67 SFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIM-LIGNKCDLAH 125
Query: 122 TWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
AV + ++ A++ + F++ SAKT V++AF +I K
Sbjct: 126 RRAVSTEEGEQFAKEHGLIFMEASAKTAQNVEEAFIKTAAKIYK 169
>gnl|CDD|206705 cd04133, Rop_like, Rho-related protein from plants (Rop)-like. The
Rop (Rho-related protein from plants) subfamily plays a
role in diverse cellular processes, including
cytoskeletal organization, pollen and vegetative cell
growth, hormone responses, stress responses, and
pathogen resistance. Rops are able to regulate several
downstream pathways to amplify a specific signal by
acting as master switches early in the signaling
cascade. They transmit a variety of extracellular and
intracellular signals. Rops are involved in establishing
cell polarity in root-hair development, root-hair
elongation, pollen-tube growth, cell-shape formation,
responses to hormones such as abscisic acid (ABA) and
auxin, responses to abiotic stresses such as oxygen
deprivation, and disease resistance and disease
susceptibility. An individual Rop can have a unique
function or an overlapping function shared with other
Rop proteins; in addition, a given Rop-regulated
function can be controlled by one or multiple Rop
proteins. For example, Rop1, Rop3, and Rop5 are all
involved in pollen-tube growth; Rop2 plays a role in
response to low-oxygen environments, cell-morphology,
and root-hair development; root-hair development is also
regulated by Rop4 and Rop6; Rop6 is also responsible for
ABA response, and ABA response is also regulated by
Rop10. Plants retain some of the regulatory mechanisms
that are shared by other members of the Rho family, but
have also developed a number of unique modes for
regulating Rops. Unique RhoGEFs have been identified
that are exclusively active toward Rop proteins, such as
those containing the domain PRONE (plant-specific Rop
nucleotide exchanger). 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 = 93.4 bits (232), Expect = 3e-24
Identities = 57/170 (33%), Positives = 88/170 (51%), Gaps = 15/170 (8%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
K V VG G VGK+ + I N F +Y PT+ D++ VV+DG T L + DTAGQE+Y
Sbjct: 3 KCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQEDY 62
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIG-SYREQIKRVKDAEEVPMVLVGNKCDL--- 120
+ +R R + FLL F++ S S+E++ + +++ A VP+VLVG K DL
Sbjct: 63 NRLRPLSYRGADVFLLAFSLISKASYENVLKKWIPELRHY--APGVPIVLVGTKLDLRDD 120
Query: 121 --------STWAVDMNQAQELAEQFNIP-FIKTSAKTRMGVDDAFYTLVR 161
+ Q +EL +Q +I+ S+KT+ V F ++
Sbjct: 121 KQFFADHPGAVPITTAQGEELRKQIGAAAYIECSSKTQQNVKAVFDAAIK 170
>gnl|CDD|133277 cd01875, RhoG, Ras homolog family, member G (RhoG) of small
guanosine triphosphatases (GTPases). RhoG is a GTPase
with high sequence similarity to members of the Rac
subfamily, including the regions involved in effector
recognition and binding. However, RhoG does not bind to
known Rac1 and Cdc42 effectors, including proteins
containing a Cdc42/Rac interacting binding (CRIB) motif.
Instead, RhoG interacts directly with Elmo, an upstream
regulator of Rac1, in a GTP-dependent manner and forms a
ternary complex with Dock180 to induce activation of
Rac1. The RhoG-Elmo-Dock180 pathway is required for
activation of Rac1 and cell spreading mediated by
integrin, as well as for neurite outgrowth induced by
nerve growth factor. Thus RhoG activates Rac1 through
Elmo and Dock180 to control cell morphology. RhoG has
also been shown to play a role in caveolar trafficking
and has a novel role in signaling the neutrophil
respiratory burst stimulated by G protein-coupled
receptor (GPCR) agonists. 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.
Length = 191
Score = 93.5 bits (232), Expect = 4e-24
Identities = 58/177 (32%), Positives = 87/177 (49%), Gaps = 15/177 (8%)
Query: 1 MAEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAG 60
M K VVVG G VGK+ L I N F EY PT+ D+Y Q +DG T L++ DTAG
Sbjct: 1 MQSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTAVDGRTVSLNLWDTAG 60
Query: 61 QEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL 120
QEEY +R F++ F++ S S+E++ ++ + VP++LVG K DL
Sbjct: 61 QEEYDRLRTLSYPQTNVFIICFSIASPSSYENV-RHKWHPEVCHHCPNVPILLVGTKKDL 119
Query: 121 -------------STWAVDMNQAQELAEQFN-IPFIKTSAKTRMGVDDAFYTLVREI 163
+ Q LA+Q + + +++ SA + GV + F VR +
Sbjct: 120 RNDADTLKKLKEQGQAPITPQQGGALAKQIHAVKYLECSALNQDGVKEVFAEAVRAV 176
>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 = 92.6 bits (230), Expect = 8e-24
Identities = 55/175 (31%), Positives = 98/175 (56%), Gaps = 4/175 (2%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFV-DEYDPTIEDSYRKQVV-IDGETALLDILDTAGQ 61
+K+++VG GVGK+ L ++ F+ + T+ + +VV +DG L I DTAGQ
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQ 60
Query: 62 EEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLS 121
E + ++ Y R LL++ V + SF++I ++ +I +V ++L+GNK D+S
Sbjct: 61 ERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYA-QSDVVIMLLGNKADMS 119
Query: 122 TW-AVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKKDKMLRGKEKK 175
V + LA+++ +PF++TSAKT + V+ AF + +E+K + + E K
Sbjct: 120 GERVVKREDGERLAKEYGVPFMETSAKTGLNVELAFTAVAKELKHRSVEQPDEPK 174
>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 = 91.0 bits (226), Expect = 2e-23
Identities = 50/163 (30%), Positives = 85/163 (52%), Gaps = 4/163 (2%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIE-DSYRKQVVIDGETALLDILDTAGQE 62
+K++++G VGK+ + + F + TI D K + I G+ L I DTAGQE
Sbjct: 4 FKIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAGQE 63
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLST 122
+ + Y R+ G ++ + + SFE + + E++++ A V ++L+GNKCDL
Sbjct: 64 RFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYG-ASNVVLLLIGNKCDLEE 122
Query: 123 W-AVDMNQAQELAEQFNIPF-IKTSAKTRMGVDDAFYTLVREI 163
V +A LAE + I ++TSAK V++AF + E+
Sbjct: 123 QREVLFEEACTLAEHYGILAVLETSAKESSNVEEAFLLMATEL 165
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 91.9 bits (228), Expect = 2e-23
Identities = 62/203 (30%), Positives = 100/203 (49%), Gaps = 19/203 (9%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVV-IDGETALLDILDTAGQE 62
+K+V++G GVGKS + + +N F E TI + + + ++G+T I DTAGQE
Sbjct: 13 FKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQE 72
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLST 122
Y A+ Y R G LLV+ + ++F+++ + +++ D+ V M + GNK DL+
Sbjct: 73 RYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNIVIM-MAGNKSDLNH 131
Query: 123 W-AVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK---DKMLRGKEKKKRG 178
+V Q LAE+ + F++TSA V+ AF T++ EI K L +E
Sbjct: 132 LRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFQTILLEIYHIISKKALAAQEAAANS 191
Query: 179 -------------ISGNKLKQCC 188
SGN + CC
Sbjct: 192 GLPGQGTTINVADTSGNNKRGCC 214
>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 = 90.7 bits (225), Expect = 2e-23
Identities = 48/162 (29%), Positives = 88/162 (54%), Gaps = 3/162 (1%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVV-IDGETALLDILDTAGQE 62
+K +++G GVGKS L Q + F+ + TI + +++ ++G+ L I DTAGQE
Sbjct: 3 FKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQE 62
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL-S 121
+ A+ Y R G L+V+ + ++ + S+ + + + V + L+GNK DL +
Sbjct: 63 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTV-IFLIGNKADLEA 121
Query: 122 TWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREI 163
V +A++ A++ + F++ SAKT V+DAF ++I
Sbjct: 122 QRDVTYEEAKQFADENGLLFLECSAKTGENVEDAFLETAKKI 163
>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 = 89.8 bits (223), Expect = 4e-23
Identities = 53/162 (32%), Positives = 90/162 (55%), Gaps = 3/162 (1%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVV-IDGETALLDILDTAGQE 62
+K +++G+ G GKS L Q I+N F + + TI + +VV + G++ L I DTAGQE
Sbjct: 1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQE 60
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLST 122
+ ++ Y R G LLV+ + S +SF + ++ + + + ++ ++LVGNK DL
Sbjct: 61 RFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLTDARTLA-SPDIVIILVGNKKDLED 119
Query: 123 -WAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREI 163
V +A A++ + F++TSA T V++AF R I
Sbjct: 120 DREVTFLEASRFAQENGLLFLETSALTGENVEEAFLKCARSI 161
>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 = 90.4 bits (225), Expect = 7e-23
Identities = 53/191 (27%), Positives = 92/191 (48%), Gaps = 9/191 (4%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIE-DSYRKQVVIDGETAL-LDILDTAGQ 61
+K++V+G GVGK+++ + + F Y TI D K + D T + L + D AGQ
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQ 60
Query: 62 EEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQI-KRVK--DAEEVPMVLVGNKC 118
E + M Y + G ++VF V +FE + ++ + +V + E +P +L+ NKC
Sbjct: 61 ERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPALLLANKC 120
Query: 119 DLS--TWAVDMNQAQELAEQFNIP-FIKTSAKTRMGVDDAFYTLVREIKKDKMLRGKEKK 175
DL A D Q + ++ + +TSAK + +++A LV+ I K + +
Sbjct: 121 DLKKERLAKDPEQMDQFCKENGFIGWFETSAKENINIEEAMRFLVKNILK-NDKGLQSPE 179
Query: 176 KRGISGNKLKQ 186
+ LKQ
Sbjct: 180 PDEDNVIDLKQ 190
>gnl|CDD|206663 cd01871, Rac1_like, Ras-related C3 botulinum toxin substrate 1 (rho
family, small GTP binding protein Rac1)-like consists of
Rac1, Rac2 and Rac3. The Rac1-like subfamily consists
of Rac1, Rac2, and Rac3 proteins, plus the splice
variant Rac1b that contains a 19-residue insertion near
switch II relative to Rac1. While Rac1 is ubiquitously
expressed, Rac2 and Rac3 are largely restricted to
hematopoietic and neural tissues respectively. Rac1
stimulates the formation of actin lamellipodia and
membrane ruffles. It also plays a role in cell-matrix
adhesion and cell anoikis. In intestinal epithelial
cells, Rac1 is an important regulator of migration and
mediates apoptosis. Rac1 is also essential for
RhoA-regulated actin stress fiber and focal adhesion
complex formation. In leukocytes, Rac1 and Rac2 have
distinct roles in regulating cell morphology, migration,
and invasion, but are not essential for macrophage
migration or chemotaxis. Rac3 has biochemical properties
that are closely related to Rac1, such as effector
interaction, nucleotide binding, and hydrolysis; Rac2
has a slower nucleotide association and is more
efficiently activated by the RacGEF Tiam1. Both Rac1 and
Rac3 have been implicated in the regulation of cell
migration and invasion in human metastatic breast
cancer. 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 = 174
Score = 89.1 bits (221), Expect = 1e-22
Identities = 50/134 (37%), Positives = 75/134 (55%), Gaps = 8/134 (5%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
K VVVG G VGK+ L I N F EY PT+ D+Y V++DG+ L + DTAGQE+Y
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDY 62
Query: 65 SAMRD-QYMRTGEGFLLVFAVNSMKSFEDI-GSYREQIKRVKDAEEVPMVLVGNKCDLST 122
+R Y +T FL+ F++ S SFE++ + +++ P++LVG K DL
Sbjct: 63 DRLRPLSYPQTDV-FLICFSLVSPASFENVRAKWYPEVRH--HCPNTPIILVGTKLDLRD 119
Query: 123 WAVDMNQAQELAEQ 136
D + ++L E+
Sbjct: 120 ---DKDTIEKLKEK 130
>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 = 87.6 bits (217), Expect = 4e-22
Identities = 55/164 (33%), Positives = 80/164 (48%), Gaps = 8/164 (4%)
Query: 5 KLVVVGAGGVGKSALTIQLIQN---HFVDEYDPTIE-DSYRKQVVI--DGETALLDILDT 58
+ VVG VGKSAL +Q+ + F Y T D K V + ++ L I D+
Sbjct: 2 QCAVVGDPAVGKSAL-VQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDS 60
Query: 59 AGQEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKC 118
AGQE +S M + +V+ V + SF + + +++ P VLVGNKC
Sbjct: 61 AGQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKC 120
Query: 119 DLSTWA-VDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVR 161
DL+ VD QAQ LA+ + F +TSAK +G + F +L R
Sbjct: 121 DLTDRREVDAAQAQALAQANTLKFYETSAKEGVGYEAPFLSLAR 164
>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 = 88.3 bits (219), Expect = 5e-22
Identities = 56/164 (34%), Positives = 93/164 (56%), Gaps = 3/164 (1%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIE-DSYRKQVVI-DGETALLDILDTAG 60
+++L+V+G VGKS+L + + F + DPT+ D + + + I G L + DTAG
Sbjct: 2 QFRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAG 61
Query: 61 QEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL 120
QE + ++ Y R G LLVF + + +SFE + + E+ + +LVG+KCDL
Sbjct: 62 QERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFILVGHKCDL 121
Query: 121 -STWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREI 163
S V +A++LA+ + +I+TSA+T V++AF L +EI
Sbjct: 122 ESQRQVTREEAEKLAKDLGMKYIETSARTGDNVEEAFELLTQEI 165
>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 = 86.3 bits (214), Expect = 1e-21
Identities = 51/165 (30%), Positives = 89/165 (53%), Gaps = 6/165 (3%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYR-KQVVIDGETALLDILDTAGQEE 63
K++ +G GVGKS + + + FV +Y PTI Y K+V + + ++ D +G E
Sbjct: 2 KVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPE 61
Query: 64 YSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIK----RVKDAEEVPMVLVGNKCD 119
Y +R+++ + +G LLV+ V +SFE + S+ +++K + E + +V+ NK D
Sbjct: 62 YLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKID 121
Query: 120 LSTW-AVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREI 163
L+ AV ++ + AE + +TSA T GV++ F TL I
Sbjct: 122 LTKHRAVSEDEGRLWAESKGFKYFETSACTGEGVNEMFQTLFSSI 166
>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 = 85.9 bits (213), Expect = 2e-21
Identities = 52/167 (31%), Positives = 87/167 (52%), Gaps = 17/167 (10%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
K V+VG G VGK++L + N + EY PT D++ V++DG+ L + DTAGQ+E+
Sbjct: 2 KCVLVGDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFSVVVLVDGKPVRLQLCDTAGQDEF 61
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGS-YREQIKRVKDAEEVPMVLVGNKCDL--- 120
+R + FLL F+V + SF++I + +I+ K + P++LVG + DL
Sbjct: 62 DKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIR--KHNPKAPIILVGTQADLRTD 119
Query: 121 ----------STWAVDMNQAQELAEQFN-IPFIKTSAKTRMGVDDAF 156
V ++A+ LAE+ +I+ SA T+ + + F
Sbjct: 120 VNVLIQLARYGEKPVSQSRAKALAEKIGACEYIECSALTQKNLKEVF 166
>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 = 86.4 bits (214), Expect = 3e-21
Identities = 49/165 (29%), Positives = 81/165 (49%), Gaps = 5/165 (3%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIE-DSYRKQVVIDGETA-LLDILDTAGQ 61
K+VV+G G GK++L + Q F Y TI D + +++ + G L + D GQ
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
Query: 62 EEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVP--MVLVGNKCD 119
+ M D+Y+ + LV+ + + +SFE++ + +K+V + E MVLVGNK D
Sbjct: 61 QIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTD 120
Query: 120 L-STWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREI 163
L V + A++ ++ I SAKT V F + E+
Sbjct: 121 LEHNRQVTAEKHARFAQENDMESIFVSAKTGDRVFLCFQRIAAEL 165
>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 = 84.6 bits (209), Expect = 5e-21
Identities = 49/158 (31%), Positives = 83/158 (52%), Gaps = 3/158 (1%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYR-KQVVIDGETALLDILDTAGQE 62
++L+++G GVGK+ L + N F + TI ++ K + +DG + I DTAGQE
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQE 60
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL-S 121
Y + QY R +G LV+ ++S +S++ I + + E V +L+GNK D
Sbjct: 61 RYQTITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAP-EGVQKILIGNKADEEQ 119
Query: 122 TWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTL 159
V Q +LA+++ + F +TSA T + ++F L
Sbjct: 120 KRQVGDEQGNKLAKEYGMDFFETSACTNKNIKESFTRL 157
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 85.1 bits (210), Expect = 8e-21
Identities = 59/197 (29%), Positives = 100/197 (50%), Gaps = 13/197 (6%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYR-KQVVIDGETALLDILDTAGQE 62
+K++++G GVGKS+L + I + V++ PTI ++ KQ+ + G+ L I DTAGQE
Sbjct: 15 FKILLIGDSGVGKSSLLVSFISSS-VEDLAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQE 73
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGS-YREQIKRVKDAEEVPMVLVGNKCDL- 120
+ + Y R +G +LV+ V ++F ++ + ++++ ++ +LVGNK D
Sbjct: 74 RFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVGNKVDRE 133
Query: 121 STWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKKDKML--RGKEKKKRG 178
S V + LA++ F++ SAKTR V+ F L +I + L G KR
Sbjct: 134 SERDVSREEGMALAKEHGCLFLECSAKTRENVEQCFEELALKIMEVPSLLEEGSTAVKRN 193
Query: 179 ISGNKLKQ-------CC 188
I K + CC
Sbjct: 194 ILKQKPEHQPPPNGGCC 210
>gnl|CDD|206702 cd04129, Rho2, Ras homology family 2 (Rho2) of small guanosine
triphosphatases (GTPases). Rho2 is a fungal GTPase that
plays a role in cell morphogenesis, control of cell wall
integrity, control of growth polarity, and maintenance
of growth direction. Rho2 activates the protein kinase C
homolog Pck2, and Pck2 controls Mok1, the major (1-3)
alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2
regulates the construction of the cell wall. Unlike
Rho1, Rho2 is not an essential protein, but its
overexpression is lethal. 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 proper intracellular localization via
membrane attachment. As with other Rho family GTPases,
the GDP/GTP cycling is regulated by GEFs (guanine
nucleotide exchange factors), GAPs (GTPase-activating
proteins) and GDIs (guanine nucleotide dissociation
inhibitors).
Length = 190
Score = 84.5 bits (209), Expect = 8e-21
Identities = 58/176 (32%), Positives = 83/176 (47%), Gaps = 27/176 (15%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
KLV+VG G GK++L F +EY PT+ ++Y +DG+ L + DTAGQEEY
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTVFENYVTDCRVDGKPVQLALWDTAGQEEY 62
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEV-------PMVLVGNK 117
+R L+ FA+++ S E++ R K EEV P++LVG K
Sbjct: 63 ERLRPLSYSKAHVILIGFAIDTPDSLENV--------RTKWIEEVRRYCPNVPVILVGLK 114
Query: 118 CDLSTWA-----------VDMNQAQELAEQFNI-PFIKTSAKTRMGVDDAFYTLVR 161
DL A V + QA+ +A +++ SA T GVDD F R
Sbjct: 115 KDLRQEAVAKGNYATDEFVPIQQAKLVARAIGAKKYMECSALTGEGVDDVFEAATR 170
>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 = 83.4 bits (206), Expect = 1e-20
Identities = 47/159 (29%), Positives = 81/159 (50%), Gaps = 3/159 (1%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETAL-LDILDTAGQE 62
+KL+++G VGK++ + + F + T+ ++ + V + + L I DTAGQE
Sbjct: 2 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQE 61
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL-S 121
Y + Y R GF+L++ + + +SF + + QIK + ++LVGNKCD+
Sbjct: 62 RYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYS-WDNAQVILVGNKCDMED 120
Query: 122 TWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLV 160
V + ++LA+Q F + SAK + V F LV
Sbjct: 121 ERVVSAERGRQLADQLGFEFFEASAKENINVKQVFERLV 159
>gnl|CDD|206662 cd01870, RhoA_like, Ras homology family A (RhoA)-like includes
RhoA, RhoB and RhoC. The RhoA subfamily consists of
RhoA, RhoB, and RhoC. RhoA promotes the formation of
stress fibers and focal adhesions, regulating cell
shape, attachment, and motility. RhoA can bind to
multiple effector proteins, thereby triggering different
downstream responses. In many cell types, RhoA mediates
local assembly of the contractile ring, which is
necessary for cytokinesis. RhoA is vital for muscle
contraction; in vascular smooth muscle cells, RhoA plays
a key role in cell contraction, differentiation,
migration, and proliferation. RhoA activities appear to
be elaborately regulated in a time- and space-dependent
manner to control cytoskeletal changes. 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. RhoA and RhoC are observed
only in geranylgeranylated forms; however, RhoB can be
present in palmitoylated, farnesylated, and
geranylgeranylated forms. RhoA and RhoC are highly
relevant for tumor progression and invasiveness;
however, RhoB has recently been suggested to be a tumor
suppressor. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 175
Score = 82.9 bits (205), Expect = 3e-20
Identities = 55/173 (31%), Positives = 87/173 (50%), Gaps = 19/173 (10%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
KLV+VG G GK+ L I ++ F + Y PT+ ++Y + +DG+ L + DTAGQE+Y
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDY 62
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQ-IKRVKD-AEEVPMVLVGNKCDL-- 120
+R + L+ F+++S S E+I E+ VK VP++LVGNK DL
Sbjct: 63 DRLRPLSYPDTDVILMCFSIDSPDSLENI---PEKWTPEVKHFCPNVPIILVGNKKDLRN 119
Query: 121 -----------STWAVDMNQAQELAEQFN-IPFIKTSAKTRMGVDDAFYTLVR 161
V + + +AE+ +++ SAKT+ GV + F R
Sbjct: 120 DEHTIRELAKMKQEPVKPEEGRAMAEKIGAFGYLECSAKTKEGVREVFEMATR 172
>gnl|CDD|206664 cd01874, Cdc42, cell division cycle 42 (Cdc42) is a small GTPase of
the Rho family. Cdc42 is an essential GTPase that
belongs to the Rho family of Ras-like GTPases. These
proteins act as molecular switches by responding to
exogenous and/or endogenous signals and relaying those
signals to activate downstream components of a
biological pathway. Cdc42 transduces signals to the
actin cytoskeleton to initiate and maintain polarized
growth and to mitogen-activated protein morphogenesis.
In the budding yeast Saccharomyces cerevisiae, Cdc42
plays an important role in multiple actin-dependent
morphogenetic events such as bud emergence,
mating-projection formation, and pseudohyphal growth. In
mammalian cells, Cdc42 regulates a variety of
actin-dependent events and induces the JNK/SAPK protein
kinase cascade, which leads to the activation of
transcription factors within the nucleus. Cdc42 mediates
these processes through interactions with a myriad of
downstream effectors, whose number and regulation we are
just starting to understand. In addition, Cdc42 has been
implicated in a number of human diseases through
interactions with its regulators and downstream
effectors. 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 = 175
Score = 81.8 bits (202), Expect = 7e-20
Identities = 54/168 (32%), Positives = 83/168 (49%), Gaps = 19/168 (11%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
K VVVG G VGK+ L I N F EY PT+ D+Y V+I GE L + DTAGQE+Y
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDY 62
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQ-IKRVK-DAEEVPMVLVGNKCDL-- 120
+R + FL+ F+V S SFE++ +E+ + + + P +LVG + DL
Sbjct: 63 DRLRPLSYPQTDVFLVCFSVVSPSSFENV---KEKWVPEITHHCPKTPFLLVGTQIDLRD 119
Query: 121 -----------STWAVDMNQAQELAEQFN-IPFIKTSAKTRMGVDDAF 156
+ ++LA + +++ SA T+ G+ + F
Sbjct: 120 DPSTIEKLAKNKQKPITPETGEKLARDLKAVKYVECSALTQKGLKNVF 167
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 82.8 bits (205), Expect = 8e-20
Identities = 50/170 (29%), Positives = 85/170 (50%), Gaps = 4/170 (2%)
Query: 1 MAEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVV-IDGETALLDILDTA 59
+ E+KL++VG GGVGK+ + + F +Y PT+ + ++ DTA
Sbjct: 7 VPEFKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNVWDTA 66
Query: 60 GQEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCD 119
GQE++ +RD Y G+ +++F V S +++++ ++ I RV E +P+VLVGNK D
Sbjct: 67 GQEKFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDIVRV--CENIPIVLVGNKVD 124
Query: 120 LSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKKDKML 169
+ V Q + N+ + SAK+ + F L R + D L
Sbjct: 125 VKDRQVKARQIT-FHRKKNLQYYDISAKSNYNFEKPFLWLARRLTNDPNL 173
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 79.4 bits (196), Expect = 1e-19
Identities = 35/116 (30%), Positives = 60/116 (51%), Gaps = 2/116 (1%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQ-VVIDGETALLDILDTAGQEE 63
K+VV+G G GKS+L QL+ F E D+ + +DG+T LL+I D G+EE
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 64 YSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAE-EVPMVLVGNKC 118
+M+ + LLV+ + +S ++ + ++ ++P++LVGNK
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVILVGNKL 116
>gnl|CDD|133342 cd04142, RRP22, Ras-related protein on chromosome 22 (RRP22)
family. RRP22 (Ras-related protein on chromosome 22)
subfamily consists of proteins that inhibit cell growth
and promote caspase-independent cell death. Unlike most
Ras proteins, RRP22 is down-regulated in many human
tumor cells due to promoter methylation. RRP22 localizes
to the nucleolus in a GTP-dependent manner, suggesting a
novel function in modulating transport of nucleolar
components. 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.
Like most Ras family proteins, RRP22 is farnesylated.
Length = 198
Score = 80.3 bits (198), Expect = 5e-19
Identities = 44/128 (34%), Positives = 64/128 (50%), Gaps = 11/128 (8%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTI-EDSYRKQVVIDGETALLDILD----- 57
++ V+GA GVGK+A+ Q + F +EY PT YR VV+ G L ILD
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQ 60
Query: 58 ---TAGQEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQI--KRVKDAEEVPMV 112
+E+ R + +R F+LV+ + S SF + R+QI R +E P+V
Sbjct: 61 RYPGTAGQEWMDPRFRGLRNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIV 120
Query: 113 LVGNKCDL 120
+VGNK D
Sbjct: 121 VVGNKRDQ 128
>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 = 78.5 bits (193), Expect = 3e-18
Identities = 49/164 (29%), Positives = 93/164 (56%), Gaps = 4/164 (2%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYR-KQVVIDGETALLDILDTAGQEE 63
+++++G+ GVGK++L + + F + T+ ++ K V + G+ L I DTAGQE
Sbjct: 2 QVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQER 61
Query: 64 YSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLST- 122
++++ Y R+ +G +LV+ + ++F+D+ + + I + +E+ ++LVGNK D T
Sbjct: 62 FNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYA-SEDAELLLVGNKLDCETD 120
Query: 123 WAVDMNQAQELAEQFN-IPFIKTSAKTRMGVDDAFYTLVREIKK 165
+ Q ++ A+Q + F + SAK VD+ F LV +I K
Sbjct: 121 REITRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVDDILK 164
>gnl|CDD|206706 cd04134, Rho3, Ras homology family 3 (Rho3) of small guanosine
triphosphatases (GTPases). Rho3 is a member of the Rho
family found only in fungi. Rho3 is believed to regulate
cell polarity by interacting with the diaphanous/formin
family protein For3 to control both the actin
cytoskeleton and microtubules. Rho3 is also believed to
have a direct role in exocytosis that is independent of
its role in regulating actin polarity. The function in
exocytosis may be two-pronged: first, in the transport
of post-Golgi vesicles from the mother cell to the bud,
mediated by myosin (Myo2); second, in the docking and
fusion of vesicles to the plasma membrane, mediated by
an exocyst (Exo70) protein. 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.
Length = 185
Score = 77.6 bits (191), Expect = 4e-18
Identities = 49/168 (29%), Positives = 85/168 (50%), Gaps = 13/168 (7%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
K+VV+G G GK++L + +F Y+PT+ ++Y + +DG L + DTAGQEE+
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTVFENYIHDIFVDGLAVELSLWDTAGQEEF 61
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKD-AEEVPMVLVGNKCDL--- 120
+R +L F+V++ S E++ S + + ++ V +VLV KCDL
Sbjct: 62 DRLRSLSYADTHVIMLCFSVDNPDSLENVES--KWLAEIRHHCPGVKLVLVALKCDLREP 119
Query: 121 ------STWAVDMNQAQELAEQFN-IPFIKTSAKTRMGVDDAFYTLVR 161
T + + +A++ N +++ SAK GV++AF R
Sbjct: 120 RNERDRGTHTISYEEGLAVAKRINACRYLECSAKLNRGVNEAFTEAAR 167
>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 = 76.9 bits (189), Expect = 5e-18
Identities = 50/162 (30%), Positives = 84/162 (51%), Gaps = 3/162 (1%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIE-DSYRKQVVIDGETALLDILDTAGQE 62
+K+V++G GVGK+ L + Q F TI D K V I GE L I DTAGQE
Sbjct: 8 FKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQE 67
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLST 122
+ ++ Y R+ +L + + +SF + + +I++ + +V +LVGNK DL+
Sbjct: 68 RFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYAN-NKVITILVGNKIDLAE 126
Query: 123 -WAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREI 163
V +A+E ++ ++ +++TSAK V+ F L +
Sbjct: 127 RREVSQQRAEEFSDAQDMYYLETSAKESDNVEKLFLDLACRL 168
>gnl|CDD|206707 cd04135, Tc10, Rho GTPase TC10 (Tc10). TC10 is a Rho family
protein that has been shown to induce microspike
formation and neurite outgrowth in vitro. Its expression
changes dramatically after peripheral nerve injury,
suggesting an important role in promoting axonal
outgrowth and regeneration. TC10 regulates translocation
of insulin-stimulated GLUT4 in adipocytes and has also
been shown to bind directly to Golgi COPI coat proteins.
GTP-bound TC10 in vitro can bind numerous potential
effectors. Depending on its subcellular localization and
distinct functional domains, TC10 can differentially
regulate two types of filamentous actin in adipocytes.
TC10 mRNAs are highly expressed in three types of mouse
muscle tissues: leg skeletal muscle, cardiac muscle, and
uterus; they were also present in brain, with higher
levels in adults than in newborns. TC10 has also been
shown to play a role in regulating the expression of
cystic fibrosis transmembrane conductance regulator
(CFTR) through interactions with CFTR-associated ligand
(CAL). The GTP-bound form of TC10 directs the
trafficking of CFTR from the juxtanuclear region to the
secretory pathway toward the plasma membrane, away from
CAL-mediated DFTR degradation in the lysosome. 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 = 174
Score = 76.2 bits (187), Expect = 1e-17
Identities = 55/167 (32%), Positives = 88/167 (52%), Gaps = 17/167 (10%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
K VVVG G VGK+ L + + F +EY PT+ D Y V + G+ LL + DTAGQE+Y
Sbjct: 2 KCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQEDY 61
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKD-AEEVPMVLVGNKCDLS-- 121
+R + FL+ F+V + SF+++ E + +K+ A VP +L+G + DL
Sbjct: 62 DRLRPLSYPMTDVFLICFSVVNPASFQNV--KEEWVPELKEYAPNVPYLLIGTQIDLRDD 119
Query: 122 --TWA---------VDMNQAQELAEQFNIP-FIKTSAKTRMGVDDAF 156
T A + + Q Q+LA++ +++ SA T+ G+ F
Sbjct: 120 PKTLARLNDMKEKPITVEQGQKLAKEIGACCYVECSALTQKGLKTVF 166
>gnl|CDD|133324 cd04124, RabL2, Rab GTPase-like family 2 (Rab-like2). RabL2
(Rab-like2) subfamily. RabL2s are novel Rab proteins
identified recently which display features that are
distinct from other Rabs, and have been termed Rab-like.
RabL2 contains RabL2a and RabL2b, two very similar Rab
proteins that share > 98% sequence identity in humans.
RabL2b maps to the subtelomeric region of chromosome
22q13.3 and RabL2a maps to 2q13, a region that suggests
it is also a subtelomeric gene. Both genes are believed
to be expressed ubiquitously, suggesting that RabL2s are
the first example of duplicated genes in human proximal
subtelomeric regions that are both expressed actively.
Like other Rab-like proteins, RabL2s lack a prenylation
site at the C-terminus. The specific functions of RabL2a
and RabL2b remain unknown. 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 = 161
Score = 72.6 bits (178), Expect = 2e-16
Identities = 44/168 (26%), Positives = 78/168 (46%), Gaps = 13/168 (7%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSY-----RKQVVIDGETALLDILDTA 59
K++++G VGKS +L++ +D Y+P +Y + +G+T L+D DTA
Sbjct: 2 KIILLGDSAVGKS----KLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTA 57
Query: 60 GQEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCD 119
GQE + M Y +LVF V +++++ + E+++ + E+P ++V NK D
Sbjct: 58 GQERFQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYR--PEIPCIVVANKID 115
Query: 120 LSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKKDK 167
L + AE+ N+P SA V F ++ K
Sbjct: 116 LDPSVT--QKKFNFAEKHNLPLYYVSAADGTNVVKLFQDAIKLAVSYK 161
>gnl|CDD|206643 cd00877, Ran, Ras-related nuclear proteins (Ran)/TC4 family of
small GTPases. Ran GTPase is involved in diverse
biological functions, such as nuclear transport, spindle
formation during mitosis, DNA replication, and cell
division. Among the Ras superfamily, Ran is a unique
small G protein. It does not have a lipid modification
motif at the C-terminus to bind to the membrane, which
is often observed within the Ras superfamily. Ran may
therefore interact with a wide range of proteins in
various intracellular locations. Like other GTPases, Ran
exists in GTP- and GDP-bound conformations that interact
differently with effectors. Conversion between these
forms and the assembly or disassembly of effector
complexes requires the interaction of regulator
proteins. The intrinsic GTPase activity of Ran is very
low, but it is greatly stimulated by a GTPase-activating
protein (RanGAP1) located in the cytoplasm. By contrast,
RCC1, a guanine nucleotide exchange factor that
generates RanGTP, is bound to chromatin and confined to
the nucleus. Ran itself is mobile and is actively
imported into the nucleus by a mechanism involving
NTF-2. Together with the compartmentalization of its
regulators, this is thought to produce a relatively high
concentration of RanGTP in the nucleus.
Length = 166
Score = 72.3 bits (178), Expect = 2e-16
Identities = 46/174 (26%), Positives = 86/174 (49%), Gaps = 18/174 (10%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIE--------DSYRKQVVIDGETALLDI 55
+KLV+VG GG GK+ + + F +Y T+ + R ++ + +
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFN-------V 53
Query: 56 LDTAGQEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVG 115
DTAGQE++ +RD Y G+ +++F V S +++++ ++ + RV E +P+VL G
Sbjct: 54 WDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDLVRV--CENIPIVLCG 111
Query: 116 NKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKKDKML 169
NK D+ V Q ++ N+ + + SAK+ + F L R++ + L
Sbjct: 112 NKVDIKDRKVKPKQITFHRKK-NLQYYEISAKSNYNFEKPFLWLARKLLGNPNL 164
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 73.2 bits (180), Expect = 3e-16
Identities = 47/168 (27%), Positives = 84/168 (50%), Gaps = 4/168 (2%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIE-DSYRKQVVIDGETALLDILDTAGQE 62
+KLV+VG GG GK+ + + F +Y+PTI + + + DTAGQE
Sbjct: 14 FKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYCWDTAGQE 73
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLST 122
++ +RD Y G+ +++F V + +++++ ++ + RV E +P+VL GNK D+
Sbjct: 74 KFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCRV--CENIPIVLCGNKVDVKN 131
Query: 123 WAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKKDKMLR 170
V Q + N+ + + SAK+ + F L R++ D L
Sbjct: 132 RQVKAKQVT-FHRKKNLQYYEISAKSNYNFEKPFLYLARKLAGDPNLH 178
>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 = 67.6 bits (165), Expect = 3e-14
Identities = 46/162 (28%), Positives = 81/162 (50%), Gaps = 9/162 (5%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVD-EYDPTIEDSY-RKQVVIDGETALLDILDTAGQE 62
K+V++G VGK++L + + + F+ Y TI ++ K++V+ L I DTAG E
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSE 61
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL-- 120
Y AM Y R + ++ + + SFE + ++++ ++ E + L G K DL
Sbjct: 62 RYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQNLE--EHCKIYLCGTKSDLIE 119
Query: 121 ---STWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTL 159
S VD + Q+ A++ +TS+KT VD+ F +
Sbjct: 120 QDRSLRQVDFHDVQDFADEIKAQHFETSSKTGQNVDELFQKV 161
>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36
(Rab36). Rab34/Rab36 subfamily. Rab34, found primarily
in the Golgi, interacts with its effector,
Rab-interacting lysosomal protein (RILP). This enables
its participation in microtubular
dynenin-dynactin-mediated repositioning of lysosomes
from the cell periphery to the Golgi. A Rab34 (Rah)
isoform that lacks the consensus GTP-binding region has
been identified in mice. This isoform is associated with
membrane ruffles and promotes macropinosome formation.
Rab36 has been mapped to human chromosome 22q11.2, a
region that is homozygously deleted in malignant
rhabdoid tumors (MRTs). However, experimental
assessments do not implicate Rab36 as a tumor suppressor
that would enable tumor formation through a
loss-of-function mechanism. 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 = 170
Score = 66.4 bits (162), Expect = 4e-14
Identities = 47/157 (29%), Positives = 74/157 (47%), Gaps = 4/157 (2%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIE-DSYRKQVVIDGETALLDILDTAGQEE 63
K++VVG VGK+ L + ++ F Y TI D ++ + G L + DTAGQE
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQER 61
Query: 64 YSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLST- 122
+ + Y R + ++VF + + S E + E + D V + LVG K DLS+
Sbjct: 62 FKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKKDLSSP 121
Query: 123 --WAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFY 157
+A+ A +LA + + SA T V D F+
Sbjct: 122 AQYALMEQDAIKLAREMKAEYWAVSALTGENVRDFFF 158
>gnl|CDD|128473 smart00176, RAN, Ran (Ras-related nuclear proteins) /TC4 subfamily
of small GTPases. Ran is involved in the active
transport of proteins through nuclear pores.
Length = 200
Score = 65.8 bits (160), Expect = 1e-13
Identities = 42/162 (25%), Positives = 76/162 (46%), Gaps = 4/162 (2%)
Query: 9 VGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETAL-LDILDTAGQEEYSAM 67
VG GG GK+ + + F +Y T+ V + ++ DTAGQE++ +
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGL 60
Query: 68 RDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLSTWAVDM 127
RD Y G+ +++F V + +++++ ++ + RV E +P+VL GNK D+ V
Sbjct: 61 RDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLVRV--CENIPIVLCGNKVDVKDRKVKA 118
Query: 128 NQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKKDKML 169
+ N+ + SAK+ + F L R++ D L
Sbjct: 119 KSIT-FHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNL 159
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 63.5 bits (155), Expect = 5e-13
Identities = 42/159 (26%), Positives = 76/159 (47%), Gaps = 9/159 (5%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
++V++G GVGKS+L + L+ F + + + + E I+DT+ + +
Sbjct: 4 RIVLIGDEGVGKSSLIMSLVSEEFPENVPRVLPE-ITIPADVTPERVPTTIVDTSSRPQD 62
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYR-EQIKRVKDAEEVPMVLVGNKCDL--- 120
A +R LV++V+ + E I + I+R+ +VP++LVGNK DL
Sbjct: 63 RANLAAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRRL--GVKVPIILVGNKSDLRDG 120
Query: 121 STWAVDMNQAQELAEQFN--IPFIKTSAKTRMGVDDAFY 157
S+ A + + +F ++ SAKT + V + FY
Sbjct: 121 SSQAGLEEEMLPIMNEFREIETCVECSAKTLINVSEVFY 159
>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 = 62.3 bits (151), Expect = 2e-12
Identities = 44/159 (27%), Positives = 75/159 (47%), Gaps = 4/159 (2%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQ-VVIDGETALLDILDTAGQEE 63
K ++VG VGK + L Y + Y+ +++DG L + DT+GQ
Sbjct: 8 KFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTSGQGR 67
Query: 64 YSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLS-T 122
+ + Y R +G +LV+ + + SF+ I + ++I + A VP +LVGN+ L+
Sbjct: 68 FCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEID--EHAPGVPKILVGNRLHLAFK 125
Query: 123 WAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVR 161
V QAQ AE+ + F + S + ++F L R
Sbjct: 126 RQVATEQAQAYAERNGMTFFEVSPLCNFNITESFTELAR 164
>gnl|CDD|133303 cd04103, Centaurin_gamma, Centaurin gamma (CENTG) GTPase. The
centaurins (alpha, beta, gamma, and delta) are large,
multi-domain proteins that all contain an ArfGAP domain
and ankyrin repeats, and in some cases, numerous
additional domains. Centaurin gamma contains an
additional GTPase domain near its N-terminus. The
specific function of this GTPase domain has not been
well characterized, but centaurin gamma 2 (CENTG2) may
play a role in the development of autism. Centaurin
gamma 1 is also called PIKE (phosphatidyl inositol (PI)
3-kinase enhancer) and centaurin gamma 2 is also known
as AGAP (ArfGAP protein with a GTPase-like domain,
ankyrin repeats and a Pleckstrin homology domain) or
GGAP. Three isoforms of PIKE have been identified.
PIKE-S (short) and PIKE-L (long) are brain-specific
isoforms, with PIKE-S restricted to the nucleus and
PIKE-L found in multiple cellular compartments. A third
isoform, PIKE-A was identified in human glioblastoma
brain cancers and has been found in various tissues.
GGAP has been shown to have high GTPase activity due to
a direct intramolecular interaction between the
N-terminal GTPase domain and the C-terminal ArfGAP
domain. In human tissue, AGAP mRNA was detected in
skeletal muscle, kidney, placenta, brain, heart, colon,
and lung. Reduced expression levels were also observed
in the spleen, liver, and small intestine.
Length = 158
Score = 61.4 bits (149), Expect = 3e-12
Identities = 39/156 (25%), Positives = 74/156 (47%), Gaps = 10/156 (6%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
KL +VG GKSAL + + +V P ++K+V++DG++ LL I D G +
Sbjct: 2 KLGIVGNLRSGKSALVHRYLTGSYVQLESPEGG-RFKKEVLVDGQSHLLLIRDEGGAPDA 60
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLSTW- 123
Q+ + + VF++ SF+ + Q+ ++ E+P++LVG + +S
Sbjct: 61 -----QFAGWVDAVIFVFSLEDEASFQTVYRLYHQLSSYRNISEIPLILVGTQDAISASN 115
Query: 124 --AVDMNQAQELAEQF-NIPFIKTSAKTRMGVDDAF 156
+D +A++L + +T A + V+ F
Sbjct: 116 PRVIDDARARQLCADMKRCSYYETCATYGLNVERVF 151
>gnl|CDD|206703 cd04131, Rnd, Rho family GTPase subfamily Rnd includes Rnd1/Rho6,
Rnd2/Rho7, and Rnd3/RhoE/Rho8. The Rnd subfamily
contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These
novel Rho family proteins have substantial structural
differences compared to other Rho members, including N-
and C-terminal extensions relative to other Rhos.
Rnd3/RhoE is farnesylated at the C-terminal prenylation
site, unlike most other Rho proteins that are
geranylgeranylated. In addition, Rnd members are unable
to hydrolyze GTP and are resistant to GAP activity. They
are believed to exist only in the GTP-bound
conformation, and are antagonists of RhoA activity. 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 = 176
Score = 61.3 bits (149), Expect = 5e-12
Identities = 43/173 (24%), Positives = 78/173 (45%), Gaps = 24/173 (13%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
K+V+VG GK+AL ++ F + Y PT+ ++Y +D + L + DT+G Y
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTVFENYTASFEVDKQRIELSLWDTSGSPYY 62
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKD-AEEVPMVLVGNKCDLSTW 123
+R + L+ F ++ ++ + + ++ V++ P++LVG K DL T
Sbjct: 63 DNVRPLSYPDSDAVLICFDISRPETLDSV--LKKWKGEVREFCPNTPVLLVGCKSDLRT- 119
Query: 124 AVDMNQAQELAEQFNIP-----------------FIKTSAKT-RMGVDDAFYT 158
D++ EL+ + IP +++ SAKT V D F
Sbjct: 120 --DLSTLTELSNKRQIPVSHEQGRNLAKQIGAAAYVECSAKTSENSVRDVFEM 170
>gnl|CDD|206741 cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc
(COR) domain family. RocCOR (or Roco) protein family is
characterized by a superdomain containing a Ras-like
GTPase domain, called Roc (Ras of complex proteins), and
a characteristic second domain called COR (C-terminal of
Roc). A kinase domain and diverse regulatory domains are
also often found in Roco proteins. Their functions are
diverse; in Dictyostelium discoideum, which encodes 11
Roco proteins, they are involved in cell division,
chemotaxis and development, while in human, where 4 Roco
proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded,
these proteins are involved in epilepsy and cancer.
Mutations in LRRK2 (leucine-rich repeat kinase 2) are
known to cause familial Parkinson's disease.
Length = 161
Score = 57.7 bits (140), Expect = 5e-11
Identities = 45/165 (27%), Positives = 72/165 (43%), Gaps = 9/165 (5%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPT--IEDSYRKQVVIDGETALLDILDTAG 60
E KL++VG GGVGK++L QLI F + T I K + + L++ D G
Sbjct: 1 EAKLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGG 60
Query: 61 QEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL 120
QE Y A ++ + +LLVF + + + + QIK P++LVG D
Sbjct: 61 QEIYHATHQFFLTSRSLYLLVFDLRTGDEVSRVPYWLRQIK--AFGGVSPVILVGTHIDE 118
Query: 121 STWAVDMNQAQELAEQFNIP---FIKTSAKTRMGVDDAFYTLVRE 162
S D+ + L ++F S K G+ + + +E
Sbjct: 119 SC-DEDILKK-ALNKKFPAIINDIHFVSCKNGKGIAELKKAIAKE 161
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 54.0 bits (129), Expect = 2e-09
Identities = 37/122 (30%), Positives = 64/122 (52%), Gaps = 3/122 (2%)
Query: 28 FVDEYDPTIE-DSYRKQVVIDGETALLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAVNS 86
F + Y TI D K + +D L + DTAGQE + ++ Y+R ++V+ + +
Sbjct: 5 FDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITN 64
Query: 87 MKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLSTW-AVDMNQAQELAEQFNIPFIKTS 145
+SFE+ + + I + ++V + LVGNK DL V + + A+++N F +TS
Sbjct: 65 RQSFENTTKWIQDILNER-GKDVIIALVGNKTDLGDLRKVTYEEGMQKAQEYNTMFHETS 123
Query: 146 AK 147
AK
Sbjct: 124 AK 125
>gnl|CDD|206736 cd04173, Rnd2_Rho7, Rnd2/Rho7 GTPases. Rnd2/Rho7 is a member of
the novel Rho subfamily Rnd, together with Rnd1/Rho6 and
Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed in
radially migrating cells in the brain while they are
within the subventricular zone of the hippocampus and
cerebral cortex. These migrating cells typically develop
into pyramidal neurons. Cells that exogenously expressed
Rnd2/Rho7 failed to migrate to upper layers of the
brain, suggesting that Rnd2/Rho7 plays a role in the
radial migration and morphological changes of developing
pyramidal neurons, and that Rnd2/Rho7 degradation is
necessary for proper cellular migration. The Rnd2/Rho7
GEF Rapostlin is found primarily in the brain and
together with Rnd2/Rho7 induces dendrite branching.
Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which are RhoA
antagonists, Rnd2/Rho7 binds the GEF Pragmin and
significantly stimulates RhoA activity and Rho-A
mediated cell contraction. Rnd2/Rho7 is also found to be
expressed in spermatocytes and early spermatids, with
male-germ-cell Rac GTPase-activating protein
(MgcRacGAP), where it localizes to the Golgi-derived
pro-acrosomal vesicle. 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.
Length = 221
Score = 52.3 bits (125), Expect = 1e-08
Identities = 37/136 (27%), Positives = 69/136 (50%), Gaps = 4/136 (2%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
K+VVVG GK+AL ++++ + Y PT+ ++Y ID L++ DT+G Y
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPESYVPTVFENYTASFEIDKHRIELNMWDTSGSSYY 62
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLSTWA 124
+R + L+ F ++ ++ + + + Q + + +VLVG K D+ T
Sbjct: 63 DNVRPLAYPDSDAVLICFDISRPETLDSV-LKKWQGETQEFCPNAKLVLVGCKLDMRT-- 119
Query: 125 VDMNQAQELAEQFNIP 140
D++ +EL++Q IP
Sbjct: 120 -DLSTLRELSKQRLIP 134
>gnl|CDD|206735 cd04172, Rnd3_RhoE_Rho8, Rnd3/RhoE/Rho8 GTPases. Rnd3/RhoE/Rho8
subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho
subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7.
Rnd3/RhoE is known to bind the serine-threonine kinase
ROCK I. Unphosphorylated Rnd3/RhoE associates primarily
with membranes, but ROCK I-phosphorylated Rnd3/RhoE
localizes in the cytosol. Phosphorylation of Rnd3/RhoE
correlates with its activity in disrupting RhoA-induced
stress fibers and inhibiting Ras-induced fibroblast
transformation. In cells that lack stress fibers, such
as macrophages and monocytes, Rnd3/RhoE induces a
redistribution of actin, causing morphological changes
in the cell. In addition, Rnd3/RhoE has been shown to
inhibit cell cycle progression in G1 phase at a point
upstream of the pRb family pocket protein checkpoint.
Rnd3/RhoE has also been shown to inhibit Ras- and
Raf-induced fibroblast transformation. In mammary
epithelial tumor cells, Rnd3/RhoE regulates the assembly
of the apical junction complex and tight junction
formation. Rnd3/RhoE is underexpressed in prostate
cancer cells both in vitro and in vivo; re-expression of
Rnd3/RhoE suppresses cell cycle progression and
increases apoptosis, suggesting it may play a role in
tumor suppression. 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 = 182
Score = 50.4 bits (120), Expect = 4e-08
Identities = 43/169 (25%), Positives = 76/169 (44%), Gaps = 18/169 (10%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
K+VVVG GK+AL ++ F + Y PT+ ++Y ID + L + DT+G Y
Sbjct: 7 KIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQRIELSLWDTSGSPYY 66
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDI-GSYREQIKRVKDAEEVPMVLVGNKCDLST- 122
+R + L+ F ++ ++ + + ++ +I+ M+LVG K DL T
Sbjct: 67 DNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEF--CPNTKMLLVGCKSDLRTD 124
Query: 123 ------------WAVDMNQAQELAEQFN-IPFIKTSA-KTRMGVDDAFY 157
V +Q +A+Q +I+ SA ++ V D F+
Sbjct: 125 VSTLVELSNHRQTPVSYDQGANMAKQIGAATYIECSALQSENSVRDIFH 173
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 50.5 bits (121), Expect = 4e-08
Identities = 39/170 (22%), Positives = 62/170 (36%), Gaps = 15/170 (8%)
Query: 1 MAEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYR----KQVVIDGETALLD-- 54
M E K+VV+G G GK+ L V S + V +D + LD
Sbjct: 8 MIETKIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIELDED 67
Query: 55 ----ILDTAGQEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVP 110
+ T GQE + M + R G +++ + +F E I + +P
Sbjct: 68 TGVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHA----EEIIDFLTSRNPIP 123
Query: 111 MVLVGNKCDLST-WAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTL 159
+V+ NK DL + + E ++P I+ A G D L
Sbjct: 124 VVVAINKQDLFDALPPEKIREALKLELLSVPVIEIDATEGEGARDQLDVL 173
>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 = 48.0 bits (115), Expect = 2e-07
Identities = 37/164 (22%), Positives = 60/164 (36%), Gaps = 28/164 (17%)
Query: 7 VVVGAGGVGKSALTIQLIQNHF--VDEYDPTIEDSYRKQVVIDGETALLDILDTAG---- 60
+ G VGKS+L L+ + V T D RK+ + + ++DT G
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLG-PVVLIDTPGLDEE 59
Query: 61 ----QEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYR-EQIKRVKDAEEVPMVLVG 115
+E R R L++ V+S D+ E + P++LV
Sbjct: 60 GGLGRERVEEARQVADRAD---LVLLVVDS-----DLTPVEEEAKLGLLRERGKPVLLVL 111
Query: 116 NKCDLST-----WAVDMNQAQELAEQFNIPFIKTSAKTRMGVDD 154
NK DL + + + L + P I SA G+D+
Sbjct: 112 NKIDLVPESEEEELLRERKLELLPDL---PVIAVSALPGEGIDE 152
>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 = 46.8 bits (112), Expect = 5e-07
Identities = 38/167 (22%), Positives = 71/167 (42%), Gaps = 22/167 (13%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
+++++G G GK+ + +L V PTI + ++ + + D GQ++
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGEVVTTI-PTIGFNVET---VEYKNVKFTVWDVGGQDKI 56
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEE---VPMVLVGNKCDLS 121
+ Y +G L+F V+S E I + ++ ++ + EE P++++ NK DL
Sbjct: 57 RPLWKHYYENTDG--LIFVVDSSDR-ERIEEAKNELHKLLNEEELKGAPLLILANKQDL- 112
Query: 122 TWAVDMNQAQELAEQFNIPFIK--------TSAKTRMGVDDAFYTLV 160
EL E + IK SA T G+D+ L+
Sbjct: 113 ---PGALTESELIELLGLESIKGRRWHIQPCSAVTGDGLDEGLDWLI 156
>gnl|CDD|206737 cd04174, Rnd1_Rho6, Rnd1/Rho6 GTPases. Rnd1/Rho6 is a member of
the novel Rho subfamily Rnd, together with Rnd2/Rho7 and
Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not
hydrolyze it to GDP, indicating that it is
constitutively active. In rat, Rnd1/Rho6 is highly
expressed in the cerebral cortex and hippocampus during
synapse formation, and plays a role in spine formation.
Rnd1/Rho6 is also expressed in the liver and in
endothelial cells, and is upregulated in uterine
myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8,
Rnd1/Rho6 is believed to function as an antagonist to
RhoA. 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 = 232
Score = 46.6 bits (110), Expect = 1e-06
Identities = 36/137 (26%), Positives = 67/137 (48%), Gaps = 6/137 (4%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
KLV+VG GK+A+ L ++ + + Y PT+ ++Y + + + L + DT+G Y
Sbjct: 15 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYY 74
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFED-IGSYREQIKRVKDAEEVPMVLVGNKCDLSTW 123
+R + LL F ++ + F+ + +R +I + + +L+G K DL T
Sbjct: 75 DNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAEILDYCPSTRI--LLIGCKTDLRT- 131
Query: 124 AVDMNQAQELAEQFNIP 140
D++ EL+ Q P
Sbjct: 132 --DLSTLMELSNQKQAP 146
>gnl|CDD|133326 cd04126, Rab20, Rab GTPase family 20 (Rab20). Rab20 is one of
several Rab proteins that appear to be restricted in
expression to the apical domain of murine polarized
epithelial cells. It is expressed on the apical side of
polarized kidney tubule and intestinal epithelial cells,
and in non-polarized cells. It also localizes to
vesico-tubular structures below the apical brush border
of renal proximal tubule cells and in the apical region
of duodenal epithelial cells. Rab20 has also been shown
to colocalize with vacuolar H+-ATPases (V-ATPases) in
mouse kidney cells, suggesting a role in the regulation
of V-ATPase traffic in specific portions of the nephron.
It was also shown to be one of several proteins whose
expression is upregulated in human myelodysplastic
syndrome (MDS) patients. 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 = 220
Score = 46.4 bits (110), Expect = 2e-06
Identities = 41/172 (23%), Positives = 77/172 (44%), Gaps = 13/172 (7%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDS-YRKQVVIDGETALLDILDTAGQEE 63
K+V++G VGK++L + ++ F D T+ + Y KQ + I DTAG+E+
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRFKD-TVSTVGGAFYLKQ----WGPYNISIWDTAGREQ 56
Query: 64 YSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLSTW 123
+ + Y R +L + V++++S E++ + + E+ +VGNK DL+
Sbjct: 57 FHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTAN-EDCLFAVVGNKLDLTE- 114
Query: 124 AVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKKDKMLRGKEKK 175
A E+ + + ++ ++DA + I K KML
Sbjct: 115 ----EGALAGQEKDAGDRVSPEDQRQVTLEDAK-AFYKRINKYKMLDEDLSP 161
>gnl|CDD|133275 cd01873, RhoBTB, RhoBTB protein is an atypical member of the Rho
family of small GTPases. Members of the RhoBTB
subfamily of Rho GTPases are present in vertebrates,
Drosophila, and Dictyostelium. RhoBTB proteins are
characterized by a modular organization, consisting of a
GTPase domain, a proline rich region, a tandem of two
BTB (Broad-Complex, Tramtrack, and Bric a brac) domains,
and a C-terminal region of unknown function. RhoBTB
proteins may act as docking points for multiple
components participating in signal transduction
cascades. RhoBTB genes appeared upregulated in some
cancer cell lines, suggesting a participation of RhoBTB
proteins in the pathogenesis of particular tumors. Note
that the Dictyostelium RacA GTPase domain is more
closely related to Rac proteins than to RhoBTB proteins,
where RacA actually belongs. Thus, the Dictyostelium
RacA is not included here. Most Rho proteins contain a
lipid modification site at the C-terminus; however,
RhoBTB is one of few Rho subfamilies that lack this
feature.
Length = 195
Score = 46.1 bits (109), Expect = 2e-06
Identities = 50/197 (25%), Positives = 80/197 (40%), Gaps = 45/197 (22%)
Query: 4 YKLVVVGAGGVGKS-----------ALTIQLIQNHF-----VDEYDPTIEDSYRKQVVID 47
K VVVG VGK+ QL+ H +D+Y E R + V+D
Sbjct: 3 IKCVVVGDNAVGKTRLICARACNKTLTQYQLLATHVPTVWAIDQYRVCQEVLERSRDVVD 62
Query: 48 GETALLDILDTAGQEEYSAMRDQYMRTGEG--FLLVFAVNSMKSFEDIGS-YREQIKRVK 104
G + L + DT G + +D+ G LL F++ S S ++ + + +I+
Sbjct: 63 GVSVSLRLWDTFGDHD----KDRRFAYGRSDVVLLCFSIASPNSLRNVKTMWYPEIRHF- 117
Query: 105 DAEEVPMVLVGNKCDLSTWAVDMN--------------------QAQELAEQFNIPFIKT 144
VP++LVG K DL +D + +A++ IP+ +T
Sbjct: 118 -CPRVPVILVGCKLDLRYADLDEVNRARRPLARPIKNADILPPETGRAVAKELGIPYYET 176
Query: 145 SAKTRMGVDDAFYTLVR 161
S T+ GV D F +R
Sbjct: 177 SVVTQFGVKDVFDNAIR 193
>gnl|CDD|206719 cd04152, Arl4_Arl7, Arf-like 4 (Arl4) and 7 (Arl7) GTPases. Arl4
(Arf-like 4) is highly expressed in testicular germ
cells, and is found in the nucleus and nucleolus. In
mice, Arl4 is developmentally expressed during
embryogenesis, and a role in somite formation and
central nervous system differentiation has been
proposed. Arl7 has been identified as the only Arf/Arl
protein to be induced by agonists of liver X-receptor
and retinoid X-receptor and by cholesterol loading in
human macrophages. Arl7 is proposed to play a role in
transport between a perinuclear compartment and the
plasma membrane, apparently linked to the ABCA1-mediated
cholesterol secretion pathway. Older literature suggests
that Arl6 is a part of the Arl4/Arl7 subfamily, but
analyses based on more recent sequence data place Arl6
in its own subfamily.
Length = 183
Score = 43.6 bits (103), Expect = 1e-05
Identities = 44/183 (24%), Positives = 80/183 (43%), Gaps = 17/183 (9%)
Query: 6 LVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDG--ETALLDILDTAGQEE 63
+V++G GK+ + +L N FV+ PT + K V G + D GQE+
Sbjct: 6 IVMLGLDSAGKTTVLYRLKFNEFVNTV-PTKGFNTEKIKVSLGNAKGVTFHFWDVGGQEK 64
Query: 64 YSAMRDQYMRTGEGFLLVFAVNS--MKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLS 121
+ Y R +G +VF V+S ++ E+ + +I + + + VP++++ NK DL
Sbjct: 65 LRPLWKSYTRCTDG--IVFVVDSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLP 122
Query: 122 TWAVDMNQAQELAEQFNIPFI-----KTSAKTRMGVD---DAFYTLVREIKKDKMLRGKE 173
+ LA A G+ + Y ++ +K+ KMLR ++
Sbjct: 123 NALPVSEVEKLLALHELSSSTPWHVQPACAIIGEGLQEGLEKLYEMI--LKRRKMLRQQK 180
Query: 174 KKK 176
KK+
Sbjct: 181 KKR 183
>gnl|CDD|206701 cd04128, Spg1, Septum-promoting GTPase (Spg1). Spg1p. Spg1p
(septum-promoting GTPase) was first identified in the
fission yeast S. pombe, where it regulates septum
formation in the septation initiation network (SIN)
through the cdc7 protein kinase. Spg1p is an essential
gene that localizes to the spindle pole bodies. When
GTP-bound, it binds cdc7 and causes it to translocate to
spindle poles. Sid4p (septation initiation defective) is
required for localization of Spg1p to the spindle pole
body, and the ability of Spg1p to promote septum
formation from any point in the cell cycle depends on
Sid4p. Spg1p is negatively regulated by Byr4 and cdc16,
which form a two-component GTPase activating protein
(GAP) for Spg1p. The existence of a SIN-related pathway
in plants has been proposed. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization.
Length = 182
Score = 42.8 bits (101), Expect = 2e-05
Identities = 37/160 (23%), Positives = 66/160 (41%), Gaps = 11/160 (6%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSY-RKQVVIDGETALLDILDTAGQEE 63
K+ ++G +GK++L ++ ++ F +EY T+ ++ K + I G I D GQ E
Sbjct: 2 KIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQRE 61
Query: 64 YSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL--- 120
+ M + L +F + + I + Q + +P +LVG K DL
Sbjct: 62 FINMLPLVCKDAVAILFMFDLTRKSTLNSIKEWYRQARGFNKT-AIP-ILVGTKYDLFAD 119
Query: 121 ----STWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAF 156
+ QA++ A+ P I S + V F
Sbjct: 120 LPPEEQEEI-TKQARKYAKAMKAPLIFCSTSHSINVQKIF 158
>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 = 42.1 bits (100), Expect = 7e-05
Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 93 IGSYREQIKRVKDAEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGV 152
G Y ++ ++P ++V NK DL + + ++L ++F +P I SA T G+
Sbjct: 99 PGEYELELIEELKERKIPYIVVINKIDLGE---ESAELEKLEKKFGLPPIFVSALTGEGI 155
Query: 153 DDAFYTLVREIKKDK 167
D+ ++ + +D
Sbjct: 156 DELKEAIIELLPEDF 170
>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 = 40.5 bits (96), Expect = 1e-04
Identities = 31/126 (24%), Positives = 54/126 (42%), Gaps = 23/126 (18%)
Query: 43 QVVIDGETALLDILDTAGQEEYSAMRDQYMRTGEG---FLLVFAVNSMKSFEDIGSY-RE 98
QV ID + + +DT G E ++ MR R +LV A + + + E
Sbjct: 41 QVPIDVKIPGITFIDTPGHEAFTNMR---ARGASVTDIAILVVAAD-----DGVMPQTIE 92
Query: 99 QIKRVKDAEEVPMVLVGNKCDLSTWAV--------DMNQAQELAEQF--NIPFIKTSAKT 148
I K A VP+++ NK D ++++ + E++ ++ + SAKT
Sbjct: 93 AINHAKAAN-VPIIVAINKIDKPYGTEADPERVKNELSELGLVGEEWGGDVSIVPISAKT 151
Query: 149 RMGVDD 154
G+DD
Sbjct: 152 GEGIDD 157
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 40.6 bits (96), Expect = 2e-04
Identities = 43/171 (25%), Positives = 68/171 (39%), Gaps = 26/171 (15%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNH--FVDEYDPTIEDSYRKQVVIDGETALLDILDTAG-- 60
K+ ++G VGKS+L ++ V + T DS + DG +L +DTAG
Sbjct: 180 KIAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDSIDIEFERDGRKYVL--IDTAGIR 237
Query: 61 --------QEEYSAMRD-QYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPM 111
E+YS R + + + LLV E I +I + + +
Sbjct: 238 RKGKITESVEKYSVARTLKAIERADVVLLVIDAT-----EGISEQDLRIAGLIEEAGRGI 292
Query: 112 VLVGNKCDL-STWAVDMNQA-QELAEQFN----IPFIKTSAKTRMGVDDAF 156
V+V NK DL M + ++L + P + SA T G+D F
Sbjct: 293 VIVVNKWDLVEEDEATMEEFKKKLRRKLPFLDFAPIVFISALTGQGLDKLF 343
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 40.1 bits (95), Expect = 3e-04
Identities = 27/87 (31%), Positives = 42/87 (48%), Gaps = 18/87 (20%)
Query: 79 LLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFN 138
LLV + + ED E ++ +KD P+++V NK DL+ +L E+
Sbjct: 299 LLVLDASEPLTEED----DEILEELKDK---PVIVVLNKADLT-------GEIDLEEENG 344
Query: 139 IPFIKTSAKTRMGVDDAFYTLVREIKK 165
P I+ SAKT G+D+ L IK+
Sbjct: 345 KPVIRISAKTGEGIDE----LREAIKE 367
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 39.0 bits (92), Expect = 4e-04
Identities = 27/138 (19%), Positives = 51/138 (36%), Gaps = 32/138 (23%)
Query: 44 VVIDGETALLDILDTAGQEEYSAMRDQYMRTG----EGFLLVFAVNS--MKSFEDIGSYR 97
V + + L++I+DT G +++ M G +G +LV M
Sbjct: 59 VSFETKKRLINIIDTPGHVDFTKE----MIRGASQADGAILVVDAVEGVM---------- 104
Query: 98 EQIK---RVKDAEEVPMVLVGNKCDLSTWAVDMNQAQELAEQF---------NIPFIKTS 145
Q + + VP+++ NK D A +E++ + +P + S
Sbjct: 105 PQTREHLLLAKTLGVPIIVFINKIDRVDDAELEEVVEEISRELLEKYGFGGETVPVVPGS 164
Query: 146 AKTRMGVDDAFYTLVREI 163
A T G+D+ L +
Sbjct: 165 ALTGEGIDELLEALDLYL 182
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 39.5 bits (93), Expect = 5e-04
Identities = 38/163 (23%), Positives = 63/163 (38%), Gaps = 28/163 (17%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNH--FVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQE 62
K+V++G VGKS+L L+ V + T D + + ++G + ++DTAG
Sbjct: 219 KVVIIGRPNVGKSSLLNALLGRDRAIVTDIAGTTRDVIEEDINLNG--IPVRLVDTAGIR 276
Query: 63 EYSAMRD-----------QYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPM 111
E D + + + L V + ED+ K + P+
Sbjct: 277 ETD---DVVERIGIERAKKAIEEADLVLFVLDASQPLDKEDLALIELLPK------KKPI 327
Query: 112 VLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDD 154
++V NK DL V + + I SAKT G+D
Sbjct: 328 IVVLNKADL----VSKIELESEKLANGDAIISISAKTGEGLDA 366
>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 = 38.9 bits (92), Expect = 7e-04
Identities = 17/55 (30%), Positives = 24/55 (43%)
Query: 110 PMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIK 164
P ++V NK DL +EL E P SA T G+D+ Y L ++
Sbjct: 275 PRIVVLNKIDLLDEEELEELLKELKEALGKPVFPISALTGEGLDELLYALAELLE 329
>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 = 38.3 bits (90), Expect = 8e-04
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 9/78 (11%)
Query: 95 SYREQI---KRVKDAEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTRMG 151
S EQ+ K +K P+++V NK DL T D+++ ++ E+ IK S T G
Sbjct: 96 SIEEQLSLFKEIKPLFNKPVIVVLNKIDLLTEE-DLSEIEKELEKEGEEVIKISTLTEEG 154
Query: 152 VDDAFYTLVREIKKDKML 169
VD+ ++ + +L
Sbjct: 155 VDE-----LKNKACELLL 167
>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 = 38.2 bits (90), Expect = 8e-04
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 10/65 (15%)
Query: 96 YREQIKRVKD------AEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTR 149
EQI+ V++ A+++P++LV NK DL +D + +E + SAKT
Sbjct: 135 REEQIETVEEVLKELGADDIPIILVLNKIDL----LDDEELEERLRAGRPDAVFISAKTG 190
Query: 150 MGVDD 154
G+D
Sbjct: 191 EGLDL 195
>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 = 37.9 bits (89), Expect = 9e-04
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 10/59 (16%)
Query: 107 EEVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
+ P+++V NK DL ++ A+ ++E P I SAKT G+D+ L + +
Sbjct: 108 AKKPVIVVLNKSDL------LSDAEGISELNGKPIIAISAKTGEGIDE----LKEALLE 156
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 38.6 bits (91), Expect = 9e-04
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 11/64 (17%)
Query: 96 YREQIKRVKD------AEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTR 149
EQI+ V+ AE++P +LV NK DL +D + + L E + + SAKT
Sbjct: 283 REEQIEAVEKVLEELGAEDIPQLLVYNKIDL----LDEPRIERLEEGYPE-AVFVSAKTG 337
Query: 150 MGVD 153
G+D
Sbjct: 338 EGLD 341
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to as
the Sar1-N-terminal activation recruitment (STAR) motif.
The STAR motif mediates the recruitment of Sar1 to ER
membranes and facilitates its interaction with mammalian
Sec12 GEF leading to activation.
Length = 191
Score = 37.6 bits (88), Expect = 0.001
Identities = 39/177 (22%), Positives = 71/177 (40%), Gaps = 38/177 (21%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEY 64
K+V +G GK+ L + ++++ + ++ PT+ + +++ I D G E
Sbjct: 21 KIVFLGLDNAGKTTL-LHMLKDDRLAQHVPTLHPT-SEELTIGNVK--FTTFDLGGHE-- 74
Query: 65 SAMR--DQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEE---VPMVLVGNKCD 119
A R Y +G +VF V++ E +E++ + + EE VP++++GNK D
Sbjct: 75 QARRVWKDYFPEVDG--IVFLVDAA-DPERFQESKEELDSLLNDEELANVPILILGNKID 131
Query: 120 LSTWAVDMNQAQELAEQFNIPFIKT--------------------SAKTRMGVDDAF 156
AV +EL E + T S R G + F
Sbjct: 132 KPG-AVSE---EELREALGLYGTTTGKGGVSLKVSNIRPVEVFMCSVVKRQGYGEGF 184
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 37.4 bits (87), Expect = 0.002
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 12/80 (15%)
Query: 91 EDIGSYREQIKRVK-DAEEVPMVLVGNKCDLSTWAVDMNQ---AQELAEQFNIPFIKTSA 146
ED + E++ + P ++V NK D N + + IP + TSA
Sbjct: 95 EDQKTLNEEVSGSFLFLKNKPEMIVANKID----MASENNLKRLKLDKLKRGIPVVPTSA 150
Query: 147 KTRMGVDDAFYTLVREIKKD 166
TR+G+D +R I+K
Sbjct: 151 LTRLGLDRV----IRTIRKL 166
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH 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.
Length = 191
Score = 36.9 bits (86), Expect = 0.003
Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 13/86 (15%)
Query: 94 GSYREQIKRVKDAEEVPMVLVGNKCDLSTWAVDMNQAQE-LAEQFNIPFIK------TSA 146
GS + + A P++LVGNK DL V N+ ++ + ++ I +K SA
Sbjct: 48 GSLIPGLAELIGA--KPVILVGNKIDLLPKDVKPNRLKQWVKKRLKIGGLKIKDVILVSA 105
Query: 147 KTRMGVDDAFYTLVREIKKDKMLRGK 172
K GV++ L+ EIKK RG
Sbjct: 106 KKGWGVEE----LIEEIKKLAKYRGD 127
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 37.0 bits (87), Expect = 0.003
Identities = 18/69 (26%), Positives = 27/69 (39%), Gaps = 13/69 (18%)
Query: 110 PMVLVGNKCDLSTWAVDMNQAQELAEQFN--------IPFIKTSAKTRMGVDDAFYTLVR 161
+V+V NK DL VD +E ++ P + SA T GVD +
Sbjct: 286 ALVIVVNKWDL----VDEKTMEEFKKELRRRLPFLDYAPIVFISALTGQGVDKLL-EAID 340
Query: 162 EIKKDKMLR 170
E ++ R
Sbjct: 341 EAYENANRR 349
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 36.7 bits (86), Expect = 0.004
Identities = 17/66 (25%), Positives = 27/66 (40%), Gaps = 6/66 (9%)
Query: 110 PMVLVGNKCDLSTWAVDMNQA-QELAEQFN----IPFIKTSAKTRMGVDDAFYTLVREIK 164
+V+V NK DL + +EL + P + SA T GVD + E+
Sbjct: 285 ALVIVVNKWDLVKDEKTREEFKKELRRKLPFLDFAPIVFISALTGQGVDKLLDA-IDEVY 343
Query: 165 KDKMLR 170
++ R
Sbjct: 344 ENANRR 349
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (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 = 190
Score = 35.9 bits (84), Expect = 0.005
Identities = 13/68 (19%), Positives = 27/68 (39%), Gaps = 6/68 (8%)
Query: 108 EVPMVLVGNKCDLSTWAVDMNQ---AQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIK 164
+P+V+ N D A ++L+E +P + TSA+ G+D+ ++ +
Sbjct: 105 GIPVVVALNMMDE---AEKKGIKIDIKKLSELLGVPVVPTSARKGEGIDELKDAIIEVAE 161
Query: 165 KDKMLRGK 172
Sbjct: 162 GKVPPAPL 169
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 36.7 bits (85), Expect = 0.005
Identities = 46/175 (26%), Positives = 68/175 (38%), Gaps = 30/175 (17%)
Query: 6 LVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDS---YRKQVVIDGETALLD--ILDTAG 60
+ +VG VGKS L N + + +ED+ R +V D E A D ++DT G
Sbjct: 278 VAIVGRPNVGKSTLV-----NRILGRREAVVEDTPGVTRDRVSYDAEWAGTDFKLVDTGG 332
Query: 61 QEE-----YSAMRDQY---MRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMV 112
E SA+ Q + + +VF V+ + S E+I R+ P+V
Sbjct: 333 WEADVEGIDSAIASQAQIAVSLAD--AVVFVVDGQVG---LTSTDERIVRMLRRAGKPVV 387
Query: 113 LVGNKCDLSTWAVDMNQ--AQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
L NK D D + L E + I SA GV D + +K
Sbjct: 388 LAVNKIDDQASEYDAAEFWKLGLGEPYPI-----SAMHGRGVGDLLDEALDSLKV 437
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 36.6 bits (86), Expect = 0.005
Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 14/66 (21%)
Query: 107 EEVPMVLVGNKCDLSTWAVDMNQAQE----LAEQFNIPFIKTSAKTRMGVD---DAFYTL 159
E P ++V NK D + +A+E E+ SA T G+D A L
Sbjct: 273 LERPQIVVANKMD-------LPEAEENLEEFKEKLGPKVFPISALTGQGLDELLYAVAEL 325
Query: 160 VREIKK 165
+ E +
Sbjct: 326 LEETPE 331
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 36.5 bits (85), Expect = 0.005
Identities = 14/57 (24%), Positives = 29/57 (50%), Gaps = 6/57 (10%)
Query: 108 EVPMVLVGNKCDLST-WAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREI 163
+PM+L N D + + ++ ++L++ +P + T AK G+++ L R I
Sbjct: 108 GIPMILALNMIDEAKKRGIRID-IEKLSKLLGVPVVPTVAKRGEGLEE----LKRAI 159
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 36.5 bits (85), Expect = 0.006
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 14/76 (18%)
Query: 96 YREQIKRVKD------AEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTR 149
E+++ V+D A+E+P++LV NK DL + + + + + SAKT
Sbjct: 286 ILEKLEAVEDVLAEIGADEIPIILVLNKIDLLEDEEILAELERGSP----NPVFISAKTG 341
Query: 150 MGVDDAFYTLVREIKK 165
G+D L I +
Sbjct: 342 EGLD----LLRERIIE 353
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a nonhistone
chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 35.0 bits (81), Expect = 0.009
Identities = 35/145 (24%), Positives = 67/145 (46%), Gaps = 14/145 (9%)
Query: 2 AEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQ 61
EYK+++VG GK+ + Q + V PTI S +++V L+ D GQ
Sbjct: 14 KEYKVIIVGLDNAGKTTILYQFLLGEVV-HTSPTI-GSNVEEIVYKNIRFLM--WDIGGQ 69
Query: 62 EEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEV---PMVLVGNKC 118
E + + Y + +LV ++S E + +E++ ++ E++ ++++ NK
Sbjct: 70 ESLRSSWNTYYTNTDAVILV--IDSTDR-ERLPLTKEELYKMLAHEDLRKAVLLVLANKQ 126
Query: 119 DLSTWAVDMNQAQELAEQFNIPFIK 143
DL M A E++E + I+
Sbjct: 127 DLK---GAMTPA-EISESLGLTSIR 147
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 35.2 bits (82), Expect = 0.014
Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 11/77 (14%)
Query: 107 EEVPMVLVGNKCDLSTWAVDMNQAQELAEQFN-----IPFIKTSAKTRMGVD---DAFYT 158
E P ++V NK DL +D + +EL + F SA TR G+D A
Sbjct: 274 AEKPRIVVLNKIDL---PLDEEELEELKKALAEALGWEVFYLISALTREGLDELLRALAE 330
Query: 159 LVREIKKDKMLRGKEKK 175
L+ E K + E+
Sbjct: 331 LLEETKAEAEAAEAEEL 347
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 35.2 bits (82), Expect = 0.015
Identities = 40/150 (26%), Positives = 58/150 (38%), Gaps = 38/150 (25%)
Query: 56 LDTAGQEEYSAMRDQYMRTGEGFL-----LVFAVNS--MKSFEDIGSYREQIKRVKDAEE 108
+DT G E ++AMR + LV A + M E I K A
Sbjct: 60 IDTPGHEAFTAMR-----ARGASVTDIAILVVAADDGVMPQTI------EAINHAKAAG- 107
Query: 109 VPMVLVGNKCDLSTWAVDM--NQAQEL---AEQF--NIPFIKTSAKTRMGVDDAFYTL-- 159
VP+V+ NK D D + QE E++ ++ F+ SAKT G+D+ +
Sbjct: 108 VPIVVAINKIDKPEANPDKVKQELQEYGLVPEEWGGDVIFVPVSAKTGEGIDELLELILL 167
Query: 160 ---VREIK--KDKMLRG-----KEKKKRGI 179
V E+K + RG K K G
Sbjct: 168 LAEVLELKANPEGPARGTVIEVKLDKGLGP 197
>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 = 34.4 bits (80), Expect = 0.016
Identities = 12/58 (20%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 109 VPMVLVGNKCDLST-WAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
+P+V+ N D + + ++ + L+E +P + TSA+ G+D+ + + +
Sbjct: 103 LPVVVALNMIDEAEKRGIKIDLDK-LSELLGVPVVPTSARKGEGIDELLDAIAKLAES 159
>gnl|CDD|206724 cd04159, Arl10_like, Arf-like 9 (Arl9) and 10 (Arl10) GTPases.
Arl10-like subfamily. Arl9/Arl10 was identified from a
human cancer-derived EST dataset. No functional
information about the subfamily is available at the
current time, but crystal structures of human Arl10b and
Arl10c have been solved.
Length = 159
Score = 34.2 bits (79), Expect = 0.017
Identities = 28/118 (23%), Positives = 57/118 (48%), Gaps = 9/118 (7%)
Query: 6 LVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEEYS 65
+ +VG GK+ L + F ++ PT+ + RK V T + + D GQ +
Sbjct: 2 ITLVGLQNSGKTTLVNVIASGQFSEDTIPTVGFNMRK-VTKGNVT--IKVWDLGGQPRFR 58
Query: 66 AMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDA---EEVPMVLVGNKCDL 120
+M ++Y R +V+ V++ E + + ++ + + E +P++++GNK DL
Sbjct: 59 SMWERYCRGVN--AIVYVVDA-ADREKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDL 113
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 34.6 bits (81), Expect = 0.017
Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 10/70 (14%)
Query: 98 EQIKRVKDAEEVPMVLVGNKCDL-STWAVDMNQAQELAEQFN-IPFIKTSAKTRMGVDDA 155
E++K+VK P++LV NK DL + +EL+E + + SA VD+
Sbjct: 107 EKLKKVK----TPVILVLNKIDLVKDKEELLPLLEELSELMDFAEIVPISALKGDNVDE- 161
Query: 156 FYTLVREIKK 165
L+ I K
Sbjct: 162 ---LLDVIAK 168
>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 = 33.9 bits (79), Expect = 0.020
Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 5/57 (8%)
Query: 110 PMVLVGNKCDLSTWA-VDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
P ++V NK DL + L E SA T G+D+ L++++ K
Sbjct: 116 PRIVVLNKIDLLDAEERFEKLKELLKELKGKKVFPISALTGEGLDE----LLKKLAK 168
>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 = 33.9 bits (79), Expect = 0.025
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 106 AEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDD 154
A + V+V NK DL ++ + E+ E+ P + SAKT G+D+
Sbjct: 31 ASGIEPVIVLNKADLVD-DEELEELLEIYEKLGYPVLAVSAKTGEGLDE 78
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 33.9 bits (79), Expect = 0.025
Identities = 8/62 (12%), Positives = 26/62 (41%), Gaps = 3/62 (4%)
Query: 108 EVPMVLVGNKCD---LSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIK 164
+P+++V K D + + ++ + + I S+ + G+D+ + + +
Sbjct: 135 GIPVLIVLTKADKLKKGERKKQLKKVRKALKFGDDEVILFSSLKKQGIDELRAAIAKWLA 194
Query: 165 KD 166
+
Sbjct: 195 EA 196
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 34.5 bits (80), Expect = 0.025
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 2/58 (3%)
Query: 110 PMVLVGNKCDLSTWAVDMNQAQELAEQFN--IPFIKTSAKTRMGVDDAFYTLVREIKK 165
P LV NK DL +A+ + E P SA + +GV + + L+ I++
Sbjct: 277 PRWLVFNKIDLLDEEEAEERAKAIVEALGWEGPVYLISAASGLGVKELCWDLMTFIEE 334
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 34.3 bits (80), Expect = 0.027
Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 1/59 (1%)
Query: 110 PMVLVGNKCD-LSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKKDK 167
P +LV NK D L +A P SA T G+D+ L +++ +
Sbjct: 273 PRILVLNKIDLLDEEEEREKRAALELAALGGPVFLISAVTGEGLDELLRALWELLEEAR 331
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 33.7 bits (78), Expect = 0.027
Identities = 38/172 (22%), Positives = 69/172 (40%), Gaps = 22/172 (12%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQE 62
E +++++G GK+ + +L V PTI + V + D GQE
Sbjct: 14 EMRILILGLDNAGKTTILYKLKLGEIV-TTIPTI-GFNVETVTYKNVK--FTVWDVGGQE 69
Query: 63 EYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEE---VPMVLVGNKCD 119
+ Y + ++F V+S + I +E++ + + EE P++++ NK D
Sbjct: 70 SLRPLWRNYFPNTDA--VIFVVDS-ADRDRIEEAKEELHALLNEEELADAPLLILANKQD 126
Query: 120 LSTWAVDMNQAQELAEQFNIPFIK--------TSAKTRMGVDDAFYTLVREI 163
L M+ E+ E + +K SA T G+D+ L I
Sbjct: 127 LPG---AMS-EAEIRELLGLHELKDRPWEIQGCSAVTGEGLDEGLDWLSNYI 174
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 33.9 bits (78), Expect = 0.032
Identities = 22/89 (24%), Positives = 42/89 (47%), Gaps = 9/89 (10%)
Query: 93 IGSYREQIKRVKDAEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGV 152
+G+ +++R+ +E P +LV NK DL+ V + ++ I I SAK+R G
Sbjct: 48 LGTRNPELERI--VKEKPKLLVLNKADLAPKEVTKKWKKYFKKEEGIKPIFVSAKSRQGG 105
Query: 153 -------DDAFYTLVREIKKDKMLRGKEK 174
+ ++ +KK +L+ K +
Sbjct: 106 KKIRKALEKLSEEKIKRLKKKGLLKRKIR 134
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however, Miro
is one of few Rho subfamilies that lack this feature.
Length = 180
Score = 33.4 bits (77), Expect = 0.033
Identities = 30/130 (23%), Positives = 47/130 (36%), Gaps = 35/130 (26%)
Query: 8 VVGAGGVGKSALTIQLIQNHFVDE-YDPTIEDSYRKQVVIDGETALLDILDTAGQEEYSA 66
V+GA G GKSAL + F Y PTI + + + + ++ GQE+Y
Sbjct: 9 VLGAKGSGKSALLQAFLGRSFSQNAYSPTI----KPRYAV-------NTVEVPGQEKYLI 57
Query: 67 MRDQYMRTGEGFLLVFAVNSM----------------KSFEDIGSYREQIKRVKDAEEVP 110
+R+ GE + ++ SF K+ E+P
Sbjct: 58 LRE----VGEDEEAILLNDAELAACDVACLVYDSSDPNSFSYCAEVY---KKYFMLGEIP 110
Query: 111 MVLVGNKCDL 120
+ V K DL
Sbjct: 111 CLFVAAKADL 120
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 33.3 bits (77), Expect = 0.067
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 10/66 (15%)
Query: 97 REQIKRVKDAEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIP--------FIKTSAKT 148
E I K A VP+++ NK D D + QEL+E +P F+ SAKT
Sbjct: 338 IEAINHAKAAG-VPIIVAINKIDKPGANPDRVK-QELSEYGLVPEEWGGDTIFVPVSAKT 395
Query: 149 RMGVDD 154
G+D+
Sbjct: 396 GEGIDE 401
>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 = 32.6 bits (75), Expect = 0.079
Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 19/77 (24%)
Query: 99 QIKRVKDAEEVPMVLVGNKCDLSTWAVDMNQAQELAEQ----------FNIPFIKTSAKT 148
+I +K ++++ NK DL V QA E EQ N P I SA+
Sbjct: 127 EIMGLKH-----IIILQNKIDL----VKEEQALENYEQIKEFVKGTIAENAPIIPISAQL 177
Query: 149 RMGVDDAFYTLVREIKK 165
+ +D +V++I
Sbjct: 178 KYNIDVLCEYIVKKIPT 194
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 32.5 bits (75), Expect = 0.088
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 6/52 (11%)
Query: 106 AEEVPMVLVGNKCDLSTWAVDMNQAQELAEQF-NI--PFIKTSAKTRMGVDD 154
A + ++V NK DL D+ +A+EL + I ++ SAK G+D+
Sbjct: 109 ANGIKPIIVLNKIDL---LDDLEEARELLALYRAIGYDVLELSAKEGEGLDE 157
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 32.5 bits (74), Expect = 0.12
Identities = 29/123 (23%), Positives = 52/123 (42%), Gaps = 14/123 (11%)
Query: 39 SYRKQVVIDGETALLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYRE 98
+Y + E + LDT G E +S+MR + + +L+ A + + I E
Sbjct: 283 AYEVEFEYKDENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTI----E 338
Query: 99 QIKRVKDAEEVPMVLVGNKCDLSTWAVDMNQAQELAEQF--------NIPFIKTSAKTRM 150
I ++ A VP+++ NK D + + + Q+LA+ + P I SA
Sbjct: 339 AINYIQAA-NVPIIVAINKIDKANANTERIK-QQLAKYNLIPEKWGGDTPMIPISASQGT 396
Query: 151 GVD 153
+D
Sbjct: 397 NID 399
>gnl|CDD|216530 pfam01494, FAD_binding_3, FAD binding domain. This domain is
involved in FAD binding in a number of enzymes.
Length = 349
Score = 32.3 bits (74), Expect = 0.13
Identities = 13/64 (20%), Positives = 27/64 (42%), Gaps = 7/64 (10%)
Query: 3 EYKLVVVGAGGVGKSA---LTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTA 59
E +++VG G G L ++ V+ + T + ++ T +++L A
Sbjct: 1 ETDVLIVGGGPAGLMLALLLARAGVRVVLVERHATTSVLP--RAGGLNQRT--MELLRQA 56
Query: 60 GQEE 63
G E+
Sbjct: 57 GLED 60
>gnl|CDD|235676 PRK06027, purU, formyltetrahydrofolate deformylase; Reviewed.
Length = 286
Score = 32.0 bits (74), Expect = 0.14
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 13/61 (21%)
Query: 108 EVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIPF--IKTSAKTRMGVDDAFYTLVREIKK 165
E+ V + N DL + L E+F IPF + + +T+ + L+ E +
Sbjct: 118 EIAAV-ISNHDDL----------RSLVERFGIPFHHVPVTKETKAEAEARLLELIDEYQP 166
Query: 166 D 166
D
Sbjct: 167 D 167
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA, an
essential protein involved in cell division control.
YihA and its orthologs are small proteins that typically
contain less than 200 amino acid residues and consists
of the GTPase domain only (some of the eukaryotic
homologs contain an N-terminal extension of about 120
residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 31.3 bits (72), Expect = 0.15
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 107 EEVPMVLVGNKCDL---STWAVDMNQAQELAEQFNI--PFIKTSAKTRMGVDDAFYTL 159
+P ++V K D S A + + +E FNI P I S+K G+D+ +
Sbjct: 109 LGIPFLIVLTKADKLKKSELAKVLKKIKEELNLFNILPPVILFSSKKGTGIDELRALI 166
>gnl|CDD|206746 cd01849, YlqF_related_GTPase, Circularly permuted YlqF-related
GTPases. These proteins are found in bacteria,
eukaryotes, and archaea. They all exhibit a circular
permutation of the GTPase signature motifs so that the
order of the conserved G box motifs is G4-G5-G1-G2-G3,
with G4 and G5 being permuted from the C-terminal region
of proteins in the Ras superfamily to the N-terminus of
YlqF-related GTPases.
Length = 146
Score = 31.2 bits (71), Expect = 0.15
Identities = 21/73 (28%), Positives = 29/73 (39%), Gaps = 5/73 (6%)
Query: 112 VLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKKDKMLRG 171
++V NK DL V EL+E + SA G+ L EI K K+
Sbjct: 32 IMVLNKADLVPKEVLRKWVAELSELYGTKTFFISATNGQGILK----LKAEITKQKLKLK 87
Query: 172 KEKKKR-GISGNK 183
+K R G+ G
Sbjct: 88 YKKGIRVGVVGLP 100
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and
chromosome partitioning / Cytoskeleton].
Length = 373
Score = 31.9 bits (73), Expect = 0.17
Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 11/66 (16%)
Query: 6 LVVVGAGGVGKSALTIQLIQNHFVDE----------YDPTIEDSYRKQVVIDGETAL-LD 54
++VVG G+GK+ L VDE PT+E K + + L L
Sbjct: 26 IMVVGESGLGKTTFINTLFGTSLVDETEIDDIRAEGTSPTLEIKITKAELEEDGFHLNLT 85
Query: 55 ILDTAG 60
++DT G
Sbjct: 86 VIDTPG 91
>gnl|CDD|234401 TIGR03925, T7SS_EccC_b, type VII secretion protein EccCb. This
model represents the C-terminal domain or EccCb subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 566
Score = 31.9 bits (73), Expect = 0.22
Identities = 15/69 (21%), Positives = 24/69 (34%), Gaps = 13/69 (18%)
Query: 6 LVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQ----VVIDGETALLDILDTAGQ 61
L+V G GK+ L + + I Y Q V++D +LL +
Sbjct: 366 LLVFGDSESGKTTLLRAIAR---------GITRRYSPQQARLVLVDYRRSLLGAVPEEHL 416
Query: 62 EEYSAMRDQ 70
Y+A
Sbjct: 417 AGYAASSAA 425
>gnl|CDD|235235 PRK04165, PRK04165, acetyl-CoA decarbonylase/synthase complex
subunit gamma; Provisional.
Length = 450
Score = 31.4 bits (72), Expect = 0.30
Identities = 23/92 (25%), Positives = 36/92 (39%), Gaps = 20/92 (21%)
Query: 42 KQVVIDGETAL--------------LDILDTAGQEEYSA-----MRDQYMRTGEGFLLVF 82
+ V I GET L +D+ DT EE A Q+ R GE L
Sbjct: 71 RAVKIGGETVLYRHEKTFFNPTGIAVDVSDTMDDEEIDARLKKINNFQFERVGEILKLDM 130
Query: 83 AVNSMKSFEDIGSYREQIKRVKDAEEVPMVLV 114
S D + + +K+V + ++P++L
Sbjct: 131 VALRNAS-GDPEKFAKAVKKVAETTDLPLILC 161
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 31.3 bits (71), Expect = 0.31
Identities = 32/109 (29%), Positives = 49/109 (44%), Gaps = 18/109 (16%)
Query: 56 LDTAGQEEYSAMRDQYMRTGEGFLLVFAVNS--MKSFEDIGSYREQIKRVKDAEEVPMVL 113
LDT G E +++MR + + + +LV A + M E I K A VP+++
Sbjct: 140 LDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQTI------EAISHAKAA-NVPIIV 192
Query: 114 VGNKCDLSTWAVDMNQAQELAEQFNIP--------FIKTSAKTRMGVDD 154
NK D D + QEL+E +P F+ SA T G+D+
Sbjct: 193 AINKIDKPEANPDRVK-QELSEYGLVPEDWGGDTIFVPVSALTGDGIDE 240
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated
with diverse processes in dividing and non-dividing
cells. They were first discovered in the budding yeast
S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of
the cell cortex and exocytosis. In humans, 12 septin
genes generate dozens of polypeptides, many of which
comprise heterooligomeric complexes. Since septin
mutants are commonly defective in cytokinesis and
formation of the neck formation of the neck
filaments/septin rings, septins have been considered to
be the primary constituents of the neck filaments.
Septins belong to the GTPase superfamily for their
conserved GTPase motifs and enzymatic activities.
Length = 275
Score = 30.6 bits (70), Expect = 0.37
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 10/68 (14%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNHFVDE---------YDPTIE-DSYRKQVVIDGETAL 52
++ ++VVG G+GKS L T+E + ++ +G
Sbjct: 4 QFNIMVVGESGLGKSTFINTLFGTKLYPSKYPPAPGEHITKTVEIKISKAELEENGVKLK 63
Query: 53 LDILDTAG 60
L ++DT G
Sbjct: 64 LTVIDTPG 71
>gnl|CDD|206722 cd04157, Arl6, Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms a
subfamily of the Arf family of small GTPases. Arl6
expression is limited to the brain and kidney in adult
mice, but it is expressed in the neural plate and
somites during embryogenesis, suggesting a possible role
for Arl6 in early development. Arl6 is also believed to
have a role in cilia or flagella function. Several
proteins have been identified that bind Arl6, including
Arl6 interacting protein (Arl6ip), and SEC61beta, a
subunit of the heterotrimeric conducting channel SEC61p.
Based on Arl6 binding to these effectors, Arl6 is also
proposed to play a role in protein transport, membrane
trafficking, or cell signaling during hematopoietic
maturation. At least three specific homozygous Arl6
mutations in humans have been found to cause
Bardet-Biedl syndrome, a disorder characterized by
obesity, retinopathy, polydactyly, renal and cardiac
malformations, learning disabilities, and
hypogenitalism. Older literature suggests that Arl6 is a
part of the Arl4/Arl7 subfamily, but analyses based on
more recent sequence data place Arl6 in its own
subfamily.
Length = 162
Score = 30.1 bits (68), Expect = 0.42
Identities = 25/112 (22%), Positives = 52/112 (46%), Gaps = 12/112 (10%)
Query: 57 DTAGQEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRV---KD--AEEVPM 111
D +GQ +Y + + Y + +G ++F ++S + +++++ + D +P+
Sbjct: 51 DMSGQGKYRGLWEHYYKNIQG--IIFVIDSSDRLR-MVVAKDELELLLNHPDIKHRRIPI 107
Query: 112 VLVGNKCDL--STWAVDMNQAQELAEQFNIPF--IKTSAKTRMGVDDAFYTL 159
+ NK DL + AV + Q L + P+ +SA T G+D+ L
Sbjct: 108 LFYANKMDLPDALTAVKITQLLCLENIKDKPWHIFASSALTGEGLDEGVDWL 159
>gnl|CDD|238991 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible
oxidation of CO to CO2. CODH contains a
nickel-iron-sulfur cluster (C-center) and an
iron-sulfur cluster (B-center). CO oxidation occurs at
the C-center. Three accessory proteins encoded by
cooCTJ genes are involved in nickel incorporation into
a nickel site. CooC functions as a nickel insertase
that mobilizes nickel to apoCODH using energy released
from ATP hydrolysis. CooC is a homodimer and has NTPase
activities. Mutation at the P-loop abolishs its
function.
Length = 116
Score = 29.5 bits (67), Expect = 0.49
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 5 KLVVVGAGGVGKSALTIQLIQ 25
K+ + G GGVGK+ + L +
Sbjct: 1 KIAITGKGGVGKTTIAALLAR 21
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 30.1 bits (69), Expect = 0.50
Identities = 43/175 (24%), Positives = 71/175 (40%), Gaps = 34/175 (19%)
Query: 5 KLVVVGAGGVGKSALTIQLI--QNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAG-- 60
K+ ++G VGKS+L L+ + V + T DS DG+ L +DTAG
Sbjct: 4 KIAIIGRPNVGKSSLLNALLGEERVIVSDIAGTTRDSIDVPFEYDGQKYTL--IDTAGIR 61
Query: 61 --------QEEYSAMRD-QYMRTGEGFLLVFAVNSMKSFED----IGSYREQIKRVKDAE 107
E+YS +R + + + LLV +++ + + I + +
Sbjct: 62 KKGKVTEGIEKYSVLRTLKAIERADVVLLV--LDASEGITEQDLRIAGLILEEGK----- 114
Query: 108 EVPMVLVGNKCDL-STWAVDMNQ-AQELAEQFN----IPFIKTSAKTRMGVDDAF 156
+++V NK DL M + +EL + P + SA T GVD F
Sbjct: 115 --ALIIVVNKWDLVEKDEKTMKEFEKELRRKLPFLDYAPIVFISALTGQGVDKLF 167
>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 = 30.3 bits (69), Expect = 0.62
Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 21/80 (26%)
Query: 110 PMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKT--------RMGV------DDA 155
PMV+ NK D+ + N ++ + + + TSA+ + G+ D
Sbjct: 216 PMVIAANKADIPD--AEENISKLRLKYPDEIVVPTSAEAELALRRAAKQGLIKYVPGDSD 273
Query: 156 FYTLVREIKKDKMLRGKEKK 175
F EI + L K+++
Sbjct: 274 F-----EITDEDGLSDKQRE 288
>gnl|CDD|223382 COG0305, DnaB, Replicative DNA helicase [DNA replication,
recombination, and repair].
Length = 435
Score = 29.9 bits (68), Expect = 0.69
Identities = 31/163 (19%), Positives = 61/163 (37%), Gaps = 34/163 (20%)
Query: 5 KLVVVGAG-GVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVI-----DGETALLDILDT 58
L++V A G+GK+AL + + N RK V I E ++ +L +
Sbjct: 197 DLIIVAARPGMGKTALALNIALN---------AAADGRKPVAIFSLEMSEEQLVMRLLSS 247
Query: 59 AGQEEYSAMRDQYMRTGEGFLLVFAVNSMKS----FEDIGSY-----REQIKRVKDAEEV 109
E S +R + E L+ A + + +D R + +R+K +
Sbjct: 248 ESGIESSKLRTGRLSDDEWERLIKAASELSEAPIFIDDTPGLTITEIRSKARRLKLKHNL 307
Query: 110 PMVLVGNKCDLSTWAVDMNQAQELAEQ----------FNIPFI 142
++++ ++ N+ QE++E +P I
Sbjct: 308 GLIVIDYLQLMTGGKKSENRKQEVSEISRSLKGLAKELGVPVI 350
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 30.1 bits (68), Expect = 0.76
Identities = 42/185 (22%), Positives = 75/185 (40%), Gaps = 32/185 (17%)
Query: 4 YKLVVVGAGGVGKSALTIQLIQNH--FVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQ 61
+KL +VG+ VGKS+L L++ V + T D ++G L+ +LDTAG
Sbjct: 204 FKLAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGI--LIKLLDTAGI 261
Query: 62 EEYSAMRDQY--------MRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVL 113
E++ ++ ++ + + V + + +D I + +++ P +L
Sbjct: 262 REHADFVERLGIEKSFKAIKQADLVIYVLDASQPLTKDD-----FLIIDLNKSKK-PFIL 315
Query: 114 VGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKT---RMGVDD------AFYTLVREIK 164
V NK DL N + + SAK + VD AFY+ R
Sbjct: 316 VLNKIDLKI-----NSLEFFVSSKVLNSSNLSAKQLKIKALVDLLTQKINAFYSKERVEL 370
Query: 165 KDKML 169
D ++
Sbjct: 371 DDYLI 375
>gnl|CDD|206752 cd01859, MJ1464, An uncharacterized, circularly permuted subfamily
of the Ras GTPases. This family represents archaeal
GTPase typified by the protein MJ1464 from Methanococcus
jannaschii. The members of this family show a circular
permutation of the GTPase signature motifs so that
C-terminal strands 5, 6, and 7 (strands 6 contain the
NKxD motif) are relocated to the N terminus.
Length = 157
Score = 29.2 bits (66), Expect = 0.87
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 5/56 (8%)
Query: 110 PMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
+++V NK DL V + + +E+ E +P + SA+ R+G L R IK+
Sbjct: 42 KLIIVLNKADLVPREV-LEKWKEVFESEGLPVVYVSARERLGTRI----LRRTIKE 92
>gnl|CDD|238941 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety
of proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion.
Length = 99
Score = 28.5 bits (64), Expect = 0.93
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 5 KLVVVGAGGVGKSALTIQLIQ 25
+VV G GGVGK+ L L
Sbjct: 1 VIVVTGKGGVGKTTLAANLAA 21
>gnl|CDD|235945 PRK07139, PRK07139, amidase; Provisional.
Length = 439
Score = 29.6 bits (67), Expect = 0.94
Identities = 13/65 (20%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 103 VKDAEEVPMVLVG-NKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVR 161
V DA + VL G ++ DL++ V +N ++ + + ++ + V + L+
Sbjct: 185 VNDAIILSKVLFGKDENDLTSVDVKINNVKKTKPK-KVAYLDCFKELEEYVAKKYKKLIN 243
Query: 162 EIKKD 166
+K +
Sbjct: 244 ILKSE 248
>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 = 29.0 bits (66), Expect = 0.96
Identities = 21/73 (28%), Positives = 29/73 (39%), Gaps = 16/73 (21%)
Query: 98 EQIKRVKDAEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFN--IPF---IKTSAKTRMGV 152
E +K+ K P++LV NK DL D L E+ PF SA V
Sbjct: 105 ELLKKSK----TPVILVLNKIDLVK---DKEDLLPLLEKLKELHPFAEIFPISALKGENV 157
Query: 153 DDAFYTLVREIKK 165
D+ L+ I +
Sbjct: 158 DE----LLEYIVE 166
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a
wide variety of presumed DNA repair proteins.
Length = 154
Score = 28.8 bits (65), Expect = 0.97
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 7 VVVGAGGVGKSALTIQLI 24
++ GA G GKS L + L
Sbjct: 37 LLAGAPGTGKSTLALDLA 54
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 28.7 bits (65), Expect = 1.1
Identities = 7/27 (25%), Positives = 14/27 (51%)
Query: 6 LVVVGAGGVGKSALTIQLIQNHFVDEY 32
+V+ G VGK+ L +Q ++ +
Sbjct: 5 IVITGPRQVGKTTLLLQFLKELLSENI 31
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 29.7 bits (67), Expect = 1.1
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 89 SFEDIGSYREQIKRVKDAEEVP 110
++ DIG QI++++DA E+P
Sbjct: 180 TYADIGGLGSQIEQIRDAVELP 201
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 29.1 bits (66), Expect = 1.1
Identities = 31/134 (23%), Positives = 49/134 (36%), Gaps = 42/134 (31%)
Query: 6 LVVVGAGGVGKSALTIQLIQNHFVDEYDPTI--EDS---YRKQVVIDGETA--------- 51
+V+ G GK+AL I L + I DS YR +D TA
Sbjct: 6 IVIAGPTASGKTALAIALAK-----RLGGEIISLDSMQVYR---GLDIGTAKPSLEELAG 57
Query: 52 ----LLDILDTAGQEEYSAMR---------DQYMRTGEGFLLV----FAVNSM-KSFEDI 93
L+DI D E YSA D + G+ +LV + ++ + +
Sbjct: 58 VPHHLIDIRDPT--ESYSAAEFQRDALAAIDDILARGKLPILVGGTGLYLKALLEGLSLL 115
Query: 94 GSYREQIKRVKDAE 107
+++R +AE
Sbjct: 116 PEADPEVRRRLEAE 129
>gnl|CDD|232968 TIGR00420, trmU, tRNA
(5-methylaminomethyl-2-thiouridylate)-methyltransferase.
tRNA
(5-methylaminomethyl-2-thiouridylate)-methyltransferase
(trmU, asuE, or mnmA) is involved in the biosynthesis of
the modified nucleoside
5-methylaminomethyl-2-thiouridine (mnm5s2U34) present in
the wobble position of some tRNAs. This enzyme appears
not to occur in the Archaea [Protein synthesis, tRNA and
rRNA base modification].
Length = 352
Score = 29.3 bits (66), Expect = 1.2
Identities = 10/29 (34%), Positives = 13/29 (44%)
Query: 115 GNKCDLSTWAVDMNQAQELAEQFNIPFIK 143
N T A D+ AQ + E+ IP K
Sbjct: 40 KNDGHGCTSAEDLRDAQAICEKLGIPLEK 68
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 29.3 bits (66), Expect = 1.2
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 8/73 (10%)
Query: 108 EVPMVLVGNKCDLS-TWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKKD 166
+PM+L N D + + ++ ++L E+ +P + TSA G++ L I
Sbjct: 99 GIPMILALNLVDEAEKKGIRID-EEKLEERLGVPVVPTSATEGRGIER----LKDAI--R 151
Query: 167 KMLRGKEKKKRGI 179
K + KE KKR I
Sbjct: 152 KAIGLKELKKRAI 164
>gnl|CDD|133356 cd04156, ARLTS1, Arf-like tumor suppressor gene 1 (ARLTS1 or
Arl11). ARLTS1 (Arf-like tumor suppressor gene 1), also
known as Arl11, is a member of the Arf family of small
GTPases that is believed to play a major role in
apoptotic signaling. ARLTS1 is widely expressed and
functions as a tumor suppressor gene in several human
cancers. ARLTS1 is a low-penetrance suppressor that
accounts for a small percentage of familial melanoma or
familial chronic lymphocytic leukemia (CLL). ARLTS1
inactivation seems to occur most frequently through
biallelic down-regulation by hypermethylation of the
promoter. In breast cancer, ARLTS1 alterations were
typically a combination of a hypomorphic polymorphism
plus loss of heterozygosity. In a case of thyroid
adenoma, ARLTS1 alterations were polymorphism plus
promoter hypermethylation. The nonsense polymorphism
Trp149Stop occurs with significantly greater frequency
in familial cancer cases than in sporadic cancer cases,
and the Cys148Arg polymorphism is associated with an
increase in high-risk familial breast cancer.
Length = 160
Score = 28.5 bits (64), Expect = 1.2
Identities = 31/119 (26%), Positives = 53/119 (44%), Gaps = 19/119 (15%)
Query: 53 LDILDTAGQEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEE---V 109
L + D GQE+ + Y+ +G LV+ V+S + ++++K + E V
Sbjct: 46 LTVWDVGGQEKMRTVWKCYLENTDG--LVYVVDSSDE-ARLDESQKELKHILKNEHIKGV 102
Query: 110 PMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKT---------SAKTRMGVDDAFYTL 159
P+VL+ NK DL A+E+ +F + + SA T G+ +AF L
Sbjct: 103 PVVLLANKQDLP----GALTAEEITRRFKLKKYCSDRDWYVQPCSAVTGEGLAEAFRKL 157
>gnl|CDD|206721 cd04155, Arl3, Arf-like 3 (Arl3) GTPase. Arl3 (Arf-like 3) is an
Arf family protein that differs from most Arf family
members in the N-terminal extension. In is inactive,
GDP-bound form, the N-terminal extension forms an
elongated loop that is hydrophobically anchored into the
membrane surface; however, it has been proposed that
this region might form a helix in the GTP-bound form.
The delta subunit of the rod-specific cyclic GMP
phosphodiesterase type 6 (PDEdelta) is an Arl3 effector.
Arl3 binds microtubules in a regulated manner to alter
specific aspects of cytokinesis via interactions with
retinitis pigmentosa 2 (RP2). It has been proposed that
RP2 functions in concert with Arl3 to link the cell
membrane and the cytoskeleton in photoreceptors as part
of the cell signaling or vesicular transport machinery.
In mice, the absence of Arl3 is associated with abnormal
epithelial cell proliferation and cyst formation.
Length = 174
Score = 28.9 bits (65), Expect = 1.3
Identities = 33/121 (27%), Positives = 51/121 (42%), Gaps = 14/121 (11%)
Query: 42 KQVVIDGETALLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIK 101
K V DG L++ D GQ + Y + + V K FE+ G ++
Sbjct: 52 KNVQADGFK--LNVWDIGGQRKIRPYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELL 109
Query: 102 RVKDAEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIK--------TSAKTRMGVD 153
+ VP+++ NK DL T A A+E+AE N+ I+ SAKT G+
Sbjct: 110 EEEKLAGVPVLVFANKQDLLT-AAP---AEEVAEALNLHDIRDRSWHIQACSAKTGEGLQ 165
Query: 154 D 154
+
Sbjct: 166 E 166
>gnl|CDD|206677 cd01890, LepA, LepA also known as Elongation Factor 4 (EF4). LepA
(also known as elongation factor 4, EF4) belongs to the
GTPase family and exhibits significant homology to the
translation factors EF-G and EF-Tu, indicating its
possible involvement in translation and association with
the ribosome. LepA is ubiquitous in bacteria and
eukaryota (e.g. yeast GUF1p), but is missing from
archaea. This pattern of phyletic distribution suggests
that LepA evolved through a duplication of the EF-G gene
in bacteria, followed by early transfer into the
eukaryotic lineage, most likely from the
promitochondrial endosymbiont. Yeast GUF1p is not
essential and mutant cells did not reveal any marked
phenotype.
Length = 179
Score = 28.7 bits (65), Expect = 1.3
Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 114 VGNKCDLSTWAVDMNQAQELAEQFNIP---FIKTSAKTRMGVDDAFYTLVREI 163
V NK DL D QE+ + + I SAKT +GV+D +V I
Sbjct: 125 VINKIDLPAADPD-RVKQEIEDVLGLDASEAILVSAKTGLGVEDLLEAIVERI 176
>gnl|CDD|213835 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members commonly
are called EngB based on homology to EngA, one of
several other GTPases of ribosome biogenesis. Cutoffs as
set find essentially all bacterial members, but also
identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about 80
percent of bacterial genomes [Protein synthesis, Other].
Length = 178
Score = 28.6 bits (65), Expect = 1.3
Identities = 9/49 (18%), Positives = 21/49 (42%), Gaps = 4/49 (8%)
Query: 109 VPMVLVGNKCD-LSTWAVDMNQA---QELAEQFNIPFIKTSAKTRMGVD 153
+P+++V K D L ++ + L + + S+ + G+D
Sbjct: 130 IPVLIVLTKADKLKKSELNKQLKKIKKALKKDADDSVQLFSSLKKTGID 178
>gnl|CDD|223107 COG0028, IlvB, Thiamine pyrophosphate-requiring enzymes
[acetolactate synthase, pyruvate dehydrogenase
(cytochrome), glyoxylate carboligase, phosphonopyruvate
decarboxylase] [Amino acid transport and metabolism /
Coenzyme metabolism].
Length = 550
Score = 29.2 bits (66), Expect = 1.5
Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 6/51 (11%)
Query: 97 REQIKRVKDAEEV---PMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKT 144
E I++ + P++L G + + +ELAE+ P + T
Sbjct: 187 PEAIRKAAELLAEAKRPVILAGGGVRRAGA---SEELRELAEKLGAPVVTT 234
>gnl|CDD|217632 pfam03599, CdhD, CO dehydrogenase/acetyl-CoA synthase delta
subunit.
Length = 384
Score = 29.0 bits (65), Expect = 1.5
Identities = 24/97 (24%), Positives = 37/97 (38%), Gaps = 23/97 (23%)
Query: 41 RKQVVIDGETAL--------------LDILDTAGQEEYSAMRDQYM--------RTGEGF 78
K VVI GE L +D+ D E A R++ R GE
Sbjct: 8 EKAVVIGGEEVLYRFELPFPNPTAITIDVFDNLSPELLKARRERIEDVMFDPKKRVGEKL 67
Query: 79 LLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVG 115
L + S D + + +++V A +VP+V+ G
Sbjct: 68 TLDMIAIRLIS-TDPKEFAKAVEKVLQAVDVPLVIGG 103
>gnl|CDD|206652 cd01853, Toc34_like, Translocon at the Outer-envelope membrane of
Chloroplasts 34-like (Toc34-like). The Toc34-like
(Translocon at the Outer-envelope membrane of
Chloroplasts) family contains several Toc proteins,
including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125,
and Toc90. The Toc complex at the outer envelope
membrane of chloroplasts is a molecular machine of ~500
kDa that contains a single Toc159 protein, four Toc75
molecules, and four or five copies of Toc34. Toc64 and
Toc12 are associated with the translocon, but do not
appear to be part of the core complex. The Toc
translocon initiates the import of nuclear-encoded
preproteins from the cytosol into the organelle. Toc34
and Toc159 are both GTPases, while Toc75 is a
beta-barrel integral membrane protein. Toc159 is equally
distributed between a soluble cytoplasmic form and a
membrane-inserted form, suggesting that assembly of the
Toc complex is dynamic. Toc34 and Toc75 act sequentially
to mediate docking and insertion of Toc159 resulting in
assembly of the functional translocon.
Length = 248
Score = 28.8 bits (65), Expect = 1.6
Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 7 VVVGAGGVGKSALTIQLI---QNHFVDEYDPTIEDSYRKQVVIDGETALLDILDTAGQEE 63
+V+G GVGKS+ TI I + V + +DG L+I+DT G E
Sbjct: 35 LVLGKTGVGKSS-TINSIFGERKVSVSAFQSETLRPREVSRTVDGFK--LNIIDTPGLLE 91
Query: 64 YSAMR--DQYMRTGEGFLL 80
R + + + FL
Sbjct: 92 SQDQRVNRKILSIIKRFLK 110
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 29.0 bits (65), Expect = 1.7
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 7/35 (20%)
Query: 84 VNSMK-------SFEDIGSYREQIKRVKDAEEVPM 111
V+ MK S+ DIG +QI+ +K+A E+P+
Sbjct: 169 VSVMKVDKAPLESYADIGGLEQQIQEIKEAVELPL 203
>gnl|CDD|206744 cd11384, RagA_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins A and B. RagA
and RagB are closely related Rag GTPases (ras-related
GTP-binding protein A and B) that constitute a unique
subgroup of the Ras superfamily, and are functional
homologs of Saccharomyces cerevisiae Gtr1. These domains
function by forming heterodimers with RagC or RagD, and
similarly, Gtr1 dimerizes with Gtr2, through the
carboxy-terminal segments. They play an essential role
in regulating amino acid-induced target of rapamycin
complex 1 (TORC1) kinase signaling, exocytic cargo
sorting at endosomes, and epigenetic control of gene
expression. In response to amino acids, the Rag GTPases
guide the TORC1 complex to activate the platform
containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 286
Score = 28.7 bits (65), Expect = 1.7
Identities = 26/114 (22%), Positives = 50/114 (43%), Gaps = 20/114 (17%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETALLDIL-------- 56
K++++G G GK+++ + N Y D+ R ID E + + L
Sbjct: 1 KVLLMGKSGSGKTSMRSIIFAN-----YLAR--DTRRLGATIDVEHSHVRFLGNLVLNLW 53
Query: 57 DTAGQEEY-----SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKD 105
D GQ+ + ++ RD R E + VF V S + +D+ +R ++ ++
Sbjct: 54 DCGGQDAFMENYFTSQRDHIFRNVEVLIYVFDVESRELEKDLTYFRSCLEALRQ 107
>gnl|CDD|223455 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
expression and maturation of urease and hydrogenase
[Posttranslational modification, protein turnover,
chaperones / Transcription].
Length = 202
Score = 28.3 bits (64), Expect = 1.8
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 7/61 (11%)
Query: 112 VLVGNKCDLSTWA-VDMNQAQELAEQFN--IPFIKTSAKTRMGVDDAFYTLVREIKKDKM 168
+LV NK DL+ + D+ A++ N P I T+ KT G+D+ +R I+ +
Sbjct: 146 LLVINKTDLAPYVGADLEVMARDAKEVNPEAPIIFTNLKTGEGLDE----WLRFIEPQAL 201
Query: 169 L 169
L
Sbjct: 202 L 202
>gnl|CDD|149458 pfam08404, Baculo_p74_N, Baculoviridae P74 N-terminal. This domain
is found at the N-terminus of P74 occlusion-derived
virus (ODV) envelope proteins which are required for
oral infectivity. The envelope proteins are found in
baculoviruses which are insect pathogens. The C-terminus
of P74 is anchored to the membrane whereas the
N-terminus is exposed to the virion surface. Furthermore
P74 is unusual for a virus envelope protein as it lacks
an N-terminal localisation signal sequence. Also see
pfam04583.
Length = 301
Score = 28.8 bits (65), Expect = 1.9
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 137 FNIPFIKTSAKTRMGVDD 154
N P+++T GVDD
Sbjct: 145 MNSPYLRTDEHLIRGVDD 162
>gnl|CDD|200432 TIGR04181, NHT_00031, aminotransferase, LLPSF_NHT_00031 family.
This clade of aminotransferases is a member of the
pfam01041 (DegT/DnrJ/EryC1/StrS) superfamily. The family
is named after the instance in Leptospira interrogans
serovar Lai, str. 56601, where it is the 31st gene in
the 91-gene lipopolysaccharide biosynthesis locus.
Members of this family are generally found within a
subcluster of seven or more genes including an
epimerase/dehydratase, four genes homologous to the
elements of the neuraminic (sialic) acid biosynthesis
cluster (NeuABCD) and a nucleotidyl transferase.
Together it is very likely that these enzymes direct the
biosynthesis of a nine-carbon sugar analogous to
CMP-neuraminic acid. These seven genes form the core of
the cassette, although they are often accompanied by
additional genes that may further modify the product
sugar.
Length = 359
Score = 28.7 bits (65), Expect = 2.0
Identities = 9/38 (23%), Positives = 22/38 (57%), Gaps = 7/38 (18%)
Query: 109 VPMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSA 146
VP+ + G+ DM++ E+ +++N+P ++ +A
Sbjct: 139 VPVHVFGH-------PADMDEIMEICDEWNLPVVEDAA 169
>gnl|CDD|198461 cd10470, FAM20B_C, C-terminal putative kinase domain of FAM20B
xylose kinase. Experiments with human FAM20B suggest
that it is a xylose kinase that participates in
proteoglycan production. It may regulate the number of
glycosaminoglycan chains by phosphorylating the xylose
residue in the glycosaminoglycan-protein linkage region
of proteoglycans. The C-terminal domain of FAM20B is a
putative kinase domain, based on mutagenesis of the
C-terminal domain of Drosophila Four-Jointed, a related
Golgi kinase. This subfamily belongs to the FAM20_C
(also known as DUF1193) domain family.
Length = 206
Score = 28.1 bits (63), Expect = 2.1
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 31 EYDPTIEDSYRKQVVIDGETALLDILDTA 59
E D D +K+ D LLD++DTA
Sbjct: 64 ETDEDYCDKVKKKSPYDSGPRLLDLIDTA 92
>gnl|CDD|130064 TIGR00991, 3a0901s02IAP34, GTP-binding protein (Chloroplast
Envelope Protein Translocase). [Transport and binding
proteins, Nucleosides, purines and pyrimidines].
Length = 313
Score = 28.3 bits (63), Expect = 2.3
Identities = 25/93 (26%), Positives = 44/93 (47%), Gaps = 2/93 (2%)
Query: 6 LVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETAL-LDILDTAGQEEY 64
++V+G GGVGKS+ T+ I + + R +V L+I+DT G E
Sbjct: 41 ILVMGKGGVGKSS-TVNSIIGERIATVSAFQSEGLRPMMVSRTRAGFTLNIIDTPGLIEG 99
Query: 65 SAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYR 97
+ DQ + + FLL ++ + + + +YR
Sbjct: 100 GYINDQAVNIIKRFLLGKTIDVLLYVDRLDAYR 132
>gnl|CDD|227444 COG5113, UFD2, Ubiquitin fusion degradation protein 2
[Posttranslational modification, protein turnover,
chaperones].
Length = 929
Score = 28.8 bits (64), Expect = 2.3
Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 8/50 (16%)
Query: 119 DLSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGVD----DAFYTLVREIK 164
D+ +DM FN P + +T++ VD D+FYT E
Sbjct: 325 DIGCSKIDMVDK----IYFNNPRVDIKEETKLNVDEKSLDSFYTKPAEGS 370
>gnl|CDD|213219 cd03252, ABCC_Hemolysin, ATP-binding cassette domain of hemolysin
B, subfamily C. The ABC-transporter hemolysin B is a
central component of the secretion machinery that
translocates the toxin, hemolysin A, in a
Sec-independent fashion across both membranes of E.
coli. The hemolysin A (HlyA) transport machinery is
composed of the ATP-binding cassette (ABC) transporter
HlyB located in the inner membrane, hemolysin D (HlyD),
also anchored in the inner membrane, and TolC, which
resides in the outer membrane. HlyD apparently forms a
continuous channel that bridges the entire periplasm,
interacting with TolC and HlyB. This arrangement
prevents the appearance of periplasmic intermediates of
HlyA during substrate transport. Little is known about
the molecular details of HlyA transport, but it is
evident that ATP-hydrolysis by the ABC-transporter HlyB
is a necessary source of energy.
Length = 237
Score = 28.2 bits (63), Expect = 2.4
Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 11/48 (22%)
Query: 8 VVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDG-ETALLD 54
+VG G GKS LT +LIQ +V E +V++DG + AL D
Sbjct: 33 IVGRSGSGKSTLT-KLIQRFYVPE---------NGRVLVDGHDLALAD 70
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 28.7 bits (64), Expect = 2.4
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 89 SFEDIGSYREQIKRVKDAEEVPM 111
++EDIG +E +++++ E+PM
Sbjct: 176 TYEDIGGLKEAKEKIREMVELPM 198
>gnl|CDD|215786 pfam00205, TPP_enzyme_M, Thiamine pyrophosphate enzyme, central
domain. The central domain of TPP enzymes contains a
2-fold Rossman fold.
Length = 136
Score = 27.5 bits (62), Expect = 2.4
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 100 IKRVKDAEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKT 144
+ + A+ P++L G S A + + + LAE+ IP + T
Sbjct: 5 AELLASAKR-PVILAGGGVRRSG-ASE--ELRALAEKLGIPVVTT 45
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family
includes the NTP binding domain of F1 and V1 H+ATPases,
DnaB and related helicases as well as bacterial RecA
and related eukaryotic and archaeal recombinases. This
group also includes bacterial conjugation proteins and
related DNA transfer proteins involved in type II and
type IV secretion.
Length = 165
Score = 27.8 bits (62), Expect = 2.7
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 5 KLVVVGAGGVGKSALTIQLIQN 26
++V G G GK+ L +QL N
Sbjct: 1 LILVFGPTGSGKTTLALQLALN 22
>gnl|CDD|200963 pfam00056, Ldh_1_N, lactate/malate dehydrogenase, NAD binding
domain. L-lactate dehydrogenases are metabolic enzymes
which catalyze the conversion of L-lactate to pyruvate,
the last step in anaerobic glycolysis.
L-2-hydroxyisocaproate dehydrogenases are also members
of the family. Malate dehydrogenases catalyze the
interconversion of malate to oxaloacetate. The enzyme
participates in the citric acid cycle. L-lactate
dehydrogenase is also found as a lens crystallin in
bird and crocodile eyes. N-terminus (this family) is a
Rossmann NAD-binding fold. C-terminus is an unusual
alpha+beta fold.
Length = 142
Score = 27.5 bits (62), Expect = 2.8
Identities = 21/73 (28%), Positives = 30/73 (41%), Gaps = 13/73 (17%)
Query: 5 KLVVVGAGG-VGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETA-LLDILDTA--- 59
K+ VVGAGG VG S+L L DE + D + +G L
Sbjct: 2 KVAVVGAGGGVG-SSLAFALALQGLADEL--VLVDINKD--KAEGVAMDLSHGSTFLSVP 56
Query: 60 ---GQEEYSAMRD 69
G ++Y A++D
Sbjct: 57 GIVGGDDYEALKD 69
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 28.0 bits (63), Expect = 2.8
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 89 SFEDIGSYREQIKRVKDAEEVPMV 112
++EDIG EQI+ +++ E+P+
Sbjct: 149 TYEDIGGLDEQIQEIREVVELPLK 172
>gnl|CDD|215955 pfam00503, G-alpha, G-protein alpha subunit. G proteins couple
receptors of extracellular signals to intracellular
signaling pathways. The G protein alpha subunit binds
guanyl nucleotide and is a weak GTPase. A set of
residues that are unique to G-alpha as compared to its
ancestor the Arf-like family form a ring of residues
centered on the nucleotide binding site. A Ggamma is
found fused to an inactive Galpha in the Dictyostelium
protein gbqA.
Length = 329
Score = 28.0 bits (63), Expect = 2.8
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQV---VIDGETALLDILDTA 59
E KL+++GAG GKS ++ ++ + + YR + +I LL+ L+
Sbjct: 2 EIKLLLLGAGESGKS-TILKQMKILHGGGFSDEEREQYRAVIYSNIIRSLKTLLEALENL 60
Query: 60 GQEE 63
E
Sbjct: 61 EIES 64
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 28.2 bits (63), Expect = 2.9
Identities = 11/23 (47%), Positives = 18/23 (78%)
Query: 89 SFEDIGSYREQIKRVKDAEEVPM 111
S+EDIG EQI+ +++A E+P+
Sbjct: 120 SYEDIGGLEEQIREIREAVELPL 142
>gnl|CDD|130618 TIGR01555, phge_rel_HI1409, phage-related protein, HI1409 family.
This model describes an uncharacterized family of
proteins found in prophage regions of a number of
bacterial genomes, including Haemophilus influenzae,
Xylella fastidiosa, Salmonella typhi, and Enterococcus
faecalis. Distantly related proteins can be found in the
prophage-bearing plasmids of Borrelia burgdorferi
[Mobile and extrachromosomal element functions, Prophage
functions].
Length = 404
Score = 28.0 bits (62), Expect = 3.0
Identities = 15/68 (22%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 91 EDIGSYREQIKRVKDAEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTRM 150
DI +Y +I +++ + P++ V +C + WA D + + +FN P +KT
Sbjct: 311 YDIMNYYSRITAIQENQLRPVLEVLMRCLM--WAEDGCDPDDWSVEFN-PLWNVDSKTDA 367
Query: 151 GVDDAFYT 158
+
Sbjct: 368 EIRKLTAE 375
>gnl|CDD|133427 cd05291, HicDH_like, L-2-hydroxyisocapronate dehydrogenases and
some bacterial L-lactate dehydrogenases.
L-2-hydroxyisocapronate dehydrogenase (HicDH) catalyzes
the conversion of a variety of 2-oxo carboxylic acids
with medium-sized aliphatic or aromatic side chains.
This subfamily is composed of HicDHs and some bacterial
L-lactate dehydrogenases (LDH). LDHs catalyze the last
step of glycolysis in which pyruvate is converted to
L-lactate. Bacterial LDHs can be non-allosteric or may
be activated by an allosteric effector such as
fructose-1,6-bisphosphate. Members of this subfamily
with known structures such as the HicDH of
Lactobacillus confusus, the non-allosteric LDH of
Lactobacillus pentosus, and the allosteric LDH of
Bacillus stearothermophilus, show that they exist as
homotetramers. The HicDH-like subfamily is part of the
NAD(P)-binding Rossmann fold superfamily, which
includes a wide variety of protein families including
the NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 306
Score = 27.8 bits (63), Expect = 3.1
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEY 32
K+V++GAG VG S+ L+ DE
Sbjct: 2 KVVIIGAGHVG-SSFAYSLVNQGIADEL 28
>gnl|CDD|226997 COG4650, RtcR, Sigma54-dependent transcription regulator containing
an AAA-type ATPase domain and a DNA-binding domain
[Transcription / Signal transduction mechanisms].
Length = 531
Score = 28.4 bits (63), Expect = 3.1
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 98 EQIKRVKDAEEVPMVLVG----NKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGVD 153
EQI+RV P++L G K L+ ++ QA+ QF+ F++ + T G D
Sbjct: 198 EQIERVAIRSRAPILLNGPTGAGKSFLARRIYELKQAR---HQFSGAFVEVNCATLRG-D 253
Query: 154 DAFYTLVREIK 164
A L +K
Sbjct: 254 TAMSALFGHVK 264
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 28.0 bits (63), Expect = 3.1
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 75 GEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPMVLVGNKCDL 120
G+ L+ V + FE GS ++KR V +LVGNK DL
Sbjct: 61 GDSNALIVYVVDIFDFE--GSLIPELKRFVGGNPV--LLVGNKIDL 102
>gnl|CDD|130460 TIGR01393, lepA, GTP-binding protein LepA. LepA (GUF1 in
Saccaromyces) is a GTP-binding membrane protein related
to EF-G and EF-Tu. Two types of phylogenetic tree,
rooted by other GTP-binding proteins, suggest that
eukaryotic homologs (including GUF1 of yeast) originated
within the bacterial LepA family. The function is
unknown [Unknown function, General].
Length = 595
Score = 28.1 bits (63), Expect = 3.4
Identities = 31/122 (25%), Positives = 62/122 (50%), Gaps = 13/122 (10%)
Query: 47 DGETALLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAVNSMKSFE--DIGSYREQIKRVK 104
DGET +L+++DT G ++S + + EG LL+ V++ + E + + ++
Sbjct: 66 DGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLL--VDAAQGIEAQTLANVYLALEN-- 121
Query: 105 DAEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIP---FIKTSAKTRMGVDDAFYTLVR 161
D E +P++ NK DL + + +E+ E + I SAKT +G+++ +V+
Sbjct: 122 DLEIIPVI---NKIDLPSADPE-RVKKEIEEVIGLDASEAILASAKTGIGIEEILEAIVK 177
Query: 162 EI 163
+
Sbjct: 178 RV 179
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 26.9 bits (60), Expect = 3.5
Identities = 28/130 (21%), Positives = 53/130 (40%), Gaps = 30/130 (23%)
Query: 5 KLVVVGAGGVGKS----ALTIQLIQNHFVDEY-----DPTIEDSYRKQVVIDGETALLDI 55
++ +VG VGKS ALT + V +Y DP + + +I +
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAI--VSDYPGTTRDPILGVLGLGRQII--------L 50
Query: 56 LDTAGQEEYSAMRDQYMRTGEGFL--------LVFAVNSMKSFEDIGSYREQIKRVKDAE 107
+DT G E A + + FL ++ V++ + + E ++ ++
Sbjct: 51 VDTPGLIE-GASEGKGVEGFNRFLEAIREADLILLVVDASEGLTE--DDEEILEELEKLP 107
Query: 108 EVPMVLVGNK 117
+ P++LV NK
Sbjct: 108 KKPIILVLNK 117
>gnl|CDD|179433 PRK02496, adk, adenylate kinase; Provisional.
Length = 184
Score = 27.4 bits (61), Expect = 3.5
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 8/51 (15%)
Query: 129 QAQELAEQFNIPFIKT--------SAKTRMGVDDAFYTLVREIKKDKMLRG 171
QA LAE +IP I T +T +G+ Y E+ D+++
Sbjct: 17 QAVVLAEHLHIPHISTGDILRQAIKEQTPLGIKAQGYMDKGELVPDQLVLD 67
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 27.9 bits (63), Expect = 3.6
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 10/53 (18%)
Query: 108 EVPMVLVGNKCDLSTWAVDMNQAQELAEQFNI------PFIKTSAKTRMGVDD 154
+ ++V NK DL +D + EQ +I + S+ T G+++
Sbjct: 150 GIEPLIVLNKIDL----LDDEGRAFVNEQLDIYRNIGYRVLMVSSHTGEGLEE 198
>gnl|CDD|238994 cd02037, MRP-like, MRP (Multiple Resistance and pH adaptation) is
a homologue of the Fer4_NifH superfamily. Like the
other members of the superfamily, MRP contains a
ATP-binding domain at the N-termini. It is found in
bacteria as a membrane-spanning protein and functions
as a Na+/H+ antiporter.
Length = 169
Score = 27.4 bits (62), Expect = 3.6
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 6 LVVVGAGGVGKSALTIQL 23
V+ G GGVGKS + + L
Sbjct: 3 AVMSGKGGVGKSTVAVNL 20
>gnl|CDD|213512 TIGR00174, miaA, tRNA dimethylallyltransferase. Alternate names
include delta(2)-isopentenylpyrophosphate transferase,
IPP transferase, 2-methylthio-N6-isopentyladenosine
tRNA modification enzyme. Catalyzes the first step in
the modification of an adenosine near the anticodon to
2-methylthio-N6-isopentyladenosine. Understanding of
substrate specificity has changed [Protein synthesis,
tRNA and rRNA base modification].
Length = 287
Score = 27.7 bits (62), Expect = 3.8
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 6 LVVVGAGGVGKSALTIQLIQN 26
+ ++G GKS L+IQL Q
Sbjct: 2 IFLMGPTASGKSQLSIQLAQK 22
>gnl|CDD|225473 COG2921, COG2921, Uncharacterized conserved protein [Function
unknown].
Length = 90
Score = 26.6 bits (59), Expect = 4.0
Identities = 8/36 (22%), Positives = 16/36 (44%)
Query: 2 AEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIE 37
+ V+GA G ++++Q H +Y P +
Sbjct: 14 CTFTYKVMGAAGPELEDQVVEVVQRHAPGDYTPRVS 49
>gnl|CDD|201420 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are
polypeptides of 30-65kDa with three characteristic
GTPase motifs (G-1, G-3 and G-4) that are similar to
those of the Ras family. The G-4 motif is strictly
conserved with a unique septin consensus of AKAD. Most
septins are thought to have at least one coiled-coil
region, which in some cases is necessary for
intermolecular interactions that allow septins to
polymerise to form rod-shaped complexes. In turn, these
are arranged into tandem arrays to form filaments. They
are multifunctional proteins, with roles in
cytokinesis, sporulation, germ cell development,
exocytosis and apoptosis.
Length = 280
Score = 27.3 bits (61), Expect = 4.9
Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 10/68 (14%)
Query: 3 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYD-PTIEDSYRKQVVIDGETALLD------- 54
++ L+VVG G+GK+ L L + E P + +K V I T ++
Sbjct: 4 DFTLMVVGESGLGKTTLINTLFLTDLIPERGIPGPSEKIKKTVEIKATTVEIEEDGVKLN 63
Query: 55 --ILDTAG 60
++DT G
Sbjct: 64 LTVIDTPG 71
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 27.5 bits (62), Expect = 5.0
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 7/62 (11%)
Query: 105 DAEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIP---FIKTSAKTRMGVDDAFYTLVR 161
+ E +P V NK DL + QE+ + I + SAKT +G++D +V
Sbjct: 128 NLEIIP---VLNKIDLPAADPER-VKQEIEDIIGIDASDAVLVSAKTGIGIEDVLEAIVE 183
Query: 162 EI 163
+I
Sbjct: 184 KI 185
>gnl|CDD|151331 pfam10882, DUF2679, Protein of unknown function (DUF2679). This
family of proteins with unknown function appear to be
restricted to Clostridium spp.
Length = 286
Score = 27.4 bits (61), Expect = 5.4
Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 2/67 (2%)
Query: 104 KDAEEVPMVLVGNKCDLSTWAVDMNQAQELA--EQFNIPFIKTSAKTRMGVDDAFYTLVR 161
++ E+ L S W N+ L+ ++F IPFI TS + F +
Sbjct: 143 ENFEKFKNFLESKGIKESDWEYKKNKNVNLSKDKRFFIPFIITSILILIITLIPFILYLM 202
Query: 162 EIKKDKM 168
DKM
Sbjct: 203 GELPDKM 209
>gnl|CDD|206730 cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.
Snu114p subfamily. Snu114p is one of several proteins
that make up the U5 small nuclear ribonucleoprotein
(snRNP) particle. U5 is a component of the spliceosome,
which catalyzes the splicing of pre-mRNA to remove
introns. Snu114p is homologous to EF-2, but typically
contains an additional N-terminal domain not found in
Ef-2. This protein is part of the GTP translation factor
family and the Ras superfamily, characterized by five
G-box motifs.
Length = 213
Score = 26.8 bits (60), Expect = 5.8
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 5/68 (7%)
Query: 52 LLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAEEVPM 111
L++I+DT G + +R +G +LV V E + S E++ R E +PM
Sbjct: 72 LINIIDTPGHVNFMDEVAAALRLCDGVVLVVDV-----VEGLTSVTERLIRHAIQEGLPM 126
Query: 112 VLVGNKCD 119
VLV NK D
Sbjct: 127 VLVINKID 134
>gnl|CDD|233596 TIGR01846, type_I_sec_HlyB, type I secretion system ABC
transporter, HlyB family. Type I protein secretion is a
system in some Gram-negative bacteria to export proteins
(often proteases) across both inner and outer membranes
to the extracellular medium. This is one of three
proteins of the type I secretion apparatus. Targeted
proteins are not cleaved at the N-terminus, but rather
carry signals located toward the extreme C-terminus to
direct type I secretion [Protein fate, Protein and
peptide secretion and trafficking].
Length = 694
Score = 27.4 bits (61), Expect = 6.1
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 11/48 (22%)
Query: 8 VVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDG-ETALLD 54
+VG G GKS LT +L+Q + + QV++DG + A+ D
Sbjct: 488 IVGPSGSGKSTLT-KLLQRLYTPQ---------HGQVLVDGVDLAIAD 525
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 27.2 bits (61), Expect = 6.2
Identities = 18/72 (25%), Positives = 27/72 (37%), Gaps = 19/72 (26%)
Query: 55 ILDTAG-----QEEYSAMR--DQYMRTGEGFLLVFAVNSMKSFEDIGSYREQIKRVKDAE 107
++DT G E ++R D G ++V E + E + R D
Sbjct: 80 LIDTPGHVDFTIEVERSLRVLD-------GAVVVVDAV-----EGVEPQTETVWRQADKY 127
Query: 108 EVPMVLVGNKCD 119
VP +L NK D
Sbjct: 128 GVPRILFVNKMD 139
>gnl|CDD|225814 COG3275, LytS, Putative regulator of cell autolysis [Signal
transduction mechanisms].
Length = 557
Score = 27.3 bits (61), Expect = 6.3
Identities = 12/62 (19%), Positives = 22/62 (35%), Gaps = 11/62 (17%)
Query: 106 AEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSAKTRMGVDDAFYTLVREIKK 165
AE + M+++ A A +L IP I + V A + + ++
Sbjct: 145 AEMLQMLII------LVIARPFADAVDLVSNIAIPMILGN-----SVGAALFMRILLDRR 193
Query: 166 DK 167
K
Sbjct: 194 AK 195
>gnl|CDD|100050 cd03360, LbH_AT_putative, Putative Acyltransferase (AT),
Left-handed parallel beta-Helix (LbH) domain; This
group is composed of mostly uncharacterized proteins
containing an N-terminal helical subdomain followed by
a LbH domain. The alignment contains 6 turns, each
containing three imperfect tandem repeats of a
hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X).
Proteins containing hexapeptide repeats are often
enzymes showing acyltransferase activity. A few members
are identified as NeuD, a sialic acid (Sia)
O-acetyltransferase that is required for Sia synthesis
and surface polysaccharide sialylation.
Length = 197
Score = 26.7 bits (60), Expect = 7.1
Identities = 12/56 (21%), Positives = 18/56 (32%), Gaps = 7/56 (12%)
Query: 8 VVGAGGVGKSALTIQLIQNH------FVDEYDPTIEDSYRKQVVIDGETALLDILD 57
++GAGG + I L + F+D+ V E LL
Sbjct: 1 IIGAGGHARVVADI-LEADSGYEVVGFLDDDPELKGTEGLGLPVGLDELLLLYPPP 55
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 154
Score = 26.4 bits (58), Expect = 7.1
Identities = 5/15 (33%), Positives = 10/15 (66%)
Query: 6 LVVVGAGGVGKSALT 20
+++ G G GK++L
Sbjct: 27 VLLTGPSGTGKTSLL 41
>gnl|CDD|206689 cd04102, RabL3, Rab GTPase-like family 3 (Rab-like3). RabL3
(Rab-like3) subfamily. RabL3s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL3 lacks a prenylation site at the
C-terminus. The specific function of RabL3 remains
unknown.
Length = 204
Score = 26.8 bits (59), Expect = 7.5
Identities = 36/169 (21%), Positives = 63/169 (37%), Gaps = 31/169 (18%)
Query: 5 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGE------TALLDILDT 58
K++V+G GVGKS+L L +N + T+ S + GE T +++ D
Sbjct: 2 KVLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHTYGEGTPEEKTFYVELWDV 61
Query: 59 AGQ----EEYSAMRDQYMRTGEGFLLVFAVNSMKSFED-----------------IGSYR 97
G E + R + G + V + + KS ++ +
Sbjct: 62 GGSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYRWSLEALNRDTFPAGLLVTN 121
Query: 98 EQIKRVKDAE-EVPMVLVGNKCDLSTWAVD---MNQAQELAEQFNIPFI 142
+ A VP++++G K D A + + L+E FN I
Sbjct: 122 GDYDSEQFAGNPVPLLVIGTKLDQIPEAKRNWVLTRTAFLSEDFNAEEI 170
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 26.7 bits (60), Expect = 7.8
Identities = 16/50 (32%), Positives = 20/50 (40%), Gaps = 8/50 (16%)
Query: 97 REQIKRVKDAEEVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIPFIKTSA 146
RE K K PMV+ NK DL + L E+ + TSA
Sbjct: 211 RELRKISK-----PMVIAANKADL---PPAEENIERLKEEKYYIVVPTSA 252
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain
only a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 26.1 bits (58), Expect = 8.0
Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 9/79 (11%)
Query: 6 LVVVGAGGVGKSALTIQLIQNHFVDEYDPTI-EDSYRKQVVIDGETALLDILDTAGQEEY 64
+++VG G GKS + + + D+ RK++ DG + A Y
Sbjct: 2 ILMVGLPGSGKS----TFARRLLRELGAVVLSSDTLRKRLRGDGPPDISY-YARASGRVY 56
Query: 65 SAMRD---QYMRTGEGFLL 80
+ + + +R G ++
Sbjct: 57 QRLLELAREALRAGRPVIV 75
>gnl|CDD|187717 cd08648, FMT_core_Formyl-FH4-Hydrolase_C, Formyltetrahydrofolate
deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase
domain. Formyl-FH4 Hydrolase catalyzes the hydrolysis
of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and
formate. Formate is the substrate of
phosphoribosylglycinamide transformylase for step three
of de novo purine nucleotide synthesis. Formyl-FH4
hydrolase has been proposed to regulate the balance of
FH4 and C1-FH4 in the cell. The enzyme uses methionine
and glycine to sense the pools of C1-FH4 and FH4,
respectively. This domain belongs to the
formyltransferase (FMT) domain superfamily. Members of
this family have an N-terminal ACT domain, which is
commonly involved in specifically bind an amino acid or
other small ligand leading to regulation of the enzyme.
The N-terminal of this protein family may be responsible
for the binding of the regulators methionine and
glycine.
Length = 196
Score = 26.4 bits (59), Expect = 8.0
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 16/72 (22%)
Query: 100 IKRVKDAE---EVPMVLVGNKCDLSTWAVDMNQAQELAEQFNIPF--IKTSAKTRMGVDD 154
+ R ++ E E+P+V + N DL + LAE+F IPF I + T+ +
Sbjct: 18 LHRWREGELPCEIPLV-ISNHPDL----------RPLAERFGIPFHHIPVTKDTKAEAEA 66
Query: 155 AFYTLVREIKKD 166
L+ E D
Sbjct: 67 EQLELLEEYGVD 78
>gnl|CDD|223563 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 265
Score = 26.6 bits (59), Expect = 8.1
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 6 LVVVGAGGVGKSALTIQL 23
V G GGVGKS + + L
Sbjct: 61 AVTSGKGGVGKSTVAVNL 78
>gnl|CDD|236375 PRK09078, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 598
Score = 26.8 bits (60), Expect = 8.4
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 3 EYKLVVVGAGGVG 15
+Y +VVVGAGG G
Sbjct: 12 KYDVVVVGAGGAG 24
>gnl|CDD|216506 pfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase.
Helicase activity for this family has been demonstrated
and NTPase activity. This helicase has multiple roles
at different stages of viral RNA replication, as
dissected by mutational analysis.
Length = 226
Score = 26.6 bits (59), Expect = 8.5
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 6 LVVVGAGGVGKSALTIQLIQNHFVDEYDPTIED 38
+VV G G GKS L I+ + + PT E
Sbjct: 1 IVVHGVPGCGKSTL-IRKLLRTDLTVIRPTAEL 32
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 26.7 bits (60), Expect = 9.3
Identities = 11/23 (47%), Positives = 18/23 (78%)
Query: 89 SFEDIGSYREQIKRVKDAEEVPM 111
++EDIG EQI+ V++A E+P+
Sbjct: 129 TYEDIGGLEEQIREVREAVELPL 151
>gnl|CDD|176221 cd08260, Zn_ADH6, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. This group has the characteristic
catalytic and structural zinc sites of the
zinc-dependent alcohol dehydrogenases. Alcohol
dehydrogenase in the liver converts ethanol and NAD+ to
acetaldehyde and NADH, while in yeast and some other
microorganisms ADH catalyzes the conversion acetaldehyde
to ethanol in alcoholic fermentation. ADH is a member of
the medium chain alcohol dehydrogenase family (MDR),
which has a NAD(P)(H)-binding domain in a Rossmann fold
of a beta-alpha form. The NAD(H)-binding region is
comprised of 2 structurally similar halves, each of
which contacts a mononucleotide. A GxGxxG motif after
the first mononucleotide contact half allows the close
contact of the coenzyme with the ADH backbone. The
N-terminal catalytic domain has a distant homology to
GroES. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit, a
catalytic zinc at the active site and a structural zinc
in a lobe of the catalytic domain. NAD(H)-binding occurs
in the cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 345
Score = 26.4 bits (59), Expect = 9.6
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 6 LVVVGAGGVGKSALTI 21
+ V G GGVG SA+ I
Sbjct: 169 VAVHGCGGVGLSAVMI 184
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
0.318 0.135 0.378
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,807,679
Number of extensions: 922658
Number of successful extensions: 2010
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1799
Number of HSP's successfully gapped: 274
Length of query: 191
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 100
Effective length of database: 6,901,388
Effective search space: 690138800
Effective search space used: 690138800
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: 56 (25.8 bits)