RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8073
(593 letters)
>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 = 218 bits (557), Expect = 2e-68
Identities = 72/165 (43%), Positives = 107/165 (64%), Gaps = 6/165 (3%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
FKIV GD+ VGK+ + RF F ST+GVDF+ KTI VD + V LQ+WDTAGQE
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQE 60
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
RFRS+T +Y+R A G +L+YDVTN SF ++ W+ ++E +IPI++ NK DL +
Sbjct: 61 RFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPPNIPIILVGNKSDLEDE 120
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSR 557
+ + E ++ A++ G +F ETS+K+G+N+ +A +L+R
Sbjct: 121 ------RQVSTEEAQQFAKENGLLFFETSAKTGENVDEAFESLAR 159
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 206 bits (527), Expect = 9e-64
Identities = 72/168 (42%), Positives = 107/168 (63%), Gaps = 6/168 (3%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
FKI+ GD+ VGKS + RF+ F + ST+GVDF+ KTI VD + V LQ+WDTAGQE
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQE 60
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
RFRS+T +Y+R A G +L+YD+TN SF +++NW++ + E ++ I++ NK DL
Sbjct: 61 RFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASPNVVIMLVGNKSDLEEQ 120
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHVY 560
Q + RE E A+++G F ETS+K+ N+ +A L+R +
Sbjct: 121 RQ------VSREEAEAFAEEHGLPFFETSAKTNTNVEEAFEELAREIL 162
>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 = 197 bits (504), Expect = 2e-60
Identities = 71/167 (42%), Positives = 104/167 (62%), Gaps = 6/167 (3%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
K+V GD VGKS + RF++ F + T+GVDF KTI VD + V LQ+WDTAGQER
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQER 60
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRADA 513
FR++ Y+R A G +L+YD+T+ SF +VK W+E + + ++PIV+ NK DL
Sbjct: 61 FRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADENVPIVLVGNKCDLEDQ- 119
Query: 514 QAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHVY 560
+ + E GE LA++ G FMETS+K+ +N+ +A L+R +
Sbjct: 120 -----RVVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELAREIL 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 = 179 bits (457), Expect = 1e-53
Identities = 68/170 (40%), Positives = 115/170 (67%), Gaps = 6/170 (3%)
Query: 390 DRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTA 449
D FK++ GD+ VGKSC + RFS++ F ST+G+DF+++TI +D + + LQ+WDTA
Sbjct: 1 DYLFKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTA 60
Query: 450 GQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDL 509
GQERFR++T +Y+R A G++L+YD+T+E+SF ++KNW+ ++E + ++ NK D+
Sbjct: 61 GQERFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHASEDVERMLVGNKCDM 120
Query: 510 RADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHV 559
+ +E GE LA++YG F+ETS+K+ N+ +A + L++ +
Sbjct: 121 EEKRV------VSKEEGEALAREYGIKFLETSAKANINVEEAFLTLAKDI 164
>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 = 166 bits (423), Expect = 1e-48
Identities = 64/165 (38%), Positives = 109/165 (66%), Gaps = 6/165 (3%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
FK++ GD+ VGKSC + RF+ + + ST+GVDF+++TI +D + V LQ+WDTAGQE
Sbjct: 3 FKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQE 62
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
RFR++T +Y+R A G++++YDVT++ SFN+VK W++ ++ ++ ++ NK DL
Sbjct: 63 RFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTDK 122
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSR 557
K +D ++ A + G F+ETS+K+ N+ +A + ++R
Sbjct: 123 ------KVVDYTEAKEFADELGIPFLETSAKNATNVEEAFMTMAR 161
>gnl|CDD|206653 cd01860, Rab5_related, Rab-related GTPase family includes Rab5 and
Rab22; regulates early endosome fusion. The
Rab5-related subfamily includes Rab5 and Rab22 of
mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants.
The members of this subfamily are involved in
endocytosis and endocytic-sorting pathways. In mammals,
Rab5 GTPases localize to early endosomes and regulate
fusion of clathrin-coated vesicles to early endosomes
and fusion between early endosomes. In yeast, Ypt51p
family members similarly regulate membrane trafficking
through prevacuolar compartments. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 165 bits (420), Expect = 3e-48
Identities = 61/168 (36%), Positives = 101/168 (60%), Gaps = 6/168 (3%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
FK+V GD++VGKS + RF K F ST+G F +T+ +D+ V ++WDTAGQE
Sbjct: 2 FKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQE 61
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
R+RS+ Y+R A +++YD+T+E SF K+WV+ ++E +I I + NK DL +
Sbjct: 62 RYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQEHGPPNIVIALAGNKADLESK 121
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHVY 560
+ + E ++ A + G +FMETS+K+G+N+ + ++R +
Sbjct: 122 ------RQVSTEEAQEYADENGLLFMETSAKTGENVNELFTEIARKLP 163
>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 = 162 bits (413), Expect = 2e-47
Identities = 67/156 (42%), Positives = 101/156 (64%), Gaps = 6/156 (3%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
K+VF GD +VGK+ I RF + F N+ +T+G+DF KT+ VD++ V LQLWDTAGQE
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQE 60
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
RFRS+ +Y R + +++YD+TN +SF++ W++ V + N + IV+ NK DL
Sbjct: 61 RFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDLSDK 120
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNI 548
Q + E GEK A++ A+F+ETS+K+G N+
Sbjct: 121 RQ------VSTEEGEKKAKENNAMFIETSAKAGHNV 150
>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 = 158 bits (403), Expect = 9e-46
Identities = 61/162 (37%), Positives = 102/162 (62%), Gaps = 6/162 (3%)
Query: 390 DRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTA 449
D FKIV GD+ VGKS + RF++ F ST+GV+F +TI++D + + Q+WDTA
Sbjct: 1 DYLFKIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRTIQIDGKTIKAQIWDTA 60
Query: 450 GQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDL 509
GQER+R++T Y+R A G +L+YD+T + +F +V+ W++ + + +++I I++ NK DL
Sbjct: 61 GQERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKELRDHADSNIVIMLVGNKSDL 120
Query: 510 RADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDA 551
R + + E + A++ G F+ETS+ G N+ +A
Sbjct: 121 RHL------RAVPTEEAKAFAEKNGLSFIETSALDGTNVEEA 156
>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 = 157 bits (399), Expect = 2e-45
Identities = 64/169 (37%), Positives = 101/169 (59%), Gaps = 14/169 (8%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
FK + G A GKSC +++F + F T+GV+F + + V ++V LQ+WDTAGQE
Sbjct: 1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQE 60
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
RFRS+T++Y+R A G +L+YD+T+ SFN++ NW+ + I I++ NK DL
Sbjct: 61 RFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLTDARTLASPDIVIILVGNKKDLED- 119
Query: 513 AQAKGVKCIDREV----GEKLAQQYGAIFMETSSKSGDNILDALIALSR 557
DREV + AQ+ G +F+ETS+ +G+N+ +A + +R
Sbjct: 120 ---------DREVTFLEASRFAQENGLLFLETSALTGENVEEAFLKCAR 159
>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 = 156 bits (397), Expect = 4e-45
Identities = 63/160 (39%), Positives = 101/160 (63%), Gaps = 8/160 (5%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
KI+ GD+ VGKS + RF+ + F L ST+GVDF++KT+ VD + V L +WDTAGQE
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE 60
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEV-TENSIPIVICANKVDLRA 511
RFR++T +Y+R A GV+L+YDVT +F+++ W+ ++ T ++ NK+D
Sbjct: 61 RFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVGNKID--- 117
Query: 512 DAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDA 551
K + + RE G+K A+++ +F+ETS+K+ + A
Sbjct: 118 ----KENREVTREEGQKFARKHNMLFIETSAKTRIGVQQA 153
>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 = 156 bits (395), Expect = 8e-45
Identities = 66/169 (39%), Positives = 106/169 (62%), Gaps = 7/169 (4%)
Query: 390 DRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTA 449
D FKI+ GD+ VGK+C + RF F + G+T+GVDF MKT+ + + V LQ+WDTA
Sbjct: 1 DFLFKIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTA 60
Query: 450 GQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDL 509
GQERFR++T++Y+R A+G ++ YD+T SF SV +W+E VE+ +++ +++ NK DL
Sbjct: 61 GQERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNVVLLLIGNKCDL 120
Query: 510 RADAQAKGVKCIDREVGEKLAQQYGAIF-METSSKSGDNILDALIALSR 557
+ + E LA+ YG + +ETS+K N+ +A + ++
Sbjct: 121 EEQRE------VLFEEACTLAEHYGILAVLETSAKESSNVEEAFLLMAT 163
>gnl|CDD|133323 cd04123, Rab21, Rab GTPase family 21 (Rab21). The localization and
function of Rab21 are not clearly defined, with
conflicting data reported. Rab21 has been reported to
localize in the ER in human intestinal epithelial cells,
with partial colocalization with alpha-glucosidase, a
late endosomal/lysosomal marker. More recently, Rab21
was shown to colocalize with and affect the morphology
of early endosomes. In Dictyostelium, GTP-bound Rab21,
together with two novel LIM domain proteins, LimF and
ChLim, has been shown to regulate phagocytosis. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 162
Score = 155 bits (393), Expect = 2e-44
Identities = 57/167 (34%), Positives = 97/167 (58%), Gaps = 6/167 (3%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
FK+V G+ VGK+ + R+ + F K ST F KT+ + + + L +WDTAGQE
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQE 60
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
R+ ++ Y+R ADG +L+YD+T+ SF VK W++ ++++ N+I +VI NK+DL
Sbjct: 61 RYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGNKIDLERQ 120
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHV 559
+ + E+ A+ GA ETS+K+G I + ++L++ +
Sbjct: 121 RV------VSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSLAKRM 161
>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 = 148 bits (376), Expect = 5e-42
Identities = 63/168 (37%), Positives = 106/168 (63%), Gaps = 6/168 (3%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
FK + GD VGKSC + +F+ + F T+GV+F + I +D + + LQ+WDTAGQE
Sbjct: 5 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQE 64
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
FRS+T++Y+R A G +L+YD+T +FN + +W+E + + +++ I++ NK DL +
Sbjct: 65 SFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIMLIGNKCDLESR 124
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHVY 560
+ + E GE A+++G IFMETS+K+ N+ +A I ++ +Y
Sbjct: 125 RE------VSYEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEIY 166
>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 = 149 bits (378), Expect = 8e-42
Identities = 65/170 (38%), Positives = 105/170 (61%), Gaps = 8/170 (4%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRV-DERNVALQLWDTAGQ 451
F+++ GD+ VGKS + RF++ F T+GVDF + I + + LQLWDTAGQ
Sbjct: 3 FRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAGQ 62
Query: 452 ERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWV-EAVEEVTENSIPIVICANKVDLR 510
ERFRS+T++Y+R + GV+L++D+TN SF V +W+ EA + + ++ +K DL
Sbjct: 63 ERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFILVGHKCDLE 122
Query: 511 ADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHVY 560
+ Q + RE EKLA+ G ++ETS+++GDN+ +A L++ +Y
Sbjct: 123 SQRQ------VTREEAEKLAKDLGMKYIETSARTGDNVEEAFELLTQEIY 166
>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 = 148 bits (375), Expect = 1e-41
Identities = 70/166 (42%), Positives = 107/166 (64%), Gaps = 7/166 (4%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFL-NKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQ 451
FK++ GD+ VGK+C + RF FL +T+G+ F K + VD V LQ+WDTAGQ
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQ 60
Query: 452 ERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRA 511
ERFRS+T Y+R A ++LLYDVTN+ SF++++ W+ + E ++ + I++ NK D+
Sbjct: 61 ERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDVVIMLLGNKADMSG 120
Query: 512 DAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSR 557
+ K RE GE+LA++YG FMETS+K+G N+ A A+++
Sbjct: 121 ERVVK------REDGERLAKEYGVPFMETSAKTGLNVELAFTAVAK 160
>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 = 145 bits (367), Expect = 7e-41
Identities = 69/167 (41%), Positives = 107/167 (64%), Gaps = 6/167 (3%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
F+++ GD+ VGK+C + RF+ F + ST+GVDF+MKTI VD V +Q+WDTAGQE
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQE 60
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
R++++TK Y+RRA G+ L+YD+++ERS+ + WV V+E + ++ NK AD
Sbjct: 61 RYQTITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKILIGNK----AD 116
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHV 559
+ K + + E G KLA++YG F ETS+ + NI ++ L+ V
Sbjct: 117 EEQK--RQVGDEQGNKLAKEYGMDFFETSACTNKNIKESFTRLTELV 161
>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 = 142 bits (359), Expect = 1e-39
Identities = 60/159 (37%), Positives = 99/159 (62%), Gaps = 6/159 (3%)
Query: 390 DRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTA 449
D FKIV G+A VGK+C + RF++ +F G+T+GVDF +KT+ + + LQ+WDTA
Sbjct: 5 DFLFKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTA 64
Query: 450 GQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDL 509
GQERFRS+T++Y+R A+ ++L YD+T E SF + W+ +E+ N + ++ NK+DL
Sbjct: 65 GQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVITILVGNKIDL 124
Query: 510 RADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNI 548
+ + ++ E+ + ++ETS+K DN+
Sbjct: 125 AERRE------VSQQRAEEFSDAQDMYYLETSAKESDNV 157
>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 = 140 bits (355), Expect = 4e-39
Identities = 57/168 (33%), Positives = 105/168 (62%), Gaps = 6/168 (3%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
FK + GD VGKSC +++F+++ F+ T+GV+F + I V+ + + LQ+WDTAGQE
Sbjct: 3 FKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQE 62
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
RFR++T++Y+R A G +++YD+T ++N + +W+ +T + I + NK DL
Sbjct: 63 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGNKADL--- 119
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHVY 560
+ + + E ++ A + G +F+E S+K+G+N+ DA + ++ +Y
Sbjct: 120 ---EAQRDVTYEEAKQFADENGLLFLECSAKTGENVEDAFLETAKKIY 164
>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 = 140 bits (354), Expect = 8e-39
Identities = 62/155 (40%), Positives = 94/155 (60%), Gaps = 8/155 (5%)
Query: 391 RAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAG 450
R FKI+ GD+ VGK+C YRF F + +T+GVDF+ +T+ +D + +QLWDTAG
Sbjct: 1 RIFKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAG 60
Query: 451 QERFR-SMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEE-VTENSIPIVICANKVD 508
QERFR SM ++Y+R V+ +YDVTN SF+S+ +W+E E+ N +P ++ NK D
Sbjct: 61 QERFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCD 120
Query: 509 LRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSK 543
LR Q + ++ ++ A + ETS+K
Sbjct: 121 LREQIQ------VPTDLAQRFADAHSMPLFETSAK 149
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 138 bits (349), Expect = 1e-37
Identities = 62/168 (36%), Positives = 102/168 (60%), Gaps = 6/168 (3%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
FK + GD VGKSC + +F+ + F T+GV+F + I +D + + LQ+WDTAGQE
Sbjct: 7 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDTAGQE 66
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
FRS+T++Y+R A G +L+YD+T +FN + +W+E + ++ I++ NK DL
Sbjct: 67 SFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKCDLAHR 126
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHVY 560
+ + E GE+ A+++G IFME S+K+ N+ +A I + +Y
Sbjct: 127 ------RAVSTEEGEQFAKEHGLIFMEASAKTAQNVEEAFIKTAAKIY 168
>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 = 136 bits (343), Expect = 2e-37
Identities = 57/156 (36%), Positives = 104/156 (66%), Gaps = 6/156 (3%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
FK++ G+++VGK+ F++R++ + F + ST+G+DF++KT+ +++ + LQ+WDTAGQE
Sbjct: 2 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQE 61
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
R+R++T Y+R A G +L+YD+TNE SFN+V++W ++ + ++ +++ NK D+ +
Sbjct: 62 RYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVILVGNKCDMEDE 121
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNI 548
+ + E G +LA Q G F E S+K N+
Sbjct: 122 ------RVVSAERGRQLADQLGFEFFEASAKENINV 151
>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 = 135 bits (342), Expect = 8e-37
Identities = 65/173 (37%), Positives = 99/173 (57%), Gaps = 11/173 (6%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVD-ERNVALQLWDTAGQ 451
FK++ GD VGK+ I R+ VF +T+GVDF +K I D V LQLWD AGQ
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQ 60
Query: 452 ERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVE-EVT---ENSIPIVICANKV 507
ERF MT+ Y++ A G ++++DVT +F +V W ++ +VT IP ++ ANK
Sbjct: 61 ERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPALLLANKC 120
Query: 508 DLRADAQAKGVKCIDREVGEKLAQQYGAI-FMETSSKSGDNILDALIALSRHV 559
DL+ + AK D E ++ ++ G I + ETS+K NI +A+ L +++
Sbjct: 121 DLKKERLAK-----DPEQMDQFCKENGFIGWFETSAKENINIEEAMRFLVKNI 168
>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 = 131 bits (331), Expect = 1e-35
Identities = 61/167 (36%), Positives = 86/167 (51%), Gaps = 8/167 (4%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
K+V G VGKS RF F+ + T+ D K I VD L + DTAGQE
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIE-DSYRKQIVVDGETYTLDILDTAGQEE 59
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTE-NSIPIVICANKVDLRAD 512
F +M Y R DG +L+Y +T+ SF +KN E + V + +PIV+ NK DL +
Sbjct: 60 FSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIVLVGNKCDLENE 119
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHV 559
Q + E GE LA+++G F+ETS+K+ NI + L R +
Sbjct: 120 RQ------VSTEEGEALAEEWGCPFLETSAKTNINIDELFNTLVREI 160
>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 = 130 bits (330), Expect = 2e-35
Identities = 61/174 (35%), Positives = 95/174 (54%), Gaps = 19/174 (10%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
K++ GD+ VGK+ + ++ + F N+ +T+G DF K + VD+R V LQ+WDTAGQE
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQE 60
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVE----AVEEVTENSIPIVICANKVD 508
RF+S+ ++R AD +L+YDVTN +SF S+ +W + + P V+ NK+D
Sbjct: 61 RFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPENFPFVVLGNKID 120
Query: 509 LRADAQAKGVKCIDREVGEKLAQQYG-----AIFMETSSKSGDNILDALIALSR 557
L R+V K AQQ+ + ETS+K N+ A ++R
Sbjct: 121 LEE----------KRQVSTKKAQQWCKSKGNIPYFETSAKEAINVDQAFETIAR 164
>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 = 129 bits (327), Expect = 3e-35
Identities = 58/157 (36%), Positives = 83/157 (52%), Gaps = 9/157 (5%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERN--VALQLWDTAGQ 451
K++ G+ VGKS I RF K +F T+GVDF K I + + + V L LWDTAGQ
Sbjct: 2 KVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQ 61
Query: 452 ERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRA 511
E F ++TK Y+R A +L++ T+ SF ++++W E VE IP+V+ K+DL
Sbjct: 62 EEFDAITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEAEC-GDIPMVLVQTKIDLLD 120
Query: 512 DAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNI 548
A I E E LA++ TS K N+
Sbjct: 121 QA------VITNEEAEALAKRLQLPLFRTSVKDDFNV 151
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 126 bits (319), Expect = 2e-33
Identities = 55/166 (33%), Positives = 84/166 (50%), Gaps = 10/166 (6%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
FKIV GD VGK+ + R + F T+G KTI RN+ LQLWDTAGQE
Sbjct: 6 FKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQE 65
Query: 453 RFRSMTKNYFRRADGVMLLYDVTN-ERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRA 511
+RS+ Y+R A+G++++YD T E S + W+E + E+ + +PI++ NK+DL
Sbjct: 66 EYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFD 125
Query: 512 DAQA------KGVKCIDREVGEKLAQQYGAI---FMETSSKSGDNI 548
+ + + + + V A +ETS+KS
Sbjct: 126 EQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGP 171
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 126 bits (319), Expect = 2e-33
Identities = 64/176 (36%), Positives = 108/176 (61%), Gaps = 6/176 (3%)
Query: 388 EPDRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWD 447
E D FKIV GD+ VGKS + RF++ F + ST+GV+F +T++V+ + V Q+WD
Sbjct: 8 EYDYLFKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWD 67
Query: 448 TAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKV 507
TAGQER+R++T Y+R A G +L+YD+T ++F++V+ W+ + + +++I I++ NK
Sbjct: 68 TAGQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNIVIMMAGNKS 127
Query: 508 DLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHVYVFI 563
DL ++ + E G+ LA++ G F+ETS+ N+ A + +Y I
Sbjct: 128 DL------NHLRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFQTILLEIYHII 177
>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 = 124 bits (314), Expect = 3e-33
Identities = 63/174 (36%), Positives = 100/174 (57%), Gaps = 17/174 (9%)
Query: 390 DRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERN--------- 440
D K++ GD+ VGK+ F+YR++ F K +T+G+DF+ K + + +
Sbjct: 2 DYLIKLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAF 61
Query: 441 -VALQLWDTAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIP 499
V LQLWDTAGQERFRS+T +FR A G +L++D+T+E+SF +V+NW+ ++ P
Sbjct: 62 RVHLQLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCENP 121
Query: 500 -IVICANKVDLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDAL 552
IV+ NK DL + + +LA +YG + ETS+ +G N+ A+
Sbjct: 122 DIVLIGNKADLPDQRE------VSERQARELADKYGIPYFETSAATGQNVEKAV 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 = 123 bits (310), Expect = 2e-32
Identities = 65/170 (38%), Positives = 100/170 (58%), Gaps = 7/170 (4%)
Query: 390 DRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTA 449
D FK++ GD+ VGKS + RF+ F +T+GVDF+++T+ ++ V LQ+WDTA
Sbjct: 4 DHLFKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTA 63
Query: 450 GQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDL 509
GQERFR++T Y+R GV+++YDVTN SF +VK W++ +E+ + + V+ NK D
Sbjct: 64 GQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQNCD-DVCKVLVGNKND- 121
Query: 510 RADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHV 559
D + K V + E K A Q G ETS+K N+ + ++ V
Sbjct: 122 --DPERKVV---ETEDAYKFAGQMGISLFETSAKENINVEEMFNCITELV 166
>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 = 119 bits (300), Expect = 3e-31
Identities = 47/171 (27%), Positives = 94/171 (54%), Gaps = 11/171 (6%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
K++ G++ VGKSC I R+ + F++K T+G+D+ +K + V + V + +D +G
Sbjct: 2 KVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPE 61
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWV-EAVEEVTEN----SIPIVICANKVD 508
+ + +++ GV+L+YDVT+ +SF ++ +W+ E +E + +I +V+CANK+D
Sbjct: 62 YLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKID 121
Query: 509 LRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHV 559
L + + + G A+ G + ETS+ +G+ + + L +
Sbjct: 122 LTKH------RAVSEDEGRLWAESKGFKYFETSACTGEGVNEMFQTLFSSI 166
>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 = 118 bits (298), Expect = 4e-31
Identities = 56/168 (33%), Positives = 89/168 (52%), Gaps = 8/168 (4%)
Query: 391 RAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAG 450
R +K+V G VGKS +F + F+++ T+ D K I +D L + DTAG
Sbjct: 1 REYKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIE-DSYRKQIEIDGEVCLLDILDTAG 59
Query: 451 QERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTEN-SIPIVICANKVDL 509
QE F +M Y R +G +L+Y +T+ +SF + + E + V + +PIV+ NK DL
Sbjct: 60 QEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDRDDVPIVLVGNKCDL 119
Query: 510 RADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSR 557
+ + E G++LA+Q+G F+ETS+K N+ +A L R
Sbjct: 120 ENERV------VSTEEGKELARQWGCPFLETSAKERINVDEAFYDLVR 161
>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 = 118 bits (297), Expect = 5e-31
Identities = 56/166 (33%), Positives = 89/166 (53%), Gaps = 8/166 (4%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
+K+V G VGKS +F + F++ T+ D K I +D L + DTAGQE
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIE-DSYRKQIEIDGEVCLLDILDTAGQE 59
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTEN-SIPIVICANKVDLRA 511
F +M Y R +G +L+Y +T+ +SF +K + E + V + +PIV+ NK DL +
Sbjct: 60 EFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVGNKCDLES 119
Query: 512 DAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSR 557
+ + E G++LA+Q+G F+ETS+K N+ +A L R
Sbjct: 120 ERV------VSTEEGKELARQWGCPFLETSAKERVNVDEAFYDLVR 159
>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 = 116 bits (294), Expect = 2e-30
Identities = 55/164 (33%), Positives = 85/164 (51%), Gaps = 13/164 (7%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
KIV GD AVGK+C + ++ F + T+ D + VD + V L LWDTAGQE
Sbjct: 2 KIVVVGDGAVGKTCLLISYTTNKFPTEYVPTV-FDNYSANVTVDGKQVNLGLWDTAGQEE 60
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKN-WVEAVEEVTEN--SIPIVICANKVDLR 510
+ + + + D +L + V + SF +VK W E+ ++PI++ K+DLR
Sbjct: 61 YDRLRPLSYPQTDVFLLCFSVDSPSSFENVKTKW---YPEIKHYCPNVPIILVGTKIDLR 117
Query: 511 ADA-----QAKGVKCIDREVGEKLAQQYGAI-FMETSSKSGDNI 548
D K K I E GEKLA++ GA+ +ME S+ + + +
Sbjct: 118 DDGNTLKKLEKKQKPITPEEGEKLAKEIGAVKYMECSALTQEGL 161
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 115 bits (289), Expect = 2e-29
Identities = 60/161 (37%), Positives = 101/161 (62%), Gaps = 9/161 (5%)
Query: 390 DRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTA 449
D +FKI+ GD+ VGKS + F + L T+GVDF++K + V + + L +WDTA
Sbjct: 12 DLSFKILLIGDSGVGKSSLLVSFISSS-VEDLAPTIGVDFKIKQLTVGGKRLKLTIWDTA 70
Query: 450 GQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKN-WVEAVEEVTENSIPI-VICANKV 507
GQERFR++T +Y+R A G++L+YDVT +F ++ + W + VE + N + ++ NKV
Sbjct: 71 GQERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVGNKV 130
Query: 508 DLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNI 548
D ++ + + RE G LA+++G +F+E S+K+ +N+
Sbjct: 131 DRESE------RDVSREEGMALAKEHGCLFLECSAKTRENV 165
>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 = 114 bits (287), Expect = 2e-29
Identities = 54/156 (34%), Positives = 85/156 (54%), Gaps = 4/156 (2%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFL-NKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
K+V G +VGK+ + R+ FL +T+G F K + V ER V L +WDTAG E
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSE 61
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
R+ +M++ Y+R A ++ YD+T+ SF K WV+ ++ + E I +C K DL
Sbjct: 62 RYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQNL-EEHCKIYLCGTKSDLI-- 118
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNI 548
Q + ++ +D + A + A ETSSK+G N+
Sbjct: 119 EQDRSLRQVDFHDVQDFADEIKAQHFETSSKTGQNV 154
>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 = 111 bits (279), Expect = 3e-28
Identities = 62/189 (32%), Positives = 107/189 (56%), Gaps = 7/189 (3%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
+++ G VGK+ + RF+ + F ST+GVDF++KT+ + + + LQ+WDTAGQER
Sbjct: 2 QVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQER 61
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRADA 513
F S+T Y+R A G++L+YD+T + +F+ + W++ +++ +++ NK+D D
Sbjct: 62 FNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLDCETD- 120
Query: 514 QAKGVKCIDREVGEKLAQQY-GAIFMETSSKSGDNILDALIALSRHVYVFIPCVYLKDLP 572
+ I R+ GEK AQQ G F E S+K N+ + + L + +P L++
Sbjct: 121 -----REITRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVDDILKKMPLDILRNEL 175
Query: 573 YTSVLIFIP 581
S+L P
Sbjct: 176 SNSILSLQP 184
>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 = 107 bits (269), Expect = 4e-27
Identities = 60/176 (34%), Positives = 90/176 (51%), Gaps = 20/176 (11%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
K++ GD VGKS + R+ F +L T+GV+F K + VD V LQ+WDTAGQE
Sbjct: 6 LKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQE 65
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAV---EEVTE-NSIPIVICANKVD 508
RFRS+ ++R +D +L + V + +SF ++ NW + +V E S P VI NK+D
Sbjct: 66 RFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKID 125
Query: 509 LRADAQAKGVKCIDREVGEKLAQQY-----GAIFMETSSKSGDNILDALIALSRHV 559
+ +R+V + AQ + + ETS+K N+ A R V
Sbjct: 126 IP-----------ERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRRV 170
>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 = 107 bits (269), Expect = 1e-26
Identities = 55/160 (34%), Positives = 83/160 (51%), Gaps = 10/160 (6%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRV-DERNVALQLWDTAGQ 451
KIV GD A GK+ I RF++E F T+G+DF + I + NV LQ+WD GQ
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
Query: 452 ERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIP---IVICANKVD 508
+ M Y A V L+YD+TN +SF ++++W+ V++V E S +V+ NK D
Sbjct: 61 QIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTD 120
Query: 509 LRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNI 548
L + Q E + AQ+ + S+K+GD +
Sbjct: 121 LEHNRQVTA------EKHARFAQENDMESIFVSAKTGDRV 154
>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 = 104 bits (262), Expect = 3e-26
Identities = 56/158 (35%), Positives = 95/158 (60%), Gaps = 5/158 (3%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
K++ GD +VGK+C I RF K+VF +T+GVDF+M+ V +LQLWDTAGQER
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQER 61
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVE-AVEEVTENSIPIVICANKVDLRAD 512
F+ + Y+R A +++++D+T+ S + W+E A++E +S+ + + K DL +
Sbjct: 62 FKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKKDLSSP 121
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILD 550
AQ ++ + KLA++ A + S+ +G+N+ D
Sbjct: 122 AQYALME----QDAIKLAREMKAEYWAVSALTGENVRD 155
>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 = 101 bits (254), Expect = 6e-25
Identities = 49/167 (29%), Positives = 84/167 (50%), Gaps = 20/167 (11%)
Query: 395 IVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE-- 452
+V GD AVGK+C + ++ F T+ ++ + VD + V L LWDTAGQE
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTVFENY-SADVEVDGKPVELGLWDTAGQEDY 59
Query: 453 -RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKN-WVEAVEEVTE--NSIPIVICANKVD 508
R R ++ + D ++ + V + SF +VK W EV ++PI++ K+D
Sbjct: 60 DRLRPLS---YPDTDVFLICFSVDSPASFENVKEKW---YPEVKHFCPNVPIILVGTKLD 113
Query: 509 LRADAQA------KGVKCIDREVGEKLAQQYGAI-FMETSSKSGDNI 548
LR D K + + E G+ LA++ GA+ ++E S+ + + +
Sbjct: 114 LRNDKSTLEELSKKKQEPVTYEQGQALAKRIGAVKYLECSALTQEGV 160
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 101 bits (252), Expect = 7e-25
Identities = 53/134 (39%), Positives = 80/134 (59%), Gaps = 6/134 (4%)
Query: 415 EVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQERFRSMTKNYFRRADGVMLLYDV 474
+ F N ST+G+DF KT+ +DE V LQLWDTAGQERFRS+ +Y R + +++YD+
Sbjct: 3 DTFDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDI 62
Query: 475 TNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRADAQAKGVKCIDREVGEKLAQQYG 534
TN +SF + W++ + + I + NK DL ++ + E G + AQ+Y
Sbjct: 63 TNRQSFENTTKWIQDILNERGKDVIIALVGNKTDL------GDLRKVTYEEGMQKAQEYN 116
Query: 535 AIFMETSSKSGDNI 548
+F ETS+K+G NI
Sbjct: 117 TMFHETSAKAGHNI 130
>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 = 100 bits (250), Expect = 1e-24
Identities = 59/173 (34%), Positives = 92/173 (53%), Gaps = 9/173 (5%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
+KIV G VGKS +F + VF+ T+ D K + +D R L++ DTAG E
Sbjct: 2 YKIVVLGAGGVGKSALTVQFVQNVFIESYDPTIE-DSYRKQVEIDGRQCDLEILDTAGTE 60
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTEN-SIPIVICANKVDLRA 511
+F +M + Y + G +L+Y VT+E S N + E V + ++ ++P+V+ NK DL
Sbjct: 61 QFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLED 120
Query: 512 DAQAKGVKCIDREVGEKLAQQYGAI-FMETSSKSGDNILDALIALSRHVYVFI 563
D Q + RE G L+QQ+G + F ETS++ N+ + I L R + I
Sbjct: 121 DRQ------VSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDLVRQIICVI 167
>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 = 99.1 bits (247), Expect = 3e-24
Identities = 52/166 (31%), Positives = 85/166 (51%), Gaps = 8/166 (4%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
+K+V G VGKS +F F+ K T+ DF K I VD L++ DTAG E
Sbjct: 2 YKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIE-DFYRKEIEVDSSPSVLEILDTAGTE 60
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTE-NSIPIVICANKVDLRA 511
+F SM Y + G +++Y + N+++F +K + + V +PI++ NKVDL +
Sbjct: 61 QFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLES 120
Query: 512 DAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSR 557
+ + + G LA+++G FMETS+KS + + + R
Sbjct: 121 ERE------VSSAEGRALAEEWGCPFMETSAKSKTMVNELFAEIVR 160
>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 = 98.9 bits (247), Expect = 4e-24
Identities = 54/165 (32%), Positives = 82/165 (49%), Gaps = 9/165 (5%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
FK+V GD GK+ F+ R F K +TLGV+ + + +WDTAGQE
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNVWDTAGQE 60
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
+F + Y+ + ++++DVT+ ++ +V NW + V EN IPIV+C NKVD++
Sbjct: 61 KFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDLVRVCEN-IPIVLCGNKVDIK-- 117
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSR 557
+ VK K QY E S+KS N + L+R
Sbjct: 118 --DRKVKPKQITFHRKKNLQY----YEISAKSNYNFEKPFLWLAR 156
>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 = 98.2 bits (245), Expect = 6e-24
Identities = 40/162 (24%), Positives = 73/162 (45%), Gaps = 10/162 (6%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSK-EVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQ 451
KIV GD VGKS + R ++ + + ++ I D + L DTAGQ
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQ 61
Query: 452 ERFRSMTKNYFRRADGVMLLYDVTN--ERSFNSVKNWVEAVEEVTENSIPIVICANKVDL 509
E + ++ + Y+R + + ++D+ ++ + + E+ +PI++ NK+DL
Sbjct: 62 EDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPIILVGNKIDL 121
Query: 510 RADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDA 551
R AK + V A+ G + S+++G NI A
Sbjct: 122 R---DAK----LKTHVAFLFAKLNGEPIIPLSAETGKNIDSA 156
>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 = 98.0 bits (244), Expect = 6e-24
Identities = 51/168 (30%), Positives = 92/168 (54%), Gaps = 8/168 (4%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
+K+V G VGKS +F + +F+ K T+ D K + VD + L++ DTAG E
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIE-DSYRKQVEVDGQQCMLEILDTAGTE 60
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTE-NSIPIVICANKVDLRA 511
+F +M Y + G +L+Y +T + +FN +++ E + V + +P+++ NK DL
Sbjct: 61 QFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLED 120
Query: 512 DAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHV 559
+ + + +E G+ LA+Q+G F+ETS+K+ N+ + L R +
Sbjct: 121 E------RVVGKEQGQNLARQWGCAFLETSAKAKINVNEIFYDLVRQI 162
>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 = 97.2 bits (242), Expect = 2e-23
Identities = 54/170 (31%), Positives = 79/170 (46%), Gaps = 11/170 (6%)
Query: 394 KIVFAGDAAVGKSCF--IYRFSKEVFLNKLGSTLGVDFQMKTIRV--DERNVALQLWDTA 449
+ GD AVGKS ++ F T G D +KT+ V +V L ++D+A
Sbjct: 2 QCAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSA 61
Query: 450 GQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTEN-SIPIVICANKVD 508
GQE F M +N + + V ++YDVTNE SFN+ W+ V + P V+ NK D
Sbjct: 62 GQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCD 121
Query: 509 LRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRH 558
L + +D + LAQ F ETS+K G ++L+R
Sbjct: 122 LTDRRE------VDAAQAQALAQANTLKFYETSAKEGVGYEAPFLSLARA 165
>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 = 96.7 bits (241), Expect = 2e-23
Identities = 46/168 (27%), Positives = 86/168 (51%), Gaps = 9/168 (5%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
+K+V G VGKS + + F+++ T+ D K + +D L + DTAGQE
Sbjct: 2 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIE-DSYRKQVVIDGETCLLDILDTAGQE 60
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTE-NSIPIVICANKVDLRA 511
+ +M Y R +G + ++ + + +SF + + E ++ V + + +P+V+ NK DL A
Sbjct: 61 EYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDLAA 120
Query: 512 DAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHV 559
+ + G+ LA+ YG ++ETS+K+ + +A L R +
Sbjct: 121 -------RTVSTRQGQDLAKSYGIPYIETSAKTRQGVEEAFYTLVREI 161
>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 = 95.3 bits (237), Expect = 6e-23
Identities = 54/169 (31%), Positives = 93/169 (55%), Gaps = 9/169 (5%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
+K+V G VGKS +F + +F++K T+ D K I VD + L++ DTAG E
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIE-DSYRKQIEVDCQQCMLEILDTAGTE 60
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTE-NSIPIVICANKVDLRA 511
+F +M Y + G L+Y +T ++SFN +++ E + V + +P+++ NK DL
Sbjct: 61 QFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVGNKCDLED 120
Query: 512 DAQAKGVKCIDREVGEKLAQQYGAI-FMETSSKSGDNILDALIALSRHV 559
+ + + +E G+ LA+Q+G F+ETS+KS N+ + L R +
Sbjct: 121 E------RVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLVRQI 163
>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 = 93.7 bits (233), Expect = 2e-22
Identities = 41/168 (24%), Positives = 69/168 (41%), Gaps = 17/168 (10%)
Query: 396 VFAGDAAVGKSCFIYRFSKEVFL---NKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
V G VGKS + + G+T D +D+ V L L DT G +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDV--YVKELDKGKVKLVLVDTPGLD 58
Query: 453 RF-----RSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKV 507
F + + R AD ++L+ D T+ S K + + IPI++ NK+
Sbjct: 59 EFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLR--KEGIPIILVGNKI 116
Query: 508 DLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIAL 555
DL + + + + E+LA+ G E S+K+G+ + + L
Sbjct: 117 DLLEEREVEELLR-----LEELAKILGVPVFEVSAKTGEGVDELFEKL 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 = 94.6 bits (235), Expect = 2e-22
Identities = 53/170 (31%), Positives = 89/170 (52%), Gaps = 7/170 (4%)
Query: 390 DRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTA 449
D K + GD+ VGK + + G +G+D++ TI +D R V LQLWDT+
Sbjct: 4 DYLLKFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTS 63
Query: 450 GQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDL 509
GQ RF ++ ++Y R A G++L+YD+TN SF+ + W++ ++E +P ++ N++ L
Sbjct: 64 GQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEIDEHAP-GVPKILVGNRLHL 122
Query: 510 RADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHV 559
Q + E + A++ G F E S NI ++ L+R V
Sbjct: 123 AFKRQ------VATEQAQAYAERNGMTFFEVSPLCNFNITESFTELARIV 166
>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 = 92.1 bits (229), Expect = 9e-22
Identities = 50/169 (29%), Positives = 86/169 (50%), Gaps = 8/169 (4%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
K++ G VGKS +F + F+ T D K + +D V L + DTAGQE
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKA-DSYRKKVVLDGEEVQLNILDTAGQE 59
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTEN-SIPIVICANKVDLRA 511
+ ++ NYFR +G +L++ +T+ SF ++ + E + V E+ ++P+++ NK DL
Sbjct: 60 DYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLLLVGNKCDLED 119
Query: 512 DAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHVY 560
Q + E LA+Q+G ++ETS+K+ N+ L R +
Sbjct: 120 KRQ------VSVEEAANLAEQWGVNYVETSAKTRANVDKVFFDLVREIR 162
>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 = 92.2 bits (229), Expect = 1e-21
Identities = 54/170 (31%), Positives = 78/170 (45%), Gaps = 8/170 (4%)
Query: 391 RAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAG 450
R +KIV G VGKS +F F + T+ ++ + R+D L + DTAG
Sbjct: 1 REYKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQ-ARIDNEPALLDILDTAG 59
Query: 451 QERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVT-ENSIPIVICANKVDL 509
Q F +M Y R +G ++ Y VT+ SF + E + V IP+V+ NKVDL
Sbjct: 60 QAEFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLTEDIPLVLVGNKVDL 119
Query: 510 RADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHV 559
Q + E G LA+++ F ETS+ I DA L R +
Sbjct: 120 EQQRQ------VTTEEGRNLAREFNCPFFETSAALRFYIDDAFHGLVREI 163
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 92.8 bits (231), Expect = 1e-21
Identities = 44/124 (35%), Positives = 67/124 (54%), Gaps = 2/124 (1%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
FK++ GD VGK+ F+ R F K TLGV+ + + +WDTAGQE
Sbjct: 10 FKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNVWDTAGQE 69
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
+F + Y+ + ++++DVT+ ++ +V NW + V EN IPIV+ NKVD+ D
Sbjct: 70 KFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDIVRVCEN-IPIVLVGNKVDV-KD 127
Query: 513 AQAK 516
Q K
Sbjct: 128 RQVK 131
>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 = 90.0 bits (224), Expect = 7e-21
Identities = 50/159 (31%), Positives = 86/159 (54%), Gaps = 8/159 (5%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
KI G +VGKS +F + F+ T+ F K I + L++ DTAGQ+
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTFS-KIITYKGQEYHLEIVDTAGQDE 61
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKN-WVEAVEEVTENSIPIVICANKVDLRAD 512
+ + + Y G +L+Y VT+ +SF VK + + ++ + + S+PIV+ NK DL +
Sbjct: 62 YSILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDLHME 121
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDA 551
+ + E G+KLA+ +GA F+E+S+K +N+ +A
Sbjct: 122 ------RQVSAEEGKKLAESWGAAFLESSAKENENVEEA 154
>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 = 88.9 bits (221), Expect = 1e-20
Identities = 48/171 (28%), Positives = 84/171 (49%), Gaps = 12/171 (7%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
KI G + VGKS RF + F+ + L + + + +D V+L++ DT GQ++
Sbjct: 1 KIAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYS-RQVTIDGEQVSLEIQDTPGQQQ 59
Query: 454 F--RSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEV--TENSIPIVICANKVDL 509
+ R ADG +L+Y +T+ SF+ V ++ + E+ + IP+++ NK DL
Sbjct: 60 NEDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVILVGNKADL 119
Query: 510 RADAQAKGVKCIDREVGEKLAQQYGAIFMETS-SKSGDNILDALIALSRHV 559
Q + E G+KLA + G +F E S +++ + + L R V
Sbjct: 120 LHSRQ------VSTEEGQKLALELGCLFFEVSAAENYLEVQNVFHELCREV 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 = 89.3 bits (222), Expect = 2e-20
Identities = 56/194 (28%), Positives = 92/194 (47%), Gaps = 26/194 (13%)
Query: 390 DRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQ--MKTIRVDERN-VALQLW 446
D KIV GD GK+C + +++ F + T+ F+ + T++V + L LW
Sbjct: 1 DLKVKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTV---FENYVTTLQVPNGKIIELALW 57
Query: 447 DTAGQE---RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKN-WVEAVEEVTENSIPIVI 502
DTAGQE R R ++ D +++ Y V N S ++V++ W V PIV+
Sbjct: 58 DTAGQEDYDRLRPLSYP---DVDVILICYSVDNPTSLDNVEDKWYPEVNHFCPG-TPIVL 113
Query: 503 CANKVDLRADAQ------AKGVKCIDREVGEKLAQQYGAI-FMETSSKSGDNI-----LD 550
K DLR D A+G++ + E GE +A+ GA+ ++E S+K +N+
Sbjct: 114 VGLKTDLRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVFDAA 173
Query: 551 ALIALSRHVYVFIP 564
+ALS+
Sbjct: 174 INVALSKSGRAARK 187
>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 = 87.5 bits (217), Expect = 4e-20
Identities = 52/168 (30%), Positives = 84/168 (50%), Gaps = 8/168 (4%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
+K+V G VGKS +F + F+ T+ D K +D + L + DTAGQE
Sbjct: 3 YKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIE-DSYTKQCEIDGQWARLDILDTAGQE 61
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTE-NSIPIVICANKVDLRA 511
F +M + Y R +G +L++ VT+ SF V + + V + + P+++ NK DL
Sbjct: 62 EFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADLEH 121
Query: 512 DAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHV 559
Q + RE G++LA+Q ++ETS+K N+ A L R +
Sbjct: 122 QRQ------VSREEGQELARQLKIPYIETSAKDRVNVDKAFHDLVRVI 163
>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 = 86.1 bits (213), Expect = 1e-19
Identities = 44/156 (28%), Positives = 79/156 (50%), Gaps = 10/156 (6%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
KI+ GD+AVGKS + RF + + + ST + + + + + + WDTAGQER
Sbjct: 2 KIILLGDSAVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQER 61
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRADA 513
F++M +Y+ +A +L++DVT + ++ ++ W E + E IP ++ ANK+DL
Sbjct: 62 FQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYRP-EIPCIVVANKIDLDPSV 120
Query: 514 QAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNIL 549
K A+++ S+ G N++
Sbjct: 121 TQKKF---------NFAEKHNLPLYYVSAADGTNVV 147
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 86.5 bits (214), Expect = 1e-19
Identities = 50/168 (29%), Positives = 87/168 (51%), Gaps = 8/168 (4%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
+K+V G VGKS +F + F+++ T+ D K +DE L + DTAGQE
Sbjct: 6 YKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIE-DSYRKQCVIDEETCLLDILDTAGQE 64
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTEN-SIPIVICANKVDLRA 511
+ +M Y R G + +Y +T+ SF + ++ E + V + +P+++ NK DL +
Sbjct: 65 EYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDS 124
Query: 512 DAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHV 559
+ Q + G++LA+ +G F+ETS+K N+ +A L R +
Sbjct: 125 ERQ------VSTGEGQELAKSFGIPFLETSAKQRVNVDEAFYELVREI 166
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 87.1 bits (216), Expect = 2e-19
Identities = 50/169 (29%), Positives = 79/169 (46%), Gaps = 15/169 (8%)
Query: 392 AFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQ 451
+FK+V GD GK+ F+ R F K T+GV+ + + WDTAGQ
Sbjct: 13 SFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYCWDTAGQ 72
Query: 452 ERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRA 511
E+F + Y+ ++++DVT ++ +V W + V EN IPIV+C NKVD++
Sbjct: 73 EKFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCRVCEN-IPIVLCGNKVDVK- 130
Query: 512 DAQAKGVKCIDREVGEKLAQ---QYGAIFMETSSKSGDNILDALIALSR 557
+R+V K + + E S+KS N + L+R
Sbjct: 131 ----------NRQVKAKQVTFHRKKNLQYYEISAKSNYNFEKPFLYLAR 169
>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 = 84.1 bits (208), Expect = 1e-18
Identities = 50/170 (29%), Positives = 88/170 (51%), Gaps = 8/170 (4%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
K+V GD A GK+ +Y F+ F + T+ + + RVD + V L LWDTAGQE
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTV-FENYVTDCRVDGKPVQLALWDTAGQEE 61
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVK-NWVEAVEEVTENSIPIVICANKVDLRAD 512
+ + + +A +++ + + S +V+ W+E V N +P+++ K DLR +
Sbjct: 62 YERLRPLSYSKAHVILIGFAIDTPDSLENVRTKWIEEVRRYCPN-VPVILVGLKKDLRQE 120
Query: 513 AQAKGV----KCIDREVGEKLAQQYGA-IFMETSSKSGDNILDALIALSR 557
A AKG + + + + +A+ GA +ME S+ +G+ + D A +R
Sbjct: 121 AVAKGNYATDEFVPIQQAKLVARAIGAKKYMECSALTGEGVDDVFEAATR 170
>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 = 83.2 bits (206), Expect = 1e-18
Identities = 48/173 (27%), Positives = 85/173 (49%), Gaps = 10/173 (5%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
K+V GD A GK+C + FSK+ F T+ ++ + I VD + V L LWDTAGQE
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENY-VADIEVDGKQVELALWDTAGQED 61
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKN-WVEAVEEVTENSIPIVICANKVDLRAD 512
+ + + D +++ + + + S ++ W V+ N +PI++ NK DLR D
Sbjct: 62 YDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPN-VPIILVGNKKDLRND 120
Query: 513 AQAK------GVKCIDREVGEKLAQQYGAI-FMETSSKSGDNILDALIALSRH 558
+ + E G +A++ GA ++E S+K+ + + + +R
Sbjct: 121 EHTIRELAKMKQEPVKPEEGRAMAEKIGAFGYLECSAKTKEGVREVFEMATRA 173
>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 = 81.2 bits (200), Expect = 1e-17
Identities = 49/162 (30%), Positives = 79/162 (48%), Gaps = 15/162 (9%)
Query: 399 GDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQERFRSMT 458
GD GK+ F+ R F K +TLGV+ + + +WDTAGQE+F +
Sbjct: 2 GDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGLR 61
Query: 459 KNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRADAQAKGV 518
Y+ + ++++DVT ++ +V NW + V EN IPIV+C NKVD++
Sbjct: 62 DGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLVRVCEN-IPIVLCGNKVDVK-------- 112
Query: 519 KCIDREVGEK---LAQQYGAIFMETSSKSGDNILDALIALSR 557
DR+V K ++ + + S+KS N + L+R
Sbjct: 113 ---DRKVKAKSITFHRKKNLQYYDISAKSNYNFEKPFLWLAR 151
>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 = 78.7 bits (194), Expect = 7e-17
Identities = 49/167 (29%), Positives = 84/167 (50%), Gaps = 10/167 (5%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
K+V GD VGK+ + F+ T+ D K + VD + L++ DTAGQE
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIE-DSYRKQVVVDGQPCMLEVLDTAGQEE 59
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENS---IPIVICANKVDLR 510
+ ++ + R +G +L+Y +T+ +F V+ + E ++ V + S +PI+I NK D
Sbjct: 60 YTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKV 119
Query: 511 ADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSR 557
+ + + E G LA++ G F+E S+K+ N+ A L R
Sbjct: 120 YERE------VSTEEGAALARRLGCEFIEASAKTNVNVERAFYTLVR 160
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 78.0 bits (192), Expect = 1e-16
Identities = 48/167 (28%), Positives = 76/167 (45%), Gaps = 7/167 (4%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
++VF G A VGK+ I RF + F K T+ + K V V + + DT+G
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVE-ELHSKEYEVAGVKVTIDILDTSGSYS 59
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENS-IPIVICANKVDLRAD 512
F +M K + D L+Y V + SF VK E + EV E+ +PIV+ NK+D A+
Sbjct: 60 FPAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNKIDSLAE 119
Query: 513 AQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHV 559
Q + + + F+E S+K +N+ + L +
Sbjct: 120 RQV-----EAADALSTVELDWNNGFVEASAKDNENVTEVFKELLQQA 161
>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 = 77.2 bits (190), Expect = 2e-16
Identities = 54/161 (33%), Positives = 82/161 (50%), Gaps = 8/161 (4%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
K V GD AVGK+C + ++ F T+ +F + VD V L LWDTAGQE
Sbjct: 3 KCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVV-VDGNTVNLGLWDTAGQED 61
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSF-NSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
+ + +R AD +L + + ++ S+ N +K W+ + +PIV+ K+DLR D
Sbjct: 62 YNRLRPLSYRGADVFLLAFSLISKASYENVLKKWIPELRHYAPG-VPIVLVGTKLDLRDD 120
Query: 513 AQ----AKGVKCIDREVGEKLAQQYGA-IFMETSSKSGDNI 548
Q G I GE+L +Q GA ++E SSK+ N+
Sbjct: 121 KQFFADHPGAVPITTAQGEELRKQIGAAAYIECSSKTQQNV 161
>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 = 73.8 bits (182), Expect = 2e-15
Identities = 41/167 (24%), Positives = 75/167 (44%), Gaps = 11/167 (6%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
+I+ G GK+ +Y+ K + T+G F ++T+ +NV +WD GQ++
Sbjct: 1 RILMLGLDGAGKTTILYKL-KLGEVVTTIPTIG--FNVETVEY--KNVKFTVWDVGGQDK 55
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENS-IPIVICANKVDLRAD 512
R + K+Y+ DG++ + D ++ KN + + E P++I ANK DL
Sbjct: 56 IRPLWKHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEEELKGAPLLILANKQDL--- 112
Query: 513 AQAKGVKCIDREVG-EKLAQQYGAIFMETSSKSGDNILDALIALSRH 558
A + +G E + + I S+ +GD + + L L
Sbjct: 113 PGALTESELIELLGLESIKGRRWHIQP-CSAVTGDGLDEGLDWLIEQ 158
>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 = 72.1 bits (177), Expect = 2e-15
Identities = 34/120 (28%), Positives = 52/120 (43%), Gaps = 12/120 (10%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVF----LNKLGSTLGVDFQMKTIRVDERNVALQLWDTA 449
K+V GD GKS + + F L G TL VD + D L +WD
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVD--TLEVDGDTG--LLNIWDFG 56
Query: 450 GQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKN---WVEAVEEVTENSIPIVICANK 506
G+E + + + AD ++L+YD+T+ S N V W+ IP+++ NK
Sbjct: 57 GREELKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWL-PNLRKLGGKIPVILVGNK 115
>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 = 72.0 bits (177), Expect = 8e-15
Identities = 37/160 (23%), Positives = 69/160 (43%), Gaps = 16/160 (10%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERN-VALQLWDTAGQE 452
K++ G VGK+ + E F ST G++ Q I ER + L +WD GQE
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGGQE 62
Query: 453 RFRSMTKNYFRRADGV-MLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRA 511
+ + T +F + + +L++D+ + V W+ ++ S P+++ +D
Sbjct: 63 IYHA-THQFFLTSRSLYLLVFDLRTGDEVSRVPYWLRQIKAFGGVS-PVILVGTHID--- 117
Query: 512 DAQAKGVKCIDREVGEKLAQQYGAI---FMETSSKSGDNI 548
C + + + L +++ AI S K+G I
Sbjct: 118 ------ESCDEDILKKALNKKFPAIINDIHFVSCKNGKGI 151
>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 = 72.7 bits (178), Expect = 9e-15
Identities = 48/166 (28%), Positives = 86/166 (51%), Gaps = 10/166 (6%)
Query: 391 RAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAG 450
++ K V GD AVGK+C + ++ F + T+ ++ +T VD R V+L LWDTAG
Sbjct: 2 QSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTA-VDGRTVSLNLWDTAG 60
Query: 451 QERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKN-WVEAVEEVTENSIPIVICANKVDL 509
QE + + + + + ++ + + + S+ +V++ W V N +PI++ K DL
Sbjct: 61 QEEYDRLRTLSYPQTNVFIICFSIASPSSYENVRHKWHPEVCHHCPN-VPILLVGTKKDL 119
Query: 510 RADAQA------KGVKCIDREVGEKLAQQYGAI-FMETSSKSGDNI 548
R DA +G I + G LA+Q A+ ++E S+ + D +
Sbjct: 120 RNDADTLKKLKEQGQAPITPQQGGALAKQIHAVKYLECSALNQDGV 165
>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 = 72.2 bits (177), Expect = 1e-14
Identities = 49/170 (28%), Positives = 82/170 (48%), Gaps = 10/170 (5%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
K+V GD A GK+ + F++ F T+ ++ + I VD V L LWDTAGQE
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTVFENY-IHDIFVDGLAVELSLWDTAGQEE 60
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKN-WVEAVEEVTEN--SIPIVICANKVDLR 510
F + + +ML + V N S +V++ W + E+ + + +V+ A K DLR
Sbjct: 61 FDRLRSLSYADTHVIMLCFSVDNPDSLENVESKW---LAEIRHHCPGVKLVLVALKCDLR 117
Query: 511 AD--AQAKGVKCIDREVGEKLAQQYGAI-FMETSSKSGDNILDALIALSR 557
+ +G I E G +A++ A ++E S+K + +A +R
Sbjct: 118 EPRNERDRGTHTISYEEGLAVAKRINACRYLECSAKLNRGVNEAFTEAAR 167
>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 = 71.7 bits (176), Expect = 1e-14
Identities = 49/164 (29%), Positives = 82/164 (50%), Gaps = 14/164 (8%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKT--IRVDERNVALQLWDTAGQ 451
KIV GD+ GK+ + F+K+ F T+ F+ T VD++ + L LWDT+G
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTV---FENYTASFEVDKQRIELSLWDTSGS 59
Query: 452 ERFRSMTKNYFRRADGVMLLYDVTNERSFNSV-KNWVEAVEEVTENSIPIVICANKVDLR 510
+ ++ + +D V++ +D++ + +SV K W V E N P+++ K DLR
Sbjct: 60 PYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEVREFCPN-TPVLLVGCKSDLR 118
Query: 511 ADAQA------KGVKCIDREVGEKLAQQYGA-IFMETSSKSGDN 547
D K + E G LA+Q GA ++E S+K+ +N
Sbjct: 119 TDLSTLTELSNKRQIPVSHEQGRNLAKQIGAAAYVECSAKTSEN 162
>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 = 70.5 bits (173), Expect = 3e-14
Identities = 45/166 (27%), Positives = 79/166 (47%), Gaps = 10/166 (6%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
K V GD AVGK+ I ++ + + T +F + + VD + V LQL DTAGQ+
Sbjct: 2 KCVLVGDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFSVV-VLVDGKPVRLQLCDTAGQDE 60
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKN-WVEAVEEVTENSIPIVICANKVDLRAD 512
F + + D +L + V N SF ++ W+ + + + PI++ + DLR D
Sbjct: 61 FDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHNPKA-PIILVGTQADLRTD 119
Query: 513 A------QAKGVKCIDREVGEKLAQQYGAI-FMETSSKSGDNILDA 551
G K + + + LA++ GA ++E S+ + N+ +
Sbjct: 120 VNVLIQLARYGEKPVSQSRAKALAEKIGACEYIECSALTQKNLKEV 165
>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 = 70.4 bits (172), Expect = 4e-14
Identities = 51/172 (29%), Positives = 84/172 (48%), Gaps = 13/172 (7%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
K V GD AVGK+C + ++ + F + T+ D ++ V + L L+DTAGQE
Sbjct: 1 LKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTV-FDHYAVSVTVGGKQYLLGLYDTAGQE 59
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVK-NWVEAVEEVTENSIPIVICANKVDLRA 511
+ + + D ++ + V N SF +VK WV ++E N +P ++ ++DLR
Sbjct: 60 DYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPN-VPYLLIGTQIDLRD 118
Query: 512 DAQAKG------VKCIDREVGEKLAQQYGA-IFMETSS---KSGDNILDALI 553
D + K I E G+KLA++ GA ++E S+ K + D I
Sbjct: 119 DPKTLARLNDMKEKPITVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAI 170
>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 = 70.2 bits (172), Expect = 4e-14
Identities = 49/162 (30%), Positives = 81/162 (50%), Gaps = 16/162 (9%)
Query: 392 AFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQ 451
A K V GD AVGK+C + ++ F + T+ D + VD + V L LWDTAGQ
Sbjct: 1 AIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPVNLGLWDTAGQ 59
Query: 452 E---RFRSMTKNYFRRADGVMLLYDVTNERSFNSVK-NWVEAVEEVTENSIPIVICANKV 507
E R R ++ + + D ++ + + + SF +V+ W V N+ PI++ K+
Sbjct: 60 EDYDRLRPLS---YPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNT-PIILVGTKL 115
Query: 508 DLRADA------QAKGVKCIDREVGEKLAQQYGAI-FMETSS 542
DLR D + K + I G +A++ GA+ ++E S+
Sbjct: 116 DLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSA 157
>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 = 69.1 bits (169), Expect = 8e-14
Identities = 45/159 (28%), Positives = 78/159 (49%), Gaps = 10/159 (6%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
+++V G VGKS + RF K F T+ D + I + LQ+ DT G
Sbjct: 2 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIE-DTYRQVISCSKSICTLQITDTTGSH 60
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTEN---SIPIVICANKVDL 509
+F +M + + +L+Y +T+++S +K E + E+ N IPI++ NK D
Sbjct: 61 QFPAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNNLEKIPIMLVGNKCD- 119
Query: 510 RADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNI 548
++ ++ V + G LA+ + FMETS+K+ N+
Sbjct: 120 --ESPSREVSSSE---GAALARTWNCAFMETSAKTNHNV 153
>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 = 69.3 bits (170), Expect = 1e-13
Identities = 37/119 (31%), Positives = 62/119 (52%), Gaps = 1/119 (0%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
KI GDA +GK+ + ++ + F + TLGV+F KTI + + +WD GQ
Sbjct: 2 KIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQRE 61
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
F +M + A ++ ++D+T + + NS+K W + +IPI++ K DL AD
Sbjct: 62 FINMLPLVCKDAVAILFMFDLTRKSTLNSIKEWYRQARGFNKTAIPILV-GTKYDLFAD 119
>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 = 67.6 bits (165), Expect = 4e-13
Identities = 51/173 (29%), Positives = 82/173 (47%), Gaps = 17/173 (9%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
K V GD AVGK+C + ++ F ++ T+ D T+ + L L+DTAGQE
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNKFPSEYVPTV-FDNYAVTVMIGGEPYTLGLFDTAGQED 61
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVK-NWVEAVEEVTENS--IPIVICANKVDLR 510
+ + + + D ++ + V + SF +VK W V E+T + P ++ ++DLR
Sbjct: 62 YDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKW---VPEITHHCPKTPFLLVGTQIDLR 118
Query: 511 ADAQA------KGVKCIDREVGEKLAQQYGAI-FMETSS---KSGDNILDALI 553
D K I E GEKLA+ A+ ++E S+ K N+ D I
Sbjct: 119 DDPSTIEKLAKNKQKPITPETGEKLARDLKAVKYVECSALTQKGLKNVFDEAI 171
>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 = 67.0 bits (164), Expect = 5e-13
Identities = 45/165 (27%), Positives = 71/165 (43%), Gaps = 29/165 (17%)
Query: 404 GKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQERFRSMTKNYFR 463
GK+ + + F T+G F M+ +V + NV +++WD GQ RFRSM + Y R
Sbjct: 11 GKTTLVNVIASGQFSEDTIPTVG--FNMR--KVTKGNVTIKVWDLGGQPRFRSMWERYCR 66
Query: 464 RADGVMLLYDVTNERSFNSVKNWVEAVEEVTE-NSIPIVICANKVDLRADAQAKGVKCI- 521
+ ++ + D + KN + + E IP+++ NK DL A + + I
Sbjct: 67 GVNAIVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDL-PGALSVD-ELIE 124
Query: 522 --------DREVGEKLAQQYGAIFMETSSKSGDNI---LDALIAL 555
DREV + + S+K NI LD LI
Sbjct: 125 QMNLKSITDREV---------SCYS-ISAKEKTNIDIVLDWLIKH 159
>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 = 67.4 bits (165), Expect = 9e-13
Identities = 46/179 (25%), Positives = 74/179 (41%), Gaps = 29/179 (16%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
+++V GD+ VGKS F+ V+ + G D +T+ VD L ++D QE
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVVYDHWEQE 60
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEV--------TENSIPIVICA 504
+ + + D +++Y VT+ SF E E+ IPI++
Sbjct: 61 DGMWLEDSCMQVGDAYVIVYSVTDRSSF-------EKASELRIQLRRARQAEDIPIILVG 113
Query: 505 NKVDLRADAQAKGVKCIDREV----GEKLAQQYGAIFMETSSKSGDNILDALIALSRHV 559
NK DL V+ REV G A + F+ETS+ N+ + + R V
Sbjct: 114 NKSDL--------VRS--REVSVQEGRACAVVFDCKFIETSAALQHNVDELFEGIVRQV 162
>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 = 65.7 bits (160), Expect = 4e-12
Identities = 52/197 (26%), Positives = 85/197 (43%), Gaps = 32/197 (16%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
K+V GD VGK+ ++R+ + F + + ST+G F +K N+++ WDTAG+E+
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRFKDTV-STVGGAFYLKQWG--PYNISI--WDTAGREQ 56
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD- 512
F + Y R A V+L YDV+N +S +++ + + + NK+DL +
Sbjct: 57 FHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVGNKLDLTEEG 116
Query: 513 AQAKGVKCIDREVGEKLAQQ---------YGAI-----------------FMETSSKSGD 546
A A K V + +Q Y I ETS+K+G
Sbjct: 117 ALAGQEKDAGDRVSPEDQRQVTLEDAKAFYKRINKYKMLDEDLSPAAEKMCFETSAKTGY 176
Query: 547 NILDALIALSRHVYVFI 563
N+ + L V I
Sbjct: 177 NVDELFEYLFNLVLPLI 193
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 64.6 bits (158), Expect = 4e-12
Identities = 42/173 (24%), Positives = 79/173 (45%), Gaps = 11/173 (6%)
Query: 389 PDRAFKIVFAG-DAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWD 447
++ +I+ G D A GK+ +Y+ + + T+G F ++T+ +NV +WD
Sbjct: 11 WNKEMRILILGLDNA-GKTTILYKLKLGEIVTTI-PTIG--FNVETVTY--KNVKFTVWD 64
Query: 448 TAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENS-IPIVICANK 506
GQE R + +NYF D V+ + D + K + A+ E + P++I ANK
Sbjct: 65 VGGQESLRPLWRNYFPNTDAVIFVVDSADRDRIEEAKEELHALLNEEELADAPLLILANK 124
Query: 507 VDLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHV 559
DL ++ + +L + I S+ +G+ + + L LS ++
Sbjct: 125 QDLPGAMSEAEIRELLGL--HELKDRPWEIQG-CSAVTGEGLDEGLDWLSNYI 174
>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 = 64.8 bits (158), Expect = 4e-12
Identities = 36/123 (29%), Positives = 61/123 (49%), Gaps = 7/123 (5%)
Query: 392 AFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRV---DERNVALQLWDT 448
+ IV G + GK+ +YR F+N + T G F + I+V + + V WD
Sbjct: 3 SLHIVMLGLDSAGKTTVLYRLKFNEFVNTV-PTKG--FNTEKIKVSLGNAKGVTFHFWDV 59
Query: 449 AGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTEN-SIPIVICANKV 507
GQE+ R + K+Y R DG++ + D + K + + + +EN +P+++ ANK
Sbjct: 60 GGQEKLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQ 119
Query: 508 DLR 510
DL
Sbjct: 120 DLP 122
>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 = 62.3 bits (151), Expect = 5e-11
Identities = 41/162 (25%), Positives = 83/162 (51%), Gaps = 10/162 (6%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
KIV GD GK+ ++ F+K+ + T+ ++ + +D+ + L +WDT+G
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPESYVPTVFENY-TASFEIDKHRIELNMWDTSGSSY 61
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSV-KNWVEAVEEVTENSIPIVICANKVDLRAD 512
+ ++ + +D V++ +D++ + +SV K W +E N+ +V+ K+D+R D
Sbjct: 62 YDNVRPLAYPDSDAVLICFDISRPETLDSVLKKWQGETQEFCPNA-KLVLVGCKLDMRTD 120
Query: 513 AQA------KGVKCIDREVGEKLAQQYGAI-FMETSSKSGDN 547
+ + + E G LA+Q GA+ ++E SS+ +N
Sbjct: 121 LSTLRELSKQRLIPVTHEQGSLLARQLGAVAYVECSSRMSEN 162
>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 = 60.1 bits (145), Expect = 2e-10
Identities = 41/162 (25%), Positives = 80/162 (49%), Gaps = 10/162 (6%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
KIV GD+ GK+ ++ F+K+ F T+ ++ + +D + + L LWDT+G
Sbjct: 7 KIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENY-TASFEIDTQRIELSLWDTSGSPY 65
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSV-KNWVEAVEEVTENSIPIVICANKVDLRAD 512
+ ++ + +D V++ +D++ + +SV K W ++E N+ +++ K DLR D
Sbjct: 66 YDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNT-KMLLVGCKSDLRTD 124
Query: 513 AQAKGVKCIDREV------GEKLAQQYGAI-FMETSSKSGDN 547
R+ G +A+Q GA ++E S+ +N
Sbjct: 125 VSTLVELSNHRQTPVSYDQGANMAKQIGAATYIECSALQSEN 166
>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 = 58.9 bits (143), Expect = 3e-10
Identities = 33/130 (25%), Positives = 55/130 (42%), Gaps = 8/130 (6%)
Query: 391 RAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVD--ERNVALQLWDT 448
+ +IV GD VGKS I E F + L TI D V + DT
Sbjct: 1 KDVRIVLIGDEGVGKSSLIMSLVSEEFPENVPRVL----PEITIPADVTPERVPTTIVDT 56
Query: 449 AGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKN-WVEAVEEVTENSIPIVICANKV 507
+ + + R+ R+A+ + L+Y V + ++ W+ + + +PI++ NK
Sbjct: 57 SSRPQDRANLAAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRRLGVK-VPIILVGNKS 115
Query: 508 DLRADAQAKG 517
DLR + G
Sbjct: 116 DLRDGSSQAG 125
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 57.5 bits (139), Expect = 1e-09
Identities = 38/130 (29%), Positives = 62/130 (47%), Gaps = 20/130 (15%)
Query: 394 KIVFAGDAAVGKSCFI----YRFSKEVFLN--------KLGSTLGVDFQMKTIRVDERNV 441
KIV G GK+ F+ + + K +T+ +DF +I +DE
Sbjct: 12 KIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFG--SIELDEDTG 69
Query: 442 ALQLWDTAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVT-ENSIPI 500
+ L+ T GQERF+ M + R A G ++L D + +F++ E ++ +T N IP+
Sbjct: 70 -VHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHA----EEIIDFLTSRNPIPV 124
Query: 501 VICANKVDLR 510
V+ NK DL
Sbjct: 125 VVAINKQDLF 134
>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 = 56.6 bits (137), Expect = 2e-09
Identities = 42/155 (27%), Positives = 73/155 (47%), Gaps = 15/155 (9%)
Query: 376 LLSLSNSLEPTGEPDRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIR 435
LLS+ L+P+ + +I+ G GK+ + + + E ++ + T G F +K ++
Sbjct: 1 LLSILRKLKPS--SRQEVRILLLGLDNAGKTTILKQLASED-ISHITPTQG--FNIKNVQ 55
Query: 436 VDERNVALQLWDTAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSV-KNWVEAVEEVT 494
D L +WD GQ + R +NYF D ++ + D + + F + VE +EE
Sbjct: 56 ADG--FKLNVWDIGGQRKIRPYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELLEEEK 113
Query: 495 ENSIPIVICANKVDLRADAQAKGVKCIDREVGEKL 529
+P+++ ANK DL A + EV E L
Sbjct: 114 LAGVPVLVFANKQDL---LTAAPAE----EVAEAL 141
>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 = 57.2 bits (138), Expect = 2e-09
Identities = 35/149 (23%), Positives = 69/149 (46%), Gaps = 28/149 (18%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLG--VDFQMKTIRV---DERNVALQLWDT 448
K++ GD+ VGKS ++ K L T+G VD + T +E+ ++LWD
Sbjct: 2 KVLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHTYGEGTPEEKTFYVELWDV 61
Query: 449 AGQ----ERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNW-VEAVEEVT--------- 494
G E +S ++ + +G++ ++D+TN++S ++ W +EA+ T
Sbjct: 62 GGSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYRWSLEALNRDTFPAGLLVTN 121
Query: 495 ---------ENSIPIVICANKVDLRADAQ 514
N +P+++ K+D +A+
Sbjct: 122 GDYDSEQFAGNPVPLLVIGTKLDQIPEAK 150
>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 = 55.4 bits (133), Expect = 1e-08
Identities = 47/188 (25%), Positives = 79/188 (42%), Gaps = 34/188 (18%)
Query: 393 FKIVFAGDAAVGKSCFI--YRFSKEVFLNKLGST-----LGVD--------FQMKTIRVD 437
K V GD AVGK+ I +K + +L +T +D + VD
Sbjct: 3 IKCVVVGDNAVGKTRLICARACNKTLTQYQLLATHVPTVWAIDQYRVCQEVLERSRDVVD 62
Query: 438 ERNVALQLWDTAG-QERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKN-WVEAVEEVTE 495
+V+L+LWDT G ++ R + R+D V+L + + + S +VK W +
Sbjct: 63 GVSVSLRLWDTFGDHDKDRRFA---YGRSDVVLLCFSIASPNSLRNVKTMWYPEIRHFCP 119
Query: 496 NSIPIVICANKVDLR-ADAQA------------KGVKCIDREVGEKLAQQYGAIFMETSS 542
+P+++ K+DLR AD K + E G +A++ G + ETS
Sbjct: 120 -RVPVILVGCKLDLRYADLDEVNRARRPLARPIKNADILPPETGRAVAKELGIPYYETSV 178
Query: 543 KSGDNILD 550
+ + D
Sbjct: 179 VTQFGVKD 186
>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 = 54.3 bits (131), Expect = 1e-08
Identities = 30/120 (25%), Positives = 67/120 (55%), Gaps = 11/120 (9%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
+++ G + GKS +Y+ + + T+G F ++ +++ E++++L +WD GQE+
Sbjct: 1 QVLLLGLDSAGKSTLLYKLKHAELVTTI-PTVG--FNVEMLQL-EKHLSLTVWDVGGQEK 56
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTEN----SIPIVICANKVDL 509
R++ K Y DG++ + D ++E + + + ++ + +N +P+V+ ANK DL
Sbjct: 57 MRTVWKCYLENTDGLVYVVDSSDEARLDESQ---KELKHILKNEHIKGVPVVLLANKQDL 113
>gnl|CDD|238008 cd00051, EFh, EF-hand, calcium binding motif; A diverse
superfamily of calcium sensors and calcium signal
modulators; most examples in this alignment model have
2 active canonical EF hands. Ca2+ binding induces a
conformational change in the EF-hand motif, leading to
the activation or inactivation of target proteins.
EF-hands tend to occur in pairs or higher copy numbers.
Length = 63
Score = 51.4 bits (124), Expect = 1e-08
Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 2/63 (3%)
Query: 5 QLEELFKTCDKKGTGQIGPEEFRELCTGFDIQPTDS--DAIFADLDHDGDGKVSLEDFAY 62
+L E F+ DK G G I +E + ++ D + ++D DGDGK+ E+F
Sbjct: 1 ELREAFRLFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLE 60
Query: 63 GFR 65
Sbjct: 61 LMA 63
Score = 29.8 bits (68), Expect = 0.48
Identities = 12/29 (41%), Positives = 20/29 (68%)
Query: 1 MSDLQLEELFKTCDKKGTGQIGPEEFREL 29
+S+ +++E+ + DK G G+I EEF EL
Sbjct: 33 LSEEEIDEMIREVDKDGDGKIDFEEFLEL 61
>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 = 55.9 bits (135), Expect = 1e-08
Identities = 45/172 (26%), Positives = 72/172 (41%), Gaps = 15/172 (8%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQE 452
+++V G + VGK+ + RF F + T+ DF K + L + DT+G
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIE-DFHRKLYSIRGEVYQLDILDTSGNH 59
Query: 453 RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVT--------EN-SIPIVIC 503
F +M + D +L++ + N SF V E + E EN IP+VIC
Sbjct: 60 PFPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVIC 119
Query: 504 ANKVDLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIAL 555
NK D + V+ EV + + + E S+K N+ + AL
Sbjct: 120 GNKADRDF---PREVQ--RDEVEQLVGGDENCAYFEVSAKKNSNLDEMFRAL 166
>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 = 53.1 bits (127), Expect = 7e-08
Identities = 54/212 (25%), Positives = 96/212 (45%), Gaps = 22/212 (10%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
K+V GD GK+ + +K+ + T+ ++ + +E+ V L LWDT+G
Sbjct: 15 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENY-TACLETEEQRVELSLWDTSGSPY 73
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNS-VKNWVEAVEEVTENSIPIVICANKVDLRAD 512
+ ++ + +D V+L +D++ F+S +K W + + ++ I++ K DLR D
Sbjct: 74 YDNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAEILDYCPST-RILLIGCKTDLRTD 132
Query: 513 AQA------KGVKCIDREVGEKLAQQYGA-IFME----TSSKSGDNI--------LDALI 553
+ I E G +A+Q GA ++E TS KS +I ++ L
Sbjct: 133 LSTLMELSNQKQAPISYEQGCAMAKQLGAEAYLECSAFTSEKSIHSIFRTASLLCINKLS 192
Query: 554 ALSRHVYVFIPCVYLKDLPYTSVLIFIPFQKQ 585
L++ V L LP S LI F+K+
Sbjct: 193 PLAKKSPVRSLSKRLLHLPSRSELISSTFKKE 224
>gnl|CDD|206725 cd04160, Arfrp1, Arf-related protein 1 (Arfrp1). Arfrp1
(Arf-related protein 1), formerly known as ARP, is a
membrane-associated Arf family member that lacks the
N-terminal myristoylation motif. Arfrp1 is mainly
associated with the trans-Golgi compartment and the
trans-Golgi network, where it regulates the targeting of
Arl1 and the GRIP domain-containing proteins, golgin-97
and golgin-245, onto Golgi membranes. It is also
involved in the anterograde transport of the vesicular
stomatitis virus G protein from the Golgi to the plasma
membrane, and in the retrograde transport of TGN38 and
Shiga toxin from endosomes to the trans-Golgi network.
Arfrp1 also inhibits Arf/Sec7-dependent activation of
phospholipase D. Deletion of Arfrp1 in mice causes
embryonic lethality at the gastrulation stage and
apoptosis of mesodermal cells, indicating its importance
in development.
Length = 168
Score = 51.6 bits (124), Expect = 1e-07
Identities = 29/94 (30%), Positives = 47/94 (50%), Gaps = 7/94 (7%)
Query: 418 LNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQERFRSMTKNYFRRADGVMLLYDVTNE 477
+K+ T+G++ ++ L WD GQE RS+ Y+ + GV+ + D T+
Sbjct: 32 PSKITPTVGLN----IGTIEVGKARLMFWDLGGQEELRSLWDKYYAESHGVIYVIDSTDR 87
Query: 478 RSFNSVKNWVEAV--EEVTENSIPIVICANKVDL 509
FN K+ E V E E +P+++ ANK DL
Sbjct: 88 ERFNESKSAFEKVINNEALEG-VPLLVLANKQDL 120
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 53.3 bits (128), Expect = 1e-07
Identities = 36/162 (22%), Positives = 72/162 (44%), Gaps = 29/162 (17%)
Query: 381 NSLEPTGEPDRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMK-------- 432
N P G+ +++ GD+ VGKS ++ K + + T+G +K
Sbjct: 14 NGGPPCGQ----VRVLVVGDSGVGKSSLVHLIVKGSSIARPPQTIGCTVGVKHITYGSPG 69
Query: 433 ----TIRVD-ERNVALQLWDTAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWV 487
+I+ D ER+ ++LWD +G ER++ ++ + +GV+ ++D++ R+ S++ W
Sbjct: 70 SSSNSIKGDSERDFFVELWDVSGHERYKDCRSLFYSQINGVIFVHDLSQRRTKTSLQKWA 129
Query: 488 EAVEEVTENS------------IPIVICANKVDLRADAQAKG 517
V S +P ++ NK D+ +G
Sbjct: 130 SEVAATGTFSAPLGSGGPGGLPVPYIVIGNKADIAPKEGTRG 171
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 49.8 bits (119), Expect = 5e-07
Identities = 39/181 (21%), Positives = 81/181 (44%), Gaps = 31/181 (17%)
Query: 391 RAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGS------TLGVDFQMKTIRVDERNVALQ 444
+ +I+ G A GK+ +Y+ KLG T+G F ++T V+ +N+
Sbjct: 16 KEVRILMVGLDAAGKTTILYKL-------KLGEVVTTIPTIG--FNVET--VEYKNLKFT 64
Query: 445 LWDTAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAV--EEVTENSIPIVI 502
+WD GQ++ R + ++Y++ +G++ + D + + +E + E+ +++ +++
Sbjct: 65 MWDVGGQDKLRPLWRHYYQNTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAV-LLV 123
Query: 503 CANKVDLRADAQAKGVKCIDREVGEKLA----QQYGAIFMETSSKSGDNILDALIALSRH 558
ANK DL EV EKL +Q + + + + L LS +
Sbjct: 124 FANKQDLPNAMSTT-------EVTEKLGLHSVRQRNWYIQGCCATTAQGLYEGLDWLSAN 176
Query: 559 V 559
+
Sbjct: 177 I 177
>gnl|CDD|206720 cd04154, Arl2, Arf-like 2 (Arl2) GTPase. Arl2 (Arf-like 2) GTPases
are members of the Arf family that bind GDP and GTP with
very low affinity. Unlike most Arf family proteins, Arl2
is not myristoylated at its N-terminal helix. The
protein PDE-delta, first identified in photoreceptor rod
cells, binds specifically to Arl2 and is structurally
very similar to RhoGDI. Despite the high structural
similarity between Arl2 and Rho proteins and between
PDE-delta and RhoGDI, the interactions between the
GTPases and their effectors are very different. In its
GTP bound form, Arl2 interacts with the protein Binder
of Arl2 (BART), and the complex is believed to play a
role in mitochondrial adenine nucleotide transport. In
its GDP bound form, Arl2 interacts with tubulin- folding
Cofactor D; this interaction is believed to play a role
in regulation of microtubule dynamics that impact the
cytoskeleton, cell division, and cytokinesis.
Length = 173
Score = 49.6 bits (119), Expect = 6e-07
Identities = 42/165 (25%), Positives = 77/165 (46%), Gaps = 11/165 (6%)
Query: 390 DRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTA 449
+R +I+ G GK+ + +F+ E ++ + TLG F +KT+ + L +WD
Sbjct: 12 EREMRILMLGLDNAGKTTILKKFNGED-ISTISPTLG--FNIKTLEYNG--YKLNIWDVG 66
Query: 450 GQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEA--VEEVTENSIPIVICANKV 507
GQ+ RS +NYF D ++ + D ++ K ++ VEE + ++I ANK
Sbjct: 67 GQKSLRSYWRNYFESTDALIWVVDSSDRARLEDCKRELQKLLVEERLAGA-TLLIFANKQ 125
Query: 508 DLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDAL 552
DL A + I + + + S+ +G+N+LD +
Sbjct: 126 DLPG---ALSPEEIREVLELDSIKSHHWRIFGCSAVTGENLLDGI 167
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 46.2 bits (110), Expect = 7e-07
Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 11 KTCDKKGTGQIGPEEFRELCTGFDIQPTDS------DAIFADLDHDGDGKVSLEDFAYGF 64
K DK G G I EE R+L ++ TD +A F ++D DGDG++S E+F
Sbjct: 1 KLLDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEFLEAM 60
>gnl|CDD|128474 smart00177, ARF, ARF-like small GTPases; ARF, ADP-ribosylation
factor. Ras homologues involved in vesicular transport.
Activator 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. Contains ATP/GTP-binding
motif (P-loop).
Length = 175
Score = 49.1 bits (117), Expect = 7e-07
Identities = 40/177 (22%), Positives = 82/177 (46%), Gaps = 27/177 (15%)
Query: 390 DRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLG----VDFQMKTIRVDERNVALQL 445
++ +I+ G A GK+ +Y+ KLG ++ + F ++T V +N++ +
Sbjct: 11 NKEMRILMVGLDAAGKTTILYKL-------KLGESVTTIPTIGFNVET--VTYKNISFTV 61
Query: 446 WDTAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAV--EEVTENSIPIVIC 503
WD GQ++ R + ++Y+ G++ + D + + + + + E+ +++ I++
Sbjct: 62 WDVGGQDKIRPLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAV-ILVF 120
Query: 504 ANKVDLRADAQAKGVKCIDREVGEKLA----QQYGAIFMETSSKSGDNILDALIALS 556
ANK DL +A E+ EKL + T + SGD + + L LS
Sbjct: 121 ANKQDLPDAMKAA-------EITEKLGLHSIRDRNWYIQPTCATSGDGLYEGLTWLS 170
>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 = 48.2 bits (115), Expect = 1e-06
Identities = 20/78 (25%), Positives = 42/78 (53%), Gaps = 4/78 (5%)
Query: 440 NVALQLWDTAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEE---VTEN 496
N++ +D +GQ ++R + ++Y++ G++ + D ++ K+ +E + +
Sbjct: 44 NLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPDIKHR 103
Query: 497 SIPIVICANKVDLRADAQ 514
IPI+ ANK+DL DA
Sbjct: 104 RIPILFYANKMDLP-DAL 120
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 50.5 bits (121), Expect = 2e-06
Identities = 46/247 (18%), Positives = 93/247 (37%), Gaps = 32/247 (12%)
Query: 121 KKLADLYHELRTSSNCPEIVTHFEGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLK 180
+ LA L E+ E + AL L++++ E+ E+ + RE E +R +
Sbjct: 772 EALAKLKEEI-------EELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRE 824
Query: 181 GLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEK 240
LE+E+ + EE + E++ L ++E +EL+ ++ E
Sbjct: 825 RLEQEI---------EELEEEIEELEEKLDELEEELEELEKELEELKEELEE-----LEA 870
Query: 241 KIEKQQDPTSDHNFSFENEELKIT-LEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGD 299
+ E+ +D + E E ++ LE L ++ + E E K + L + +
Sbjct: 871 EKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERLEELEAKLERLEVELPE 930
Query: 300 YLELDQGSDKQFAIQRLMEDIDSGRSTMRDCMDCSSDYKSNNEENMSSLSEYDYNKRDYP 359
E + + L +I+ + N+ ++ EY+ + Y
Sbjct: 931 LEEELEEEYEDTLETELEREIERLEEEIEALGPV----------NLRAIEEYEEVEERYE 980
Query: 360 ELRRQHS 366
EL+ Q
Sbjct: 981 ELKSQRE 987
Score = 41.2 bits (97), Expect = 0.002
Identities = 42/228 (18%), Positives = 90/228 (39%), Gaps = 6/228 (2%)
Query: 144 EGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEE-ELDVQVAKVVTQAKEEAR 202
+ L +++ L + E+L E +E LE + +EE E ++ + + + E
Sbjct: 259 QEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENEL 318
Query: 203 AKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELK 262
+ E+ L K+E +EL+ L +++ +L E + K++ E EEL
Sbjct: 319 EELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELF 378
Query: 263 ITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDYLELDQGSDKQFAIQRLMEDIDS 322
E + L + AE+A++++E E +E+ L L + + + L E
Sbjct: 379 ---EALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDL--KEELKELEAE 433
Query: 323 GRSTMRDCMDCSSDYKSNNEENMSSLSEYDYNKRDYPELRRQHSNKSD 370
+ + + + + E+ +R+ EL+ +
Sbjct: 434 LEELQTELEELNEELEELEEQLEELRDRLKELERELAELQEELQRLEK 481
Score = 39.7 bits (93), Expect = 0.004
Identities = 51/233 (21%), Positives = 106/233 (45%), Gaps = 32/233 (13%)
Query: 146 ALSSLLDD---VKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAK--EE 200
L+++ V + E E+ E E +LERL+ L EEL+ Q+ K+ QA+ E
Sbjct: 156 ERRKLIEEAAGVSKYKERKEEAERKL-ERTEENLERLEDLLEELEKQLEKLERQAEKAER 214
Query: 201 ARAKYEQ----EKAILMRKMEHETQELQAHLNLFQKVNNVLKE-KKIEKQQDPTSDHNFS 255
+ + E A+L+ K++ +EL+ L ++++ + +E ++++++ +
Sbjct: 215 YQELKAELRELELALLLAKLKELRKELEE---LEEELSRLEEELEELQEELEEAEK---- 267
Query: 256 FENEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDYLELDQGSDKQFAIQR 315
E EELK LE+ + L+ + E+ +LK E E E++ L ++ + + ++
Sbjct: 268 -EIEELKSELEELREELEELQEELLELKEEIEELEGEISLLR------ERLEELENELEE 320
Query: 316 LMEDIDSGRSTMRDCMDCSSDYKSNNEENMSSLSEYDYNKRDYPELRRQHSNK 368
L E ++ + + K EE + L E + + E + + K
Sbjct: 321 LEERLEELKEKI-------EALKEELEERETLLEELEQLLAELEEAKEELEEK 366
Score = 38.2 bits (89), Expect = 0.013
Identities = 52/231 (22%), Positives = 96/231 (41%), Gaps = 26/231 (11%)
Query: 81 AGAMSSEGPERRNSDVQNAWSLLLAGIGEANVHKFLNTSGKKLADLYHELRTSSNCPEIV 140
+G+++ +R+S Q L + L +L L EL++ N +
Sbjct: 649 SGSITGGSRNKRSSLAQKRELKELE--------EELAELEAQLEKLEEELKSLKN---EL 697
Query: 141 THFEGALSSL---LDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEE----------LD 187
E L L L++++R E+ ++ E E RL+ LEEE L
Sbjct: 698 RSLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQ 757
Query: 188 VQVAKVVTQ--AKEEARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQ 245
++ ++ + + EEA AK ++E L K + +EL+ ++ L + E +
Sbjct: 758 ERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELE 817
Query: 246 QDPTSDHNFSFENEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQL 296
E EEL+ +E+ + LD + E+ +L+ E E +EL +L
Sbjct: 818 SLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEEL 868
Score = 35.1 bits (81), Expect = 0.14
Identities = 46/186 (24%), Positives = 80/186 (43%), Gaps = 9/186 (4%)
Query: 138 EIVTHFEGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQA 197
E + E L L + L E E+LEE + E E + L EEL
Sbjct: 337 EELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELA---------E 387
Query: 198 KEEARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFE 257
E A+ E L R++E + L+ + + LKE + E ++ T + E
Sbjct: 388 LEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELEELQTELEELNEE 447
Query: 258 NEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDYLELDQGSDKQFAIQRLM 317
EEL+ LE+ ++ L + E+A+L+ E + +EL+ L L+ ++ ++
Sbjct: 448 LEELEEQLEELRDRLKELERELAELQEELQRLEKELSSLEARLDRLEAEQRASQGVRAVL 507
Query: 318 EDIDSG 323
E ++SG
Sbjct: 508 EALESG 513
>gnl|CDD|206717 cd04150, Arf1_5_like, ADP-ribosylation factor-1 (Arf1) and
ADP-ribosylation factor-5 (Arf5). The Arf1-Arf5-like
subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and
related proteins. Arfs1-5 are soluble proteins that are
crucial for assembling coat proteins during vesicle
formation. Each contains an N-terminal myristoylated
amphipathic helix that is folded into the protein in the
GDP-bound state. GDP/GTP exchange exposes the helix,
which anchors to the membrane. Following GTP hydrolysis,
the helix dissociates from the membrane and folds back
into the protein. A general feature of Arf1-5 signaling
may be the cooperation of two Arfs at the same site.
Arfs1-5 are generally considered to be interchangeable
in function and location, but some specific functions
have been assigned. Arf1 localizes to the
early/cis-Golgi, where it is activated by GBF1 and
recruits the coat protein COPI. It also localizes to the
trans-Golgi network (TGN), where it is activated by
BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA
proteins. Humans, but not rodents and other lower
eukaryotes, lack Arf2. Human Arf3 shares 96% sequence
identity with Arf1 and is believed to generally function
interchangeably with Arf1. Human Arf4 in the activated
(GTP-bound) state has been shown to interact with the
cytoplasmic domain of epidermal growth factor receptor
(EGFR) and mediate the EGF-dependent activation of
phospholipase D2 (PLD2), leading to activation of the
activator protein 1 (AP-1) transcription factor. Arf4
has also been shown to recognize the C-terminal sorting
signal of rhodopsin and regulate its incorporation into
specialized post-Golgi rhodopsin transport carriers
(RTCs). There is some evidence that Arf5 functions at
the early-Golgi and the trans-Golgi to affect
Golgi-associated alpha-adaptin homology Arf-binding
proteins (GGAs).
Length = 159
Score = 47.4 bits (113), Expect = 3e-06
Identities = 35/147 (23%), Positives = 70/147 (47%), Gaps = 27/147 (18%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGS------TLGVDFQMKTIRVDERNVALQLWD 447
+I+ G A GK+ +Y+ KLG T+G F ++T V+ +N++ +WD
Sbjct: 2 RILMVGLDAAGKTTILYKL-------KLGEIVTTIPTIG--FNVET--VEYKNISFTVWD 50
Query: 448 TAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAV--EEVTENSIPIVICAN 505
GQ++ R + ++YF+ G++ + D + + ++ + E+ +++ +++ AN
Sbjct: 51 VGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERIGEAREELQRMLNEDELRDAV-LLVFAN 109
Query: 506 KVDLRADAQAKGVKCIDREVGEKLAQQ 532
K DL A EV +KL
Sbjct: 110 KQDLPNAMSA-------AEVTDKLGLH 129
>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 = 46.5 bits (111), Expect = 7e-06
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 440 NVALQLWDTAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAV---EEVTEN 496
NV +D G E+ R + K+YF DG++ L D + F K ++++ EE+
Sbjct: 62 NVKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDAADPERFQESKEELDSLLNDEELAN- 120
Query: 497 SIPIVICANKVDLR 510
+PI+I NK+D
Sbjct: 121 -VPILILGNKIDKP 133
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 47.9 bits (115), Expect = 1e-05
Identities = 27/123 (21%), Positives = 53/123 (43%), Gaps = 20/123 (16%)
Query: 146 ALSSLLDDVKRLHED-NEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEA--- 201
+LL + ++L E+ EK E++ E + L EE + + + + +AK+EA
Sbjct: 538 EAEALLKEAEKLKEELEEKKEKLQEEEDK--------LLEEAEKEAQQAIKEAKKEADEI 589
Query: 202 -RAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEE 260
+ + +K HE E + LN K N ++KK ++++ +E
Sbjct: 590 IKELRQLQKGGYASVKAHELIEARKRLN---KANEKKEKKKKKQKEKQEELK----VGDE 642
Query: 261 LKI 263
+K
Sbjct: 643 VKY 645
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 45.7 bits (108), Expect = 1e-05
Identities = 38/173 (21%), Positives = 83/173 (47%), Gaps = 15/173 (8%)
Query: 391 RAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTL-GVDFQMKTIRVDERNVALQLWDTA 449
+ +I+ G A GK+ +Y+ L ++ +T+ + F ++T V+ +N++ +WD
Sbjct: 16 KEMRILMVGLDAAGKTTILYKLK----LGEIVTTIPTIGFNVET--VEYKNISFTVWDVG 69
Query: 450 GQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSI---PIVICANK 506
GQ++ R + ++YF+ G++ + D + ++ E + E+ + +++ ANK
Sbjct: 70 GQDKIRPLWRHYFQNTQGLIFVVDSNDRDRVVEARD--ELHRMLNEDELRDAVLLVFANK 127
Query: 507 VDLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRHV 559
DL A I ++G +Q T + SG+ + + L LS ++
Sbjct: 128 QDL---PNAMNAAEITDKLGLHSLRQRHWYIQSTCATSGEGLYEGLDWLSNNI 177
>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 = 45.2 bits (108), Expect = 2e-05
Identities = 31/125 (24%), Positives = 49/125 (39%), Gaps = 31/125 (24%)
Query: 447 DTAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTE--------NSI 498
DT G F +ADG +L+ D VE V T +
Sbjct: 72 DTPGHVDFTKEMIRGASQADGAILVVDA------------VEGVMPQTREHLLLAKTLGV 119
Query: 499 PIVICANKVDLRADAQAKGVKCIDREVGEKLAQQYG-----AIFMETSSKSGDNI---LD 550
PI++ NK+D DA+ + V E+ +L ++YG + S+ +G+ I L+
Sbjct: 120 PIIVFINKIDRVDDAELEEVV---EEISRELLEKYGFGGETVPVVPGSALTGEGIDELLE 176
Query: 551 ALIAL 555
AL
Sbjct: 177 ALDLY 181
>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 = 44.6 bits (106), Expect = 3e-05
Identities = 33/126 (26%), Positives = 59/126 (46%), Gaps = 12/126 (9%)
Query: 389 PDRAFKIVFAGDAAVGKSCFIYRFS-KEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWD 447
P + +K++ G GK+ +Y+F EV T+G + + + +N+ +WD
Sbjct: 12 PRKEYKVIIVGLDNAGKTTILYQFLLGEVVHTS--PTIGSNVE----EIVYKNIRFLMWD 65
Query: 448 TAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVE---AVEEVTENSIPIVICA 504
GQE RS Y+ D V+L+ D T+ K + A E++ + +++ A
Sbjct: 66 IGGQESLRSSWNTYYTNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKA--VLLVLA 123
Query: 505 NKVDLR 510
NK DL+
Sbjct: 124 NKQDLK 129
>gnl|CDD|206716 cd04149, Arf6, ADP ribosylation factor 6 (Arf6). Arf6 subfamily.
Arf6 (ADP ribosylation factor 6) proteins localize to
the plasma membrane, where they perform a wide variety
of functions. In its active, GTP-bound form, Arf6 is
involved in cell spreading, Rac-induced formation of
plasma membrane ruffles, cell migration, wound healing,
and Fc-mediated phagocytosis. Arf6 appears to change the
actin structure at the plasma membrane by activating
Rac, a Rho family protein involved in membrane ruffling.
Arf6 is required for and enhances Rac formation of
ruffles. Arf6 can regulate dendritic branching in
hippocampal neurons, and in yeast it localizes to the
growing bud, where it plays a role in polarized growth
and bud site selection. In leukocytes, Arf6 is required
for chemokine-stimulated migration across endothelial
cells. Arf6 also plays a role in down-regulation of
beta2-adrenergic receptors and luteinizing hormone
receptors by facilitating the release of sequestered
arrestin to allow endocytosis. Arf6 is believed to
function at multiple sites on the plasma membrane
through interaction with a specific set of GEFs, GAPs,
and effectors. Arf6 has been implicated in breast cancer
and melanoma cell invasion, and in actin remodelling at
the invasion site of Chlamydia infection.
Length = 168
Score = 44.0 bits (104), Expect = 5e-05
Identities = 36/172 (20%), Positives = 83/172 (48%), Gaps = 13/172 (7%)
Query: 390 DRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTL-GVDFQMKTIRVDERNVALQLWDT 448
++ +I+ G A GK+ +Y+ L + +T+ V F ++T V +NV +WD
Sbjct: 7 NKEMRILMLGLDAAGKTTILYKLK----LGQSVTTIPTVGFNVET--VTYKNVKFNVWDV 60
Query: 449 AGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAV--EEVTENSIPIVICANK 506
GQ++ R + ++Y+ G++ + D + + + + + + +++ +++ ANK
Sbjct: 61 GGQDKIRPLWRHYYTGTQGLIFVVDSADRDRIDEARQELHRIINDREMRDAL-LLVFANK 119
Query: 507 VDLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRH 558
DL DA K + ++ ++ + + + + SGD + + L LS +
Sbjct: 120 QDL-PDAM-KPHEIQEKLGLTRIRDRNWYV-QPSCATSGDGLYEGLTWLSSN 168
>gnl|CDD|227455 COG5126, FRQ1, Ca2+-binding protein (EF-Hand superfamily) [Signal
transduction mechanisms / Cytoskeleton / Cell division
and chromosome partitioning / General function
prediction only].
Length = 160
Score = 40.4 bits (95), Expect = 6e-04
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 6 LEELFKTCDKKGTGQIGPEEFRELCT--GFDIQPTDSDAIFADLDHDGDGKVSLEDFA 61
L E FK DK G I E R + G + + + + + D DGDG++ E+F
Sbjct: 94 LREAFKLFDKDHDGYISIGELRRVLKSLGERLSDEEVEKLLKEYDEDGDGEIDYEEFK 151
>gnl|CDD|206723 cd04158, ARD1, (ADP-ribosylation factor domain protein 1 (ARD1).
ARD1 (ADP-ribosylation factor domain protein 1) is an
unusual member of the Arf family. In addition to the
C-terminal Arf domain, ARD1 has an additional 46-kDa
N-terminal domain that contains a RING finger domain,
two predicted B-Boxes, and a coiled-coil protein
interaction motif. This domain belongs to the TRIM
(tripartite motif) or RBCC (RING, B-Box, coiled-coil)
family. Like most Arfs, the ARD1 Arf domain lacks
detectable GTPase activity. However, unlike most Arfs,
the full-length ARD1 protein has significant GTPase
activity due to the GAP (GTPase-activating protein)
activity exhibited by the 46-kDa N-terminal domain. The
GAP domain of ARD1 is specific for its own Arf domain
and does not bind other Arfs. The rate of GDP
dissociation from the ARD1 Arf domain is slowed by the
adjacent 15 amino acids, which act as a GDI
(GDP-dissociation inhibitor) domain. ARD1 is
ubiquitously expressed in cells and localizes to the
Golgi and to the lysosomal membrane. Two Tyr-based
motifs in the Arf domain are responsible for Golgi
localization, while the GAP domain controls lysosomal
localization.
Length = 169
Score = 40.0 bits (93), Expect = 8e-04
Identities = 27/119 (22%), Positives = 61/119 (51%), Gaps = 10/119 (8%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQER 453
++V G GK+ +++ ++ F+ + T+G F ++T V+ +N+ +WD G+ +
Sbjct: 1 RVVTLGLDGAGKTTILFKLKQDEFMQPI-PTIG--FNVET--VEYKNLKFTIWDVGGKHK 55
Query: 454 FRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIP---IVICANKVDL 509
R + K+Y+ V+ + D ++ + + E + +TE + ++I ANK D+
Sbjct: 56 LRPLWKHYYLNTQAVVFVIDSSHRDRVSEAHS--ELAKLLTEKELRDALLLIFANKQDV 112
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 42.1 bits (99), Expect = 8e-04
Identities = 39/225 (17%), Positives = 85/225 (37%), Gaps = 26/225 (11%)
Query: 155 KRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMR 214
++L + LEE+ + ++ L++LK +L K E+ L+R
Sbjct: 533 EKLEKLENLLEELEELKEKLQLQQLKEELRQL----------EDRLQELKELLEELRLLR 582
Query: 215 KMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENE---------ELKITL 265
+ E +EL+ L +K L+E+ + ++ S ENE L
Sbjct: 583 TRKEELEELRERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEAEEELESELEKL 642
Query: 266 EKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDYLELDQGSDKQFAIQRLMEDIDSGRS 325
+L+ A + +L+ + E E+ + + +Q +K +++L E+++ R
Sbjct: 643 NLQAELEELLQAALEELEEKVEELEAEIRRELQRIENEEQLEEKLEELEQLEEELEQLRE 702
Query: 326 TMRDCMDCSSDYKSNNEENMSSLSEYDYNKRDYPELRRQHSNKSD 370
+ + E + E + K + EL+++
Sbjct: 703 EL-------EELLKKLGEIEQLIEELESRKAELEELKKELEKLEK 740
Score = 35.9 bits (83), Expect = 0.074
Identities = 34/154 (22%), Positives = 61/154 (39%), Gaps = 5/154 (3%)
Query: 143 FEGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEAR 202
+E L + +K E+LE + E + L+ LEEEL Q ++E
Sbjct: 169 YEKLSELLKEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQEEE 228
Query: 203 AKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELK 262
++ +A+ E EL+ +++ L E + + + E E L
Sbjct: 229 ELEQEIEAL-----EERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELERLL 283
Query: 263 ITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQL 296
LE+ L+ + E+ +L+ E EG L +L
Sbjct: 284 EELEEKIERLEELEREIEELEEELEGLRALLEEL 317
Score = 31.3 bits (71), Expect = 1.9
Identities = 44/263 (16%), Positives = 97/263 (36%), Gaps = 35/263 (13%)
Query: 143 FEGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAK---- 198
E L L + +++L + E+L E N ++ ERLK LEE L+ ++ +
Sbjct: 327 LEERLEKLEEKLEKLESELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERLKQ 386
Query: 199 -EEARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKK---------------- 241
EEA + ++E A L +E +EL+ +++ L+E +
Sbjct: 387 LEEAIQELKEELAELSAALEEIQEELEELEKELEELERELEELEEEIKKLEEQINQLESK 446
Query: 242 ------IEKQQDPTSDHNFSFENEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQ 295
+ + E K LE + L+ + E+++ K E E + +E+ +
Sbjct: 447 ELMIAELAGAGEKCPVCGQELPEEHEKELLELYELELEELEEELSREKEEAELR-EEIEE 505
Query: 296 LVGDYLELDQGSDKQFAIQRLMEDIDSGRSTMRDCMDCSSDYKSNNEENMSS-----LSE 350
L + EL++ + ++ + + + + + E+ L +
Sbjct: 506 LEKELRELEEELIEL--LELEEALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQ 563
Query: 351 YDYNKRDYPELRRQHSNKSDSQS 373
+ ++ EL + +
Sbjct: 564 LEDRLQELKELLEELRLLRTRKE 586
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 42.0 bits (99), Expect = 0.001
Identities = 41/199 (20%), Positives = 79/199 (39%), Gaps = 20/199 (10%)
Query: 144 EGALSSLLDDVKRLH---EDNEKLEEMFNREREVHLE----RLKGLEEELD---VQVAKV 193
E L+ L +K L E E+ +E+ RE+ L RL+ L EEL+ ++ +
Sbjct: 192 EDILNELERQLKSLERQAEKAERYKELKAELRELELALLVLRLEELREELEELQEELKEA 251
Query: 194 VTQAKEEARAKYEQEKAI---------LMRKMEHETQELQAHLNLFQKVNNVLKEKKIEK 244
+ +E E E+ + L ++E +EL A N ++ + +
Sbjct: 252 EEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERL 311
Query: 245 QQDPTSDHNFSFENEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDYLELD 304
+ EEL+ L++ L + ++ +LK E E EL +L + EL+
Sbjct: 312 ANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELE 371
Query: 305 QGSDKQF-AIQRLMEDIDS 322
++ ++ L +
Sbjct: 372 SRLEELEEQLETLRSKVAQ 390
Score = 38.1 bits (89), Expect = 0.017
Identities = 40/182 (21%), Positives = 79/182 (43%), Gaps = 10/182 (5%)
Query: 147 LSSLLDDVKRLHEDNEKLEEMFNR---EREVHLERLKGLEEELDVQVAKV--VTQAKEEA 201
L+ L+ ++ L E+ E+L+E E E L+ LEE+L+ +V + + EE
Sbjct: 227 LALLVLRLEELREELEELQEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEEL 286
Query: 202 RAKYEQEKAILMRKMEHETQELQAHL----NLFQKVNNVLKEKKIEKQQDPTSDHNFSFE 257
+ + A + ++E + Q L+ L +++ L+E + + + +
Sbjct: 287 QKEL-YALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEK 345
Query: 258 NEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDYLELDQGSDKQFAIQRLM 317
EELK LE + L+ + AE+ +L+S E ++L L +L+ +
Sbjct: 346 LEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERL 405
Query: 318 ED 319
E
Sbjct: 406 EA 407
Score = 37.7 bits (88), Expect = 0.018
Identities = 39/179 (21%), Positives = 75/179 (41%), Gaps = 15/179 (8%)
Query: 146 ALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKY 205
L+ L + ++ L E+ E LE LE L+ EEL+ Q+ + +
Sbjct: 338 ELAELEEKLEELKEELESLEAELEELEAE-LEELESRLEELEEQL----ETLRSKVAQLE 392
Query: 206 EQEKAIL--MRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKI 263
Q ++ + ++E + L+ Q+ L +K E + E EEL+
Sbjct: 393 LQIASLNNEIERLEARLERLEDRRERLQQEIEELLKKLEEAELKELQA-----ELEELEE 447
Query: 264 TLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDYLELDQGSDKQFAIQRLMEDIDS 322
LE+ + L+ + + +L+ E E Q L+ EL Q + +++RL E+++
Sbjct: 448 ELEELQEELERLEEALEELREELEEAEQALDAAER---ELAQLQARLDSLERLQENLEG 503
Score = 32.7 bits (75), Expect = 0.60
Identities = 44/191 (23%), Positives = 76/191 (39%), Gaps = 9/191 (4%)
Query: 124 ADLYHELRTSSNCPEIVTHFEGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLE 183
DL E + L+ L +++ L E E+ EE E E +E L+
Sbjct: 733 KDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEEL-AEAEAEIEELEAQI 791
Query: 184 EELDVQVAKVVTQAKEEARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIE 243
E+L + K + +A +E RA+ + + L+ + ++ L+E+ E
Sbjct: 792 EQLKEE-LKALREALDELRAELTLLN-EEAANLRERLESLERRIAATERRLEDLEEQIEE 849
Query: 244 KQQDPTSDHNFSFEN-----EELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVG 298
+D S E EEL+ LE N + +A L+SE E +EL +L
Sbjct: 850 LSEDIES-LAAEIEELEELIEELESELEALLNERASLEEALALLRSELEELSEELRELES 908
Query: 299 DYLELDQGSDK 309
EL + ++
Sbjct: 909 KRSELRRELEE 919
Score = 32.0 bits (73), Expect = 1.3
Identities = 33/150 (22%), Positives = 67/150 (44%), Gaps = 23/150 (15%)
Query: 154 VKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILM 213
+ + E ++ E R RE +L+RL+ + EL+ Q+ + QA EKA
Sbjct: 167 ISKYKERRKETERKLERTRE-NLDRLEDILNELERQLKSLERQA----------EKAERY 215
Query: 214 RKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNLD 273
++++ E +EL+ L + L+E + E ++ E +E + LE+ L
Sbjct: 216 KELKAELRELELALLV-----LRLEELREELEE-------LQEELKEAEEELEELTAELQ 263
Query: 274 LVHAEMAQLKSEYEGKCQELNQLVGDYLEL 303
+ ++ +L+ E +E+ +L + L
Sbjct: 264 ELEEKLEELRLEVSELEEEIEELQKELYAL 293
Score = 30.4 bits (69), Expect = 3.5
Identities = 34/196 (17%), Positives = 82/196 (41%), Gaps = 20/196 (10%)
Query: 167 MFNREREVHLERLKGLEEELDVQVA--KVVTQAKEEARAKYEQEKAILMRKMEHETQELQ 224
+ R RE +E L+ EEL+ ++A + + + E+E L +++E ++++
Sbjct: 672 ILERRRE--IEELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQIS 729
Query: 225 AHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNLDLVHAE--MAQL 282
A ++ + +++E++ S E E ++ + +L AE + +L
Sbjct: 730 ALRKDLARLEA--EVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEEL 787
Query: 283 KSEYEGKCQELNQLVGDYLEL--------DQGSDKQFAIQRLMEDIDSGRSTMRDCMDCS 334
+++ E +EL L EL ++ ++ + ++ L I + + D
Sbjct: 788 EAQIEQLKEELKALREALDELRAELTLLNEEAANLRERLESLERRIAATERRLED----L 843
Query: 335 SDYKSNNEENMSSLSE 350
+ E++ SL+
Sbjct: 844 EEQIEELSEDIESLAA 859
Score = 29.6 bits (67), Expect = 6.2
Identities = 19/134 (14%), Positives = 55/134 (41%), Gaps = 1/134 (0%)
Query: 194 VTQAKEEARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHN 253
+ + E++ L K+ + L +++ L++ + E ++
Sbjct: 671 SILERRREIEELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISA 730
Query: 254 FSFENEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDYLELDQGSDKQFA- 312
+ L+ +E+ + + + E+ +L++E E + L + + E + ++ A
Sbjct: 731 LRKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQ 790
Query: 313 IQRLMEDIDSGRST 326
I++L E++ + R
Sbjct: 791 IEQLKEELKALREA 804
>gnl|CDD|222407 pfam13833, EF_hand_6, EF-hand domain pair.
Length = 53
Score = 36.7 bits (86), Expect = 0.001
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 17 GTGQIGPEEFRELCTGFDIQPTDS--DAIFADLDHDGDGKVSLEDF 60
G I EE + I ++ D +F + D DGDGK+S E+F
Sbjct: 1 EKGLITREELKRALALLGISLSEEEVDILFREFDTDGDGKISFEEF 46
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2-like protein 1 (Arl2l1) and Arl13.
Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily
of the Arf family of small GTPases. Arl2l1 was
identified in human cells during a search for the
gene(s) responsible for Bardet-Biedl syndrome (BBS).
Like Arl6, the identified BBS gene, Arl2l1 is proposed
to have cilia-specific functions. Arl13 is found on the
X chromosome, but its expression has not been confirmed;
it may be a pseudogene.
Length = 167
Score = 39.3 bits (92), Expect = 0.002
Identities = 30/116 (25%), Positives = 54/116 (46%), Gaps = 7/116 (6%)
Query: 395 IVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQERF 454
+ D A GK+ + E+ K+ T+G F +R+D+ V + +D G F
Sbjct: 3 LTVGLDNA-GKTTLVSALQGEIPK-KVAPTVG--FTPTKLRLDKYEVCI--FDLGGGANF 56
Query: 455 RSMTKNYFRRADGVMLLYDVTNERSFNSVKN-WVEAVEEVTENSIPIVICANKVDL 509
R + NY+ A G++ + D +++ VK E ++ + PI++ ANK D
Sbjct: 57 RGIWVNYYAEAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDK 112
>gnl|CDD|206718 cd04151, Arl1, ADP ribosylation factor 1 (Arf1). Arl1 subfamily.
Arl1 (Arf-like 1) localizes to the Golgi complex, where
it is believed to recruit effector proteins to the
trans-Golgi network. Like most members of the Arf
family, Arl1 is myristoylated at its N-terminal helix
and mutation of the myristoylation site disrupts Golgi
targeting. In humans, the Golgi-localized proteins
golgin-97 and golgin-245 have been identified as Arl1
effectors. Golgins are large coiled-coil proteins found
in the Golgi, and these golgins contain a C-terminal
GRIP domain, which is the site of Arl1 binding.
Additional Arl1 effectors include the GARP
(Golgi-associated retrograde protein)/VFT (Vps53)
vesicle-tethering complex and Arfaptin 2. Arl1 is not
required for exocytosis, but appears necessary for
trafficking from the endosomes to the Golgi. In
Drosophila zygotes, mutation of Arl1 is lethal, and in
the host-bloodstream form of Trypanosoma brucei, Arl1 is
essential for viability.
Length = 158
Score = 38.9 bits (91), Expect = 0.002
Identities = 29/118 (24%), Positives = 56/118 (47%), Gaps = 8/118 (6%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTL-GVDFQMKTIRVDERNVALQLWDTAGQE 452
+I+ G GK+ +YR + ++ +T+ + F ++T V +N+ Q+WD GQ
Sbjct: 1 RILILGLDGAGKTTILYRLQ----VGEVVTTIPTIGFNVET--VTYKNLKFQVWDLGGQT 54
Query: 453 RFRSMTKNYFRRADGVMLLYDVTN-ERSFNSVKNWVEAVEEVTENSIPIVICANKVDL 509
R + Y+ D ++ + D T+ +R S +EE +++ ANK D+
Sbjct: 55 SIRPYWRCYYSNTDAIIYVVDSTDRDRLGISKSELHAMLEEEELKDAVLLVFANKQDM 112
>gnl|CDD|197556 smart00178, SAR, Sar1p-like members of the Ras-family of small
GTPases. Yeast SAR1 is an essential gene required for
transport of secretory proteins from the endoplasmic
reticulum to the Golgi apparatus.
Length = 184
Score = 39.1 bits (91), Expect = 0.003
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 440 NVALQLWDTAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTE-NSI 498
N+ +D G ++ R + K+YF +G++ L D ++ F K ++A+ E ++
Sbjct: 60 NIKFTTFDLGGHQQARRLWKDYFPEVNGIVYLVDAYDKERFAESKRELDALLSDEELATV 119
Query: 499 PIVICANKVD 508
P +I NK+D
Sbjct: 120 PFLILGNKID 129
>gnl|CDD|183426 PRK12309, PRK12309, transaldolase/EF-hand domain-containing
protein; Provisional.
Length = 391
Score = 39.7 bits (93), Expect = 0.004
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 11/58 (18%)
Query: 7 EELFKTCDKKGTGQIGPEEFRELCTGFDIQPTDSDAIFADLDHDGDGKVSLEDFAYGF 64
+E+F+ D G G I EE SDA+F LD + DGK++ E+ G
Sbjct: 337 QEIFRLYDLDGDGFITREE-----------WLGSDAVFDALDLNHDGKITPEEMRAGL 383
>gnl|CDD|227512 COG5185, HEC1, Protein involved in chromosome segregation,
interacts with SMC proteins [Cell division and
chromosome partitioning].
Length = 622
Score = 39.6 bits (92), Expect = 0.004
Identities = 31/164 (18%), Positives = 62/164 (37%), Gaps = 2/164 (1%)
Query: 138 EIVTHFEGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQA 197
E+ FE + + D+ L N+ L E ++ + E+ ++ +
Sbjct: 257 ELKLGFEKFVHIINTDIANLKTQNDNLYEKIQEAMKISQKIKTLREKWRALKSDSNKYEN 316
Query: 198 KEEARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSD-HNFSF 256
A + QE + K++ E + + + Q + L K++ KQ T +
Sbjct: 317 YVNAMKQKSQEWPGKLEKLKSEIELKEEEIKALQSNIDELH-KQLRKQGISTEQFELMNQ 375
Query: 257 ENEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDY 300
E E+L L+K D + + K E +G + L + + Y
Sbjct: 376 EREKLTRELDKINIQSDKLTKSVKSRKLEAQGIFKSLEKTLRQY 419
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 39.6 bits (93), Expect = 0.004
Identities = 34/133 (25%), Positives = 64/133 (48%), Gaps = 7/133 (5%)
Query: 121 KKLADLYHELRTSSNCPEIVTHFEGALSSLLDDVKRLHED----NEKLEEMFNRE-REVH 175
++L ++++L S + E ++S +++ +L + + EE R +E
Sbjct: 139 QELVSIFNDLIDSIKEDNLKDDLESLIASAKEELDQLSKKLAELKAEEEEELERALKEKR 198
Query: 176 LERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRKMEHE-TQELQAHLNLF-QKV 233
E L LEEEL ++ +++ R ++E+EK L +K E + QEL+ QK+
Sbjct: 199 EELLSKLEEELLARLESKEAALEKQLRLEFEREKEELRKKYEEKLRQELERQAEAHEQKL 258
Query: 234 NNVLKEKKIEKQQ 246
N L + IE Q+
Sbjct: 259 KNELALQAIELQR 271
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 39.7 bits (93), Expect = 0.005
Identities = 50/244 (20%), Positives = 89/244 (36%), Gaps = 41/244 (16%)
Query: 146 ALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDV-------------QVAK 192
LS L D R + EK E +E E ERL+ LEE+L ++
Sbjct: 706 ELSQELSDASRKIGEIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEA 765
Query: 193 VVTQAKEEARAKYEQEKAILMRKMEHE-TQELQAHLNLFQK-----------VNNVLKEK 240
+ + EE K E+ L ++ H E+QA L+ ++ + L
Sbjct: 766 RI-EELEEDLHKLEEALNDLEARLSHSRIPEIQAELSKLEEEVSRIEARLREIEQKLNRL 824
Query: 241 KIEKQQDPTSDHNFSFENEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDY 300
+EK+ + +LK ++ + ++ ++ + +L+ E E L L
Sbjct: 825 TLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALRDLESRL 884
Query: 301 LELD--------QGSDKQFAIQRLMEDIDSGRSTMRDCMDCSSDYKSNNEENMSSLSEYD 352
+L Q + + I+ L I+ R + S+ K+ E LSE +
Sbjct: 885 GDLKKERDELEAQLRELERKIEELEAQIEKKRKRL-------SELKAKLEALEEELSEIE 937
Query: 353 YNKR 356
K
Sbjct: 938 DPKG 941
Score = 35.4 bits (82), Expect = 0.11
Identities = 40/210 (19%), Positives = 83/210 (39%), Gaps = 24/210 (11%)
Query: 144 EGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARA 203
E +++ +++ E KLE E + L ++ LE E++ + K + EE
Sbjct: 307 ERSIAEKERELEDAEERLAKLEA----EIDKLLAEIEELEREIE-EERKRRDKLTEEYAE 361
Query: 204 KYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKI 263
++E L ++E +E ++ + +K+EK + E ELK
Sbjct: 362 L-KEELEDLRAELEEVDKEFAE---TRDELKDY--REKLEKLKR---------EINELKR 406
Query: 264 TLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDYLELDQGSDKQ-FAIQRLMEDIDS 322
L++ + L + E+A L + G ++N+L + + KQ + +++L D+
Sbjct: 407 ELDRLQEELQRLSEELADLNAAIAGIEAKINELEEEKEDKALEIKKQEWKLEQLAADLSK 466
Query: 323 GRSTMRDCMDCSSDYKSNNEENMSSLSEYD 352
+ D +Y +E E
Sbjct: 467 YEQELY---DLKEEYDRVEKELSKLQRELA 493
Score = 33.1 bits (76), Expect = 0.54
Identities = 36/203 (17%), Positives = 83/203 (40%), Gaps = 32/203 (15%)
Query: 168 FNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRKMEHETQELQAHL 227
F+R++E LE L+ +EE ++ + + ++ R + E+EKA + + E +E + +
Sbjct: 168 FDRKKEKALEELEEVEENIERLDLIIDEKRQQLERLRREREKAERYQALLKEKREYEGYE 227
Query: 228 NLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNLDLVHAEMAQLKSEYE 287
L +K + +E+Q E + L + E+ +L E
Sbjct: 228 LLKEK-------EALERQ-------------------KEAIERQLASLEEELEKLTEEIS 261
Query: 288 GKCQELNQLVGDYLEL-----DQGSDKQFAIQRLMEDIDSGRSTMRDCMD-CSSDYKSNN 341
+ L ++ EL D G ++Q ++ + ++++ +++ + + +
Sbjct: 262 ELEKRLEEIEQLLEELNKKIKDLGEEEQLRVKEKIGELEAEIASLERSIAEKERELEDAE 321
Query: 342 EENMSSLSEYDYNKRDYPELRRQ 364
E +E D + EL R+
Sbjct: 322 ERLAKLEAEIDKLLAEIEELERE 344
Score = 31.2 bits (71), Expect = 2.2
Identities = 28/150 (18%), Positives = 56/150 (37%), Gaps = 9/150 (6%)
Query: 159 EDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRKMEH 218
E E+ +E R+ E L+ L EE+ ++ EE E+ + E
Sbjct: 233 EALERQKEAIERQLASLEEELEKLTEEISELEKRL-----EEIEQLLEELNKKIKDLGEE 287
Query: 219 ETQELQAHLNLFQ----KVNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNLDL 274
E ++ + + + + EK+ E + E ++L +E+ + ++
Sbjct: 288 EQLRVKEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEE 347
Query: 275 VHAEMAQLKSEYEGKCQELNQLVGDYLELD 304
+L EY +EL L + E+D
Sbjct: 348 ERKRRDKLTEEYAELKEELEDLRAELEEVD 377
>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 = 37.9 bits (88), Expect = 0.006
Identities = 33/134 (24%), Positives = 54/134 (40%), Gaps = 21/134 (15%)
Query: 393 FKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWD----- 447
++ G VGK+ + +F + F + T + + R L + D
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQ 60
Query: 448 ----TAGQE----RFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVT---EN 496
TAGQE RFR + R + +L+YD+ + SF+ VK + + E
Sbjct: 61 RYPGTAGQEWMDPRFRGL-----RNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNK 115
Query: 497 SIPIVICANKVDLR 510
PIV+ NK D +
Sbjct: 116 EPPIVVVGNKRDQQ 129
>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein. Function of MutS2 is
unknown. It should not be considered a DNA mismatch
repair protein. It is likely a DNA mismatch binding
protein of unknown cellular function [DNA metabolism,
Other].
Length = 771
Score = 38.6 bits (90), Expect = 0.008
Identities = 23/112 (20%), Positives = 45/112 (40%), Gaps = 15/112 (13%)
Query: 146 ALSSLLDDVKRLHEDNEKLEEM----------FNREREVHLERLKGLEEELDVQVAKVVT 195
+ L K L + NE LE++ +E E ER + + EL+ + + +
Sbjct: 516 LIEKLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNKKLELEKEAQEALK 575
Query: 196 QAKEEARAKYEQEKAILMRKMEHETQELQAHLNLFQ-KVNNVLKEKKIEKQQ 246
K+E + + L K H+ +E+++ +L + K +K Q
Sbjct: 576 ALKKEVESIIRE----LKEKKIHKAKEIKSIEDLVKLKETKQKIPQKPTNFQ 623
Score = 29.4 bits (66), Expect = 6.2
Identities = 19/121 (15%), Positives = 44/121 (36%), Gaps = 9/121 (7%)
Query: 177 ERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNV 236
+EE++V + K+ + EQ+ L + ++ + + + +++
Sbjct: 504 TFYGEFKEEINVLIEKL-----SALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKER 558
Query: 237 LKEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQL 296
+ KK+E +++ + E I K K +H E K +E Q
Sbjct: 559 ERNKKLELEKEAQEALKALKKEVESIIRELKEKK----IHKAKEIKSIEDLVKLKETKQK 614
Query: 297 V 297
+
Sbjct: 615 I 615
>gnl|CDD|218636 pfam05557, MAD, Mitotic checkpoint protein. This family consists
of several eukaryotic mitotic checkpoint (Mitotic arrest
deficient or MAD) proteins. The mitotic spindle
checkpoint monitors proper attachment of the bipolar
spindle to the kinetochores of aligned sister chromatids
and causes a cell cycle arrest in prometaphase when
failures occur. Multiple components of the mitotic
spindle checkpoint have been identified in yeast and
higher eukaryotes. In S.cerevisiae, the existence of a
Mad1-dependent complex containing Mad2, Mad3, Bub3 and
Cdc20 has been demonstrated.
Length = 722
Score = 38.8 bits (90), Expect = 0.009
Identities = 35/153 (22%), Positives = 63/153 (41%), Gaps = 12/153 (7%)
Query: 155 KRLHEDNEKLEEM---FNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAI 211
+ L +L+ +ER+ L ++EL + E Q+
Sbjct: 395 EALKALVRRLQRRLTLVTKERDGLRAILNSYDKELTETSVSGQLMKRLEEAEDLVQKVQS 454
Query: 212 LMRKMEHETQELQAHLNLFQKVNNVL-KEKKIEKQQDPTSDHNFSFENEE---LKITLEK 267
+ KME++ EL+ + + NN L E K+ K+Q +++ SF E L++ +E
Sbjct: 455 HLAKMENQLSELEEDVGQQKDRNNTLETEIKLLKEQLVSNERLLSFVKEATNALRLKIET 514
Query: 268 TKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDY 300
+ D + E + L+ + E C L GDY
Sbjct: 515 LERERDRLRQEKSLLEMKLEHLC-----LQGDY 542
Score = 29.1 bits (65), Expect = 8.1
Identities = 34/186 (18%), Positives = 71/186 (38%), Gaps = 15/186 (8%)
Query: 146 ALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAK-----VVTQAKEE 200
L + +L + + E R + + L E + ++ + V +A EE
Sbjct: 62 ELIRSKSKLIQLENELMQKELEHKRAQIELERKASTLAENYERELDRNLELEVRLKALEE 121
Query: 201 ARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEE 260
K E E + E E + L+ L+ KE ++++ ++ S + E
Sbjct: 122 LEKKAENE----AAEAEEEAKLLKDKLDAESLKLQNEKEDQLKEAKESIS--RIKNDLSE 175
Query: 261 LKITLEKTKNNLDLVHAEMAQLKSEYEGKCQEL----NQLVGDYLELDQGSDKQFAIQRL 316
++ + L L+ +E+ +L+ + E +EL +L E +D I+ L
Sbjct: 176 MQCRAQNADTELKLLESELEELREQLEECQKELAEAEKKLQSLTSEQASSADNSVKIKHL 235
Query: 317 MEDIDS 322
E++
Sbjct: 236 EEELKR 241
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 36.0 bits (84), Expect = 0.027
Identities = 47/196 (23%), Positives = 76/196 (38%), Gaps = 46/196 (23%)
Query: 387 GEPDRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLW 446
PDR +IVF G + VGKS + + + ++G GV K D + L
Sbjct: 4 TRPDRKPEIVFVGRSNVGKSTLVRELTGKKV--RVGKRPGVTR--KPNHYDWGD--FILT 57
Query: 447 DTAG-----------QERFRSMTKNYFRR-ADGVMLLYDVTNERSF-NSVKNW------- 486
D G QE+ + Y AD ++ V + +SF ++ W
Sbjct: 58 DLPGFGFMSGVPKEVQEKIKDEIVRYIEDNADRILAAVLVVDGKSFIEIIERWEGRGEIP 117
Query: 487 --VEAVEEVTENSIPIVICANKVDLRADAQAKGVKCIDR---EVGEKLA-----QQYGAI 536
VE + + E IP ++ NK+D +K D E+ E+L +Q+ I
Sbjct: 118 IDVEMFDFLRELGIPPIVAVNKMD--------KIKNRDEVLDEIAERLGLYPPWRQWQDI 169
Query: 537 FMETSSKSGDNILDAL 552
S+K G ++ L
Sbjct: 170 IAPISAKKGG--IEEL 183
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 36.8 bits (86), Expect = 0.030
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 15/78 (19%)
Query: 149 SLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKE----EARAK 204
L + K L E E+LEE+ +RE LER+ GL +E +AKE E +
Sbjct: 112 ELSNKEKNLDEKEEELEELIAEQRE-ELERISGLTQE----------EAKEILLEEVEEE 160
Query: 205 YEQEKAILMRKMEHETQE 222
E A L++++E E +E
Sbjct: 161 ARHEAAKLIKEIEEEAKE 178
>gnl|CDD|185503 PTZ00183, PTZ00183, centrin; Provisional.
Length = 158
Score = 35.4 bits (82), Expect = 0.031
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 4 LQLEELFKTCDKKGTGQIGPEEF----RELCTGFDIQPTDSDAIFADLDHDGDGKVSLED 59
++ E F D G+G I P+E R L GF+ + + + AD+D DG GK+ E+
Sbjct: 17 KEIREAFDLFDTDGSGTIDPKELKVAMRSL--GFEPKKEEIKQMIADVDKDGSGKIDFEE 74
Query: 60 F 60
F
Sbjct: 75 F 75
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 36.7 bits (86), Expect = 0.032
Identities = 34/132 (25%), Positives = 62/132 (46%), Gaps = 28/132 (21%)
Query: 178 RLKGLEEELDVQVAKVVTQAKEEA-----RAKYEQEKAILMRKMEHETQELQAHLNLFQK 232
++K EEE +++ +AK+EA A E ++ I + E E +EL+ N QK
Sbjct: 32 KIKEAEEEAK----RILEEAKKEAEAIKKEALLEAKEEIHKLRNEFE-KELRERRNELQK 86
Query: 233 VNNVL--KEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNLDLVHAEMAQLKSEYEGKC 290
+ L KE+ ++++ + LEK + L+ E+ Q + E E K
Sbjct: 87 LEKRLLQKEENLDRKLE----------------LLEKREEELEKKEKELEQKQQELEKKE 130
Query: 291 QELNQLVGDYLE 302
+EL +L+ + L+
Sbjct: 131 EELEELIEEQLQ 142
Score = 34.4 bits (80), Expect = 0.20
Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 18/89 (20%)
Query: 138 EIVTHFEGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQA 197
E + E L ++++ E+ E+L E E+ LER+ GL E +A
Sbjct: 110 EELEKKEKELEQKQQELEKKEEELEELIE----EQLQELERISGLTAE----------EA 155
Query: 198 K----EEARAKYEQEKAILMRKMEHETQE 222
K E+ + E A+L++++E E +E
Sbjct: 156 KEILLEKVEEEARHEAAVLIKEIEEEAKE 184
Score = 31.3 bits (72), Expect = 1.6
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 11/77 (14%)
Query: 161 NEKLEEMFNREREV--HLERLKGLEEELDVQVAKVVTQAKEEARAKYE--------QEKA 210
+ KLE + RE E+ + L+ ++EL+ + + + + EE + E + K
Sbjct: 99 DRKLELLEKREEELEKKEKELEQKQQELEKK-EEELEELIEEQLQELERISGLTAEEAKE 157
Query: 211 ILMRKMEHETQELQAHL 227
IL+ K+E E + A L
Sbjct: 158 ILLEKVEEEARHEAAVL 174
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 35.3 bits (82), Expect = 0.039
Identities = 29/120 (24%), Positives = 52/120 (43%), Gaps = 16/120 (13%)
Query: 447 DTAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANK 506
DT G E F T +ADG +L+ D + ++ A+ +PI++ NK
Sbjct: 68 DTPGHEDFSKETVRGLAQADGALLVVDANEGVEPQTREHLNIALAGG----LPIIVAVNK 123
Query: 507 VDLRADAQAKGVKCIDREVGEKLAQQYGAIFME--------TSSKSGDNILDALIALSRH 558
+D + V RE+ ++L + G F++ S+ +G+ I + L A+ H
Sbjct: 124 IDRVGEEDFDEVL---REI-KELLKLIGFTFLKGKDVPIIPISALTGEGIEELLDAIVEH 179
>gnl|CDD|185504 PTZ00184, PTZ00184, calmodulin; Provisional.
Length = 149
Score = 34.7 bits (80), Expect = 0.046
Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 2 SDLQLEELFKTCDKKGTGQIGPEEFRELCTGFDIQPTDS--DAIFADLDHDGDGKVSLED 59
S+ +++E FK D+ G G I E R + T + TD D + + D DGDG+++ E+
Sbjct: 82 SEEEIKEAFKVFDRDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADVDGDGQINYEE 141
Query: 60 F 60
F
Sbjct: 142 F 142
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. All proteins in this family for
which functions are known are part of an exonuclease
complex with sbcD homologs. This complex is involved in
the initiation of recombination to regulate the levels
of palindromic sequences in DNA. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1042
Score = 36.5 bits (84), Expect = 0.048
Identities = 43/217 (19%), Positives = 86/217 (39%), Gaps = 19/217 (8%)
Query: 122 KLADLYHELRTSSNCPEIVTHFEGALSSLLDDVKRLHEDNEKLEEM-------FNREREV 174
L + E + E++ + L L ++ + ++E +
Sbjct: 681 ALQKMQSEKEQLTYWKEMLAQCQTLLRELETHIEEYDREFNEIENASSSLGSDLAAREDA 740
Query: 175 HLERLKGLEEELDVQVAKVVTQAKEEARA-KYEQEKAILMR--KMEHETQELQAHLNLFQ 231
+ LK L + A+ V +A+ EA E+ A L ++ H E+Q L +
Sbjct: 741 LNQSLKELMHQ-----ARTVLKARTEAHFNNNEEVTAALQTGAELSHLAAEIQFFNRLRE 795
Query: 232 KVNNVLKEKKIEKQQDPTSDHN-FSFENEELKITLEKTKNNLDLVHAEMAQLKS---EYE 287
+ ++LK + E Q+ SD + + + E L E+ + L+ A + ++ +YE
Sbjct: 796 EDTHLLKTLEAEIGQEIPSDEDILNLQCETLVQEEEQFLSRLEEKSATLGEITHQLLKYE 855
Query: 288 GKCQELNQLVGDYLELDQGSDKQFAIQRLMEDIDSGR 324
++L QL + ++ Q SDK I ++ D
Sbjct: 856 ECSKQLAQLTQEQAKIIQLSDKLNGINQIKIQFDGDA 892
Score = 29.2 bits (65), Expect = 8.0
Identities = 21/126 (16%), Positives = 40/126 (31%), Gaps = 6/126 (4%)
Query: 150 LLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEK 209
+L E + ER+ LK +E+ Q ++TQ ++ +
Sbjct: 533 GEQTYAQLETSEEDVYHQLTSERK-QRASLKEQMQEIQ-QSFSILTQCDNRSKEDIPNLQ 590
Query: 210 AILMRKMEHETQELQAH---LNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKITLE 266
I +R ++ T++L L Q + + + Q S E L
Sbjct: 591 NITVR-LQDLTEKLSEAEDMLACEQHALLRKLQPEQDLQDVRLHLQQCSQELALKLTALH 649
Query: 267 KTKNNL 272
+ L
Sbjct: 650 ALQLTL 655
>gnl|CDD|133362 cd04162, Arl9_Arfrp2_like, Arf-like 9 (Arl9)/Arfrp2-like GTPase.
Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first
identified as part of the Human Cancer Genome Project.
It maps to chromosome 4q12 and is sometimes referred to
as Arfrp2 (Arf-related protein 2). This is a novel
subfamily identified in human cancers that is
uncharacterized to date.
Length = 164
Score = 34.3 bits (79), Expect = 0.068
Identities = 33/149 (22%), Positives = 67/149 (44%), Gaps = 11/149 (7%)
Query: 395 IVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQERF 454
I+ G GK+ ++ S E L + T G + ++ + ++ ++L + G +
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPTTGFN----SVAIPTQDAIMELLEIGGSQNL 57
Query: 455 RSMTKNYFRRADGVMLLYDVTNERSFNSVKNWV-EAVEEVTENSIPIVICANKVDLRADA 513
R K Y + G++ + D + + + + ++ +P+V+ ANK DL A
Sbjct: 58 RKYWKRYLSGSQGLIFVVDSADSERLPLARQELHQLLQH--PPDLPLVVLANKQDLPA-- 113
Query: 514 QAKGVKCIDREVG-EKLAQQYGAIFMETS 541
A+ V+ I +E+ E +A+ I TS
Sbjct: 114 -ARSVQEIHKELELEPIARGRRWILQGTS 141
>gnl|CDD|200946 pfam00036, efhand, EF hand. The EF-hands can be divided into two
classes: signaling proteins and buffering/transport
proteins. The first group is the largest and includes
the most well-known members of the family such as
calmodulin, troponin C and S100B. These proteins
typically undergo a calcium-dependent conformational
change which opens a target binding site. The latter
group is represented by calbindin D9k and do not
undergo calcium dependent conformational changes.
Length = 29
Score = 30.9 bits (71), Expect = 0.11
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 5 QLEELFKTCDKKGTGQIGPEEFRELCTGF 33
+L+E FK DK G G+I EEF+EL
Sbjct: 1 ELKEAFKEFDKDGDGKISFEEFKELLKKL 29
Score = 29.7 bits (68), Expect = 0.20
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 41 DAIFADLDHDGDGKVSLEDFAYGFREF 67
F + D DGDGK+S E+F ++
Sbjct: 3 KEAFKEFDKDGDGKISFEEFKELLKKL 29
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 34.8 bits (81), Expect = 0.12
Identities = 33/129 (25%), Positives = 54/129 (41%), Gaps = 39/129 (30%)
Query: 447 DTAGQERFRSMTKNYFRRADG------VMLLYDVTNERSFNSVK-NWVEAVEEVTENSIP 499
DT G E F +M RA G +L+ + V +EA+ +P
Sbjct: 61 DTPGHEAFTAM------RARGASVTDIAILVVAADD-----GVMPQTIEAINHAKAAGVP 109
Query: 500 IVICANKVDLRADAQAKGVKCIDREVGEKLAQQYG---------AIFMETSSKSGDNI-- 548
IV+ NK+D + +A D+ E Q+YG IF+ S+K+G+ I
Sbjct: 110 IVVAINKID-KPEAN------PDKVKQEL--QEYGLVPEEWGGDVIFVPVSAKTGEGIDE 160
Query: 549 -LDALIALS 556
L+ ++ L+
Sbjct: 161 LLELILLLA 169
>gnl|CDD|205692 pfam13514, AAA_27, AAA domain. This domain is found in a number of
double-strand DNA break proteins. This domain contains a
P-loop motif.
Length = 1118
Score = 35.1 bits (81), Expect = 0.13
Identities = 40/214 (18%), Positives = 85/214 (39%), Gaps = 43/214 (20%)
Query: 145 GALSSLLDDVKRLHEDNEKLEEMF-----NREREVHLERLKGLEEELDVQVAKVVT-QAK 198
G+L S+ D++++ + +E++ E V L+ LK LE E+ K T +
Sbjct: 126 GSLGSVRDELEK------EADELWKPRGRKPEINVALKELKELEAEIREVQLKTRTWKDL 179
Query: 199 EEARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVL----KEKKIEKQQDPTSDH-- 252
+A + E+E A L E ++L+ +++ +L + K +E+Q +
Sbjct: 180 VKALDEAEEELANL----RKELRQLEKEKQRLERLRRLLPLLAERKALEQQLAALGEVID 235
Query: 253 ---NFSFENEELKITLEKTKNNLDLVHAEMAQLKSEYEG------------KCQELNQLV 297
+ EE + L + NL+L+ + L++E + + L+Q
Sbjct: 236 LPPDAVERYEEARAELRAARRNLELLTERLEALQAELDEISLDEELLAQAAAIEALHQQR 295
Query: 298 GDYLELDQGSDKQFAIQRLMEDIDSGRSTMRDCM 331
G+Y + + + +I + R +
Sbjct: 296 GEY------RNAEQDLPDREGEIANAREAAAALL 323
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 34.9 bits (80), Expect = 0.14
Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 431 MKTIRVDERNVALQLWDTAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAV 490
+K ++ + + L DT G E F S+ K AD +L+ D+ NE F +EA+
Sbjct: 516 LKLLKAEIKIPGLLFIDTPGHEAFTSLRKRGGSLADLAVLVVDI-NE-GFKP--QTIEAI 571
Query: 491 EEVTENSIPIVICANKVDL 509
+ + P V+ ANK+DL
Sbjct: 572 NILRQYKTPFVVAANKIDL 590
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 34.2 bits (79), Expect = 0.15
Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 6/69 (8%)
Query: 495 ENSIPIVICANKVDLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIA 554
I VI NK+DL D +A + + + G + S+K+GD + +
Sbjct: 108 AGGIEPVIVLNKIDLLDDEEAA------VKELLREYEDIGYPVLFVSAKNGDGLEELAEL 161
Query: 555 LSRHVYVFI 563
L+ + V +
Sbjct: 162 LAGKITVLL 170
>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 = 33.2 bits (77), Expect = 0.15
Identities = 19/66 (28%), Positives = 39/66 (59%), Gaps = 7/66 (10%)
Query: 492 EVTENSIPIVICANKVDLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDA 551
++ E +P+V+ N +D A+ +G+K ID +KL++ G + TS++ G+ I +
Sbjct: 97 QLLELGLPVVVALNMIDE---AEKRGIK-IDL---DKLSELLGVPVVPTSARKGEGIDEL 149
Query: 552 LIALSR 557
L A+++
Sbjct: 150 LDAIAK 155
>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 = 33.6 bits (78), Expect = 0.15
Identities = 29/135 (21%), Positives = 50/135 (37%), Gaps = 48/135 (35%)
Query: 447 DTAGQERFRSMTKNYFRRADG------VMLLYDVTNERSFNSVKNWVEAVEEVTENSI-- 498
DT G E F +M RA G +L+ + V T +I
Sbjct: 55 DTPGHEAFTNM------RARGASVTDIAILVVAA------------DDGVMPQTIEAINH 96
Query: 499 ------PIVICANKVDLRADAQAKGVKCIDREVGEKLAQQYGA--------IFMETSSKS 544
PI++ NK+D +A +R V +L++ + S+K+
Sbjct: 97 AKAANVPIIVAINKIDKPYGTEAD----PER-VKNELSELGLVGEEWGGDVSIVPISAKT 151
Query: 545 GDNI---LDALIALS 556
G+ I L+A++ L+
Sbjct: 152 GEGIDDLLEAILLLA 166
>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional.
Length = 508
Score = 34.3 bits (79), Expect = 0.17
Identities = 30/123 (24%), Positives = 57/123 (46%), Gaps = 22/123 (17%)
Query: 152 DDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEAR--------A 203
+ + L E+ E+ + RE+ LE LE++LD ++ +V E+AR A
Sbjct: 98 EKLDNLENQLEEREKALS-ARELELE---ELEKQLDNELYRVAGLTPEQARKLLLKLLDA 153
Query: 204 KYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSF----ENE 259
+ E+EKA ++K+E E A L +K N+L + +++ T+ ++
Sbjct: 154 ELEEEKAQRVKKIEEE-----ADLEAERKAQNILA-QAMQRIASETASDLSVSVVPIPSD 207
Query: 260 ELK 262
+K
Sbjct: 208 AMK 210
>gnl|CDD|221198 pfam11740, KfrA_N, Plasmid replication region DNA-binding N-term.
The broad host-range plasmid RK2 is able to replicate in
and be inherited in a stable manner in diverse
Gram-negative bacterial species. It encodes a number of
co-ordinately regulated operons including a central
control korF1 operon that represses the kfrA operon. The
KfrA polypeptide is a site-specific DNA-binding protein
whose operator overlaps the kfrA promoter. The
N-terminus, containing an helix-turn-helix motif, is
essential for function. Downstream from this family is
an extended coiled-coil domain containing a heptad
repeat segment which is probably responsible for
formation of multimers, and may provide an example of a
bridge to host structures required for plasmid
partitioning.
Length = 120
Score = 32.3 bits (74), Expect = 0.19
Identities = 15/61 (24%), Positives = 21/61 (34%), Gaps = 3/61 (4%)
Query: 170 REREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRK---MEHETQELQAH 226
E L E L VA + A+EEA + +A + +E E E A
Sbjct: 51 ALAPAAPELPDALSEALAELVAALWEAAQEEAEERLAAARAAAEAERAELEAELAEAAAE 110
Query: 227 L 227
Sbjct: 111 A 111
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 34.1 bits (79), Expect = 0.20
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 13/69 (18%)
Query: 498 IPIVICANKVDLRADAQAKGVKCIDREVGEKLAQQYGAI---FMETSSKSGDNILDALIA 554
I +I NK+DL D V + Y I + SS +G+ + + L A
Sbjct: 151 IEPLIVLNKIDLLDDEGRAFV--------NEQLDIYRNIGYRVLMVSSHTGEGL-EELEA 201
Query: 555 -LSRHVYVF 562
L+ + +F
Sbjct: 202 ALTGRISIF 210
>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 = 33.5 bits (78), Expect = 0.21
Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 16/70 (22%)
Query: 498 IPIVICANKVDLRADAQAKGVKCIDREVGEKLAQQYGAI---FMETSSKSGDNILDALIA 554
I VI NK DL D + E+L + Y + + S+K+G+ + D L
Sbjct: 34 IEPVIVLNKADLVDDEEL-----------EELLEIYEKLGYPVLAVSAKTGEGL-DELRE 81
Query: 555 -LSRHVYVFI 563
L V +
Sbjct: 82 LLKGKTSVLV 91
>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 = 33.2 bits (77), Expect = 0.22
Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 10/62 (16%)
Query: 498 IPIVICANKVDLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNI---LDALIA 554
IP+V+ N +D A+ KG+K ID +KL++ G + TS++ G+ I DA+I
Sbjct: 106 IPVVVALNMMDE---AEKKGIK-IDI---KKLSELLGVPVVPTSARKGEGIDELKDAIIE 158
Query: 555 LS 556
++
Sbjct: 159 VA 160
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 33.0 bits (76), Expect = 0.22
Identities = 26/122 (21%), Positives = 44/122 (36%), Gaps = 18/122 (14%)
Query: 403 VGKSCFIYR-FSKEVFL--NKLGSTLGVDFQMKTIRVDERNVALQLWDTAG------QER 453
VGKS + + V + G+T K + + L DT G R
Sbjct: 8 VGKSSLLNALLGQNVGIVSPIPGTTRDP--VRKEWELLP-LGPVVLIDTPGLDEEGGLGR 64
Query: 454 FRS-MTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRAD 512
R + RAD V+L+ D + + E P+++ NK+DL +
Sbjct: 65 ERVEEARQVADRADLVLLVVDSDLTP-----VEEEAKLGLLRERGKPVLLVLNKIDLVPE 119
Query: 513 AQ 514
++
Sbjct: 120 SE 121
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 33.0 bits (76), Expect = 0.24
Identities = 44/189 (23%), Positives = 76/189 (40%), Gaps = 31/189 (16%)
Query: 389 PDRAFKIVFAGDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVA--LQLW 446
D +I FAG + VGKS I + + L + T G +T ++ V L+L
Sbjct: 21 EDDLPEIAFAGRSNVGKSSLINALTNQKNLARTSKTPG-----RTQLINFFEVDDELRLV 75
Query: 447 DTAG----------QERFRSMTKNYFR-RAD--GVMLLYDVTNERSFNSVKNWVEAVEEV 493
D G +E+++ + + Y RA+ GV+LL D R E +E +
Sbjct: 76 DLPGYGYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDA---RHPPK-DLDREMIEFL 131
Query: 494 TENSIPIVICANKVD-LRADAQAKGVKCIDREVGEKLAQQYGA--IFMETSSKSGDNILD 550
E IP+++ K D L+ + K + +V E+L + + SS I +
Sbjct: 132 LELGIPVIVVLTKADKLKKSERNKQLN----KVAEELKKPPPDDQWVVLFSSLKKKGIDE 187
Query: 551 ALIALSRHV 559
+ +
Sbjct: 188 LKAKILEWL 196
>gnl|CDD|205583 pfam13405, EF_hand_4, EF-hand domain.
Length = 30
Score = 29.9 bits (68), Expect = 0.25
Identities = 12/27 (44%), Positives = 14/27 (51%)
Query: 5 QLEELFKTCDKKGTGQIGPEEFRELCT 31
+L E FK DK G G I EE R+
Sbjct: 1 ELREAFKLFDKDGDGYISAEELRKALR 27
Score = 27.9 bits (63), Expect = 1.0
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 43 IFADLDHDGDGKVSLEDFAYGFREF 67
F D DGDG +S E+ R
Sbjct: 5 AFKLFDKDGDGYISAEELRKALRSL 29
>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 = 33.6 bits (78), Expect = 0.26
Identities = 27/121 (22%), Positives = 51/121 (42%), Gaps = 23/121 (19%)
Query: 447 DTAG--------QERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSI 498
DTAG + R T+ + D +L+ D + +E +EE+ E I
Sbjct: 61 DTAGLDDEGELGELRVEK-TREVLDKTDLALLVVDAGVGPG----EYELELIEELKERKI 115
Query: 499 PIVICANKVDLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALSRH 558
P ++ NK+DL ++ EKL +++G + S+ +G+ I + A+
Sbjct: 116 PYIVVINKIDLGEESAEL----------EKLEKKFGLPPIFVSALTGEGIDELKEAIIEL 165
Query: 559 V 559
+
Sbjct: 166 L 166
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 33.3 bits (77), Expect = 0.27
Identities = 22/72 (30%), Positives = 30/72 (41%), Gaps = 15/72 (20%)
Query: 496 NSIPIVICANKVDLRADAQAKGVKCIDREVGEKLAQQYGAI---FMETSSKSGDNILDAL 552
N I +I NK+DL D E +L Y AI +E S+K G+ + D L
Sbjct: 110 NGIKPIIVLNKIDLLD----------DLEEARELLALYRAIGYDVLELSAKEGEGL-DEL 158
Query: 553 IA-LSRHVYVFI 563
L+ V V
Sbjct: 159 KPLLAGKVTVLA 170
>gnl|CDD|219478 pfam07586, HXXSHH, Protein of unknown function (DUF1552). A family
of proteins identified in Rhodopirellula baltica.
Length = 298
Score = 33.4 bits (77), Expect = 0.29
Identities = 21/53 (39%), Positives = 26/53 (49%), Gaps = 10/53 (18%)
Query: 147 LSSLLDDVKRLH-----EDNEKLEEMFN--REREVHLERLKGLEEELDVQVAK 192
L ++L+D K L ED KL+E RE E RL+ E LDV AK
Sbjct: 161 LDAVLEDAKSLRRKLGKEDRAKLDEYLTSVREIEK---RLEKAEAWLDVPKAK 210
>gnl|CDD|218704 pfam05701, DUF827, Plant protein of unknown function (DUF827).
This family consists of several plant proteins of
unknown function. Several sequences in this family are
described as being "myosin heavy chain-like".
Length = 484
Score = 33.8 bits (77), Expect = 0.30
Identities = 34/154 (22%), Positives = 62/154 (40%), Gaps = 7/154 (4%)
Query: 144 EGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARA 203
E A+ + + K++ E +++ M H L+ EE + K++ R
Sbjct: 152 EEAICASKVNEKKVEELTKEIIAMKESLERAHAAHLEAEEERIGA------ALEKDQDRE 205
Query: 204 KYEQEKAILMRKMEHETQELQAHLNLFQ-KVNNVLKEKKIEKQQDPTSDHNFSFENEELK 262
YE+E +++E Q+L +L + + E ++ S + E EE K
Sbjct: 206 TYEKELKEAEKELERLKQDLDPEKDLEKLAEASAELESLQKEISIMASVASVLKELEEAK 265
Query: 263 ITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQL 296
LEK + + LK E E + +EL +L
Sbjct: 266 ANLEKAAEEEKSLRNLVESLKQELEEEKKELEEL 299
>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 = 32.4 bits (75), Expect = 0.31
Identities = 19/100 (19%), Positives = 40/100 (40%), Gaps = 22/100 (22%)
Query: 462 FRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRADAQAKGVKCI 521
+ D V+ + D + ++ +E + ++ P+++ NK+DL
Sbjct: 80 LKDVDLVLFVVDASEWIGEGD--EFI--LELLKKSKTPVILVLNKIDL----------VK 125
Query: 522 DREVGEKLAQQYG------AIFMETSSKSGDNILDALIAL 555
D+E L ++ IF S+ G+N+ D L+
Sbjct: 126 DKEDLLPLLEKLKELHPFAEIFP-ISALKGENV-DELLEY 163
>gnl|CDD|172948 PRK14473, PRK14473, F0F1 ATP synthase subunit B; Provisional.
Length = 164
Score = 32.2 bits (73), Expect = 0.34
Identities = 15/47 (31%), Positives = 28/47 (59%)
Query: 177 ERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRKMEHETQEL 223
ER + E E+ Q + + KEEARA+ EQE+ ++ +++ + +L
Sbjct: 85 ERARAQEAEIIAQARREAEKIKEEARAQAEQERQRMLSELKSQIADL 131
>gnl|CDD|184062 PRK13455, PRK13455, F0F1 ATP synthase subunit B; Provisional.
Length = 184
Score = 32.5 bits (74), Expect = 0.37
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 11/62 (17%)
Query: 151 LDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKA 210
L++ + L E+ + L + R+ + E+ Q ++V AK+EA+A EQ KA
Sbjct: 67 LEEARALREEAQTLLASYERK-----------QREVQEQADRIVAAAKDEAQAAAEQAKA 115
Query: 211 IL 212
L
Sbjct: 116 DL 117
>gnl|CDD|197477 smart00027, EH, Eps15 homology domain. Pair of EF hand motifs
that recognise proteins containing Asn-Pro-Phe (NPF)
sequences.
Length = 96
Score = 31.1 bits (71), Expect = 0.38
Identities = 13/59 (22%), Positives = 27/59 (45%)
Query: 7 EELFKTCDKKGTGQIGPEEFRELCTGFDIQPTDSDAIFADLDHDGDGKVSLEDFAYGFR 65
E++F++ DK G + + + + + T I+ D D DG++ ++FA
Sbjct: 13 EQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWNLADIDNDGELDKDEFALAMH 71
>gnl|CDD|197492 smart00054, EFh, EF-hand, calcium binding motif. EF-hands are
calcium-binding motifs that occur at least in pairs.
Links between disease states and genes encoding
EF-hands, particularly the S100 subclass, are emerging.
Each motif consists of a 12 residue loop flanked on
either side by a 12 residue alpha-helix. EF-hands
undergo a conformational change unpon binding calcium
ions.
Length = 29
Score = 28.9 bits (66), Expect = 0.42
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 41 DAIFADLDHDGDGKVSLEDFAYGFREF 67
F D DGDGK+ E+F +
Sbjct: 3 KEAFRLFDKDGDGKIDFEEFKDLLKAL 29
Score = 28.5 bits (65), Expect = 0.68
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 5 QLEELFKTCDKKGTGQIGPEEFRELCT 31
+L+E F+ DK G G+I EEF++L
Sbjct: 1 ELKEAFRLFDKDGDGKIDFEEFKDLLK 27
>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 = 33.2 bits (77), Expect = 0.43
Identities = 51/210 (24%), Positives = 72/210 (34%), Gaps = 59/210 (28%)
Query: 379 LSNSLEPTGEPDRAFKIVFAGDAAVGKSCFIYRFSKE----VFLNKLGSTL-GVDFQMKT 433
L E E D KI G VGKS + E V + G+T +D
Sbjct: 159 LPEEEEEEEEEDGPIKIAIIGRPNVGKSTLVNALLGEERVIVS-DIAGTTRDSID----- 212
Query: 434 IRVDERNVALQLWDTAGQER----------------FRSMTKNYFRRADGVMLLYDVTNE 477
I + L DTAG R +++ RAD V+L+ D T
Sbjct: 213 IPFERNGKKYTLIDTAGIRRKGKVTEGVEKYSVLRTLKAI-----ERADVVLLVLDAT-- 265
Query: 478 RSFNSVKNWVEAVEE--------VTENSIPIVICANKVDLRAD-AQAKGVKCIDREVGEK 528
E + E E +VI NK DL D + K +E+ K
Sbjct: 266 ----------EGITEQDLRIAGLALEAGKALVIVVNKWDLVKDEKTREEFK---KELRRK 312
Query: 529 LAQQYGAIFMETSSKSG---DNILDALIAL 555
L A + S+ +G D +LDA+ +
Sbjct: 313 LPFLDFAPIVFISALTGQGVDKLLDAIDEV 342
>gnl|CDD|191111 pfam04849, HAP1_N, HAP1 N-terminal conserved region. This family
represents an N-terminal conserved region found in
several huntingtin-associated protein 1 (HAP1)
homologues. HAP1 binds to huntingtin in a polyglutamine
repeat-length-dependent manner. However, its possible
role in the pathogenesis of Huntington's disease is
unclear. This family also includes a similar N-terminal
conserved region from hypothetical protein products of
ALS2CR3 genes found in the human juvenile amyotrophic
lateral sclerosis critical region 2q33-2q34.
Length = 307
Score = 32.9 bits (75), Expect = 0.45
Identities = 35/155 (22%), Positives = 66/155 (42%), Gaps = 18/155 (11%)
Query: 149 SLLDDVKRLHEDNEKLEEMFN--REREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYE 206
SLL K L E NEKLEE R+ + L L++EL + + A EE+ +
Sbjct: 88 SLLKQNKVLMEKNEKLEEQLGKARDEILQLRHELNLKDEL----LQFYSDADEESEDESS 143
Query: 207 QEKAILMRKMEHETQE------LQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEE 260
+ + ++ + LQ L L ++ N L+ + + + ++E +E
Sbjct: 144 ESTPLRPQESSSSSHGCFQLEALQEKLKLLEEENEHLRSEASHLKTE-----TVTYEEKE 198
Query: 261 LKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQ 295
++ + K L + ++A L E K ++L +
Sbjct: 199 QQLVNDCVK-QLREANDQIASLSEELAKKTEDLER 232
>gnl|CDD|116500 pfam07888, CALCOCO1, Calcium binding and coiled-coil domain
(CALCOCO1) like. Proteins found in this family are
similar to the coiled-coil transcriptional coactivator
protein coexpressed by Mus musculus (CoCoA/CALCOCO1).
This protein binds to a highly conserved N-terminal
domain of p160 coactivators, such as GRIP1, and thus
enhances transcriptional activation by a number of
nuclear receptors. CALCOCO1 has a central coiled-coil
region with three leucine zipper motifs, which is
required for its interaction with GRIP1 and may regulate
the autonomous transcriptional activation activity of
the C-terminal region.
Length = 546
Score = 33.0 bits (75), Expect = 0.48
Identities = 44/196 (22%), Positives = 93/196 (47%), Gaps = 17/196 (8%)
Query: 173 EVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRKMEHETQELQAHLNLFQK 232
E+H RL+ ++ +Q++++ KE ++++ QE+ L + E + +Q K
Sbjct: 326 ELHQSRLE--SAQMSLQLSQLNLALKEG-QSQWAQERETLRQSAEADKDRIQKLSAELLK 382
Query: 233 VNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQE 292
+ L+E++ ++++ E + ++ L + + L + + + L+ E E + QE
Sbjct: 383 LEEWLQEERSQREKLEVE---LGIEKDCNRVQLSENRRELSELRSALRVLQKEKE-QLQE 438
Query: 293 LNQLVGDY-----LELDQGSDKQFAIQR-LMEDIDS--GRSTMRDCMDCSSDYKSNNEEN 344
Q + DY L LD+ +D+++A ED S R+ D +D S +S +E+
Sbjct: 439 EKQELLDYIRVLELRLDKEADEKWAEDAATCEDAKSYLHRAAYIDLLD--SIDESPLDES 496
Query: 345 MSSLSEYDYNKRDYPE 360
S LS ++ + E
Sbjct: 497 SSELSPSALDEEQHNE 512
Score = 29.6 bits (66), Expect = 6.0
Identities = 29/145 (20%), Positives = 53/145 (36%), Gaps = 23/145 (15%)
Query: 121 KKLADLYHELRTSSNCPEIVTHFEGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLK 180
++ L LR S+ E L + + E +R + +R+
Sbjct: 171 SRIEQLETALRHSTE-----KTEE--LEEQHKEAQSSSESMSAERNALLAQRAENQQRIL 223
Query: 181 GLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEK 240
LE+++ + +TQ K+E E + I E EL+ LK+
Sbjct: 224 ELEQDI-----QTLTQKKQENDRVLEGTQDIEAEL-ERMKGELKQR----------LKKM 267
Query: 241 KIEKQQDPTSDHNFSFENEELKITL 265
I+++ + T + ENE+L L
Sbjct: 268 TIQRRDEETERIDLQLENEQLHEDL 292
>gnl|CDD|227204 COG4867, COG4867, Uncharacterized protein with a von Willebrand
factor type A (vWA) domain [General function prediction
only].
Length = 652
Score = 33.0 bits (75), Expect = 0.49
Identities = 44/217 (20%), Positives = 78/217 (35%), Gaps = 45/217 (20%)
Query: 147 LSSLLDDVKRLHEDNEKLE--------EMFNREREVHLERLKGLEEELDVQVAKVVTQAK 198
L L ++K+L ++ E + R E+ L+ L AK V +
Sbjct: 84 LDGTLQEIKKLLDEAVLAERKELARALDDDARFAELQLDALP-------ESPAKAVQELA 136
Query: 199 E------EARAKYEQEKAILMRK------------MEHETQELQAHLNLFQKVNNVLKEK 240
E +AR KYEQ K +L R+ + T + + + N L +K
Sbjct: 137 EYRWRSGQAREKYEQIKDLLGRELLDQRFAGMKQALAGATDDDRRRVTEMLDDLNDLLDK 196
Query: 241 KIEKQQDPTSDHNFSFENEELKITLEKTKNNLDLVHAEMAQLK--SEYEGKCQELNQLVG 298
+ F ++ E E +N +L+ + A+ S + L+Q
Sbjct: 197 HARGEDTQRDFDEFMTKHGEF--FPENPRNVEELLDSLAARAAAASRFRN---SLSQEQR 251
Query: 299 DYLELDQGSDKQF---AIQRLMEDIDSGRSTMRDCMD 332
D EL + + F A+ R ++ +D+ R D
Sbjct: 252 D--ELMALAQQAFGSPALMRALDRLDAHLQGARPGED 286
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor of
a mutation in RCC1. Biochemical analysis revealed that
Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 32.2 bits (74), Expect = 0.53
Identities = 33/133 (24%), Positives = 58/133 (43%), Gaps = 27/133 (20%)
Query: 394 KIVFAGDAAVGKSCFIYRFSKEVFLN-------KLGSTLGVDFQMKTIRVDERNVALQLW 446
K++ G GKS +F N +LG+T+ V+ +R N+ L LW
Sbjct: 1 KVLLMGLRGSGKSSMR----SIIFSNYSPRDTLRLGATIDVEQS--HVRF-LGNLTLNLW 53
Query: 447 DTAGQERFRSMTKNYFRRAD-------GVML-LYDVTNERSFNSVKNWVEAVEEVTENS- 497
D GQ+ F +NY R GV++ ++DV + + V+ +E + + S
Sbjct: 54 DCPGQDDF---MENYLTRQKEHIFSNVGVLIYVFDVESREYEEDLATLVKIIEALYQYSP 110
Query: 498 -IPIVICANKVDL 509
+ + +K+DL
Sbjct: 111 NAKVFVLIHKMDL 123
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 32.8 bits (75), Expect = 0.57
Identities = 17/90 (18%), Positives = 27/90 (30%), Gaps = 8/90 (8%)
Query: 144 EGALSSLLDDVKRLHEDNEKLEEMFNRE---REVHLERLKGLEEELDVQVAKVVTQA--- 197
+ + +L E+ +K N E + LE L+ E L ++A A
Sbjct: 191 LSEQRAQQAKLAQLLEERKKTLAQLNSELSADQKKLEELRANESRLKNEIASAEAAAAKA 250
Query: 198 --KEEARAKYEQEKAILMRKMEHETQELQA 225
A K ET + A
Sbjct: 251 REAAAAAEAAAARARAAEAKRTGETYKPTA 280
Score = 32.0 bits (73), Expect = 0.92
Identities = 34/204 (16%), Positives = 58/204 (28%), Gaps = 39/204 (19%)
Query: 147 LSSLLDDVKRLHEDNEKLEEM----------FNREREVHLERLKGLEEELDVQ---VAKV 193
+ L +K L + LE ++ RL LE + Q +A+
Sbjct: 61 RAKLEKQLKSLETEIASLEAQLIETADDLKKLRKQIADLNARLNALEVQEREQRRRLAEQ 120
Query: 194 VTQAKEEARAKYEQEK------------AILMRKMEHETQELQAHLNLFQKVNNVLKEKK 241
+ + R AI + E L K ++ +
Sbjct: 121 LAALQRSGRNPPPALLVSPEDAQRSVRLAIYYGALNPARAERIDALKATLKQLAAVRAEI 180
Query: 242 IEKQQDPTSDHNFSFENEE-LKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDY 300
+Q + T+ + + L LE+ K L AQL SE ++L +L +
Sbjct: 181 AAEQAELTTLLSEQRAQQAKLAQLLEERKKTL-------AQLNSELSADQKKLEELRANE 233
Query: 301 LELDQGSDKQFAIQRLMEDIDSGR 324
L I R
Sbjct: 234 SRLKN------EIASAEAAAAKAR 251
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 32.7 bits (75), Expect = 0.57
Identities = 25/141 (17%), Positives = 63/141 (44%), Gaps = 21/141 (14%)
Query: 162 EKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRKMEHETQ 221
+LE F+ E + +E+L+ L ++ + + K + + E+ E+E + + + +
Sbjct: 270 AELEAHFDEEYQELIEQLEELIDKYESHIEKALEEL--ESILDTEKENSEF----KLDVE 323
Query: 222 ELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNLDLVHAEMAQ 281
EL+A L +++ +K EK +DP++ I LE + ++ ++ +
Sbjct: 324 ELKALLEALEEILEKNLQKLEEKLKDPST-----------SIELESITDLIESINDIIDA 372
Query: 282 LKSEYEGKCQELNQLVGDYLE 302
+ +E N+ + + +
Sbjct: 373 I----NELIREHNEKIDNLKK 389
>gnl|CDD|221389 pfam12037, DUF3523, Domain of unknown function (DUF3523). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 257 to 277 amino acids in length. This domain is
found associated with pfam00004. This domain has a
conserved LER sequence motif.
Length = 276
Score = 32.4 bits (74), Expect = 0.62
Identities = 35/151 (23%), Positives = 58/151 (38%), Gaps = 21/151 (13%)
Query: 156 RLHEDNEKLEEM--------FNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQ 207
R E K++E R R ER K L+E+ +E+ RA+Y+
Sbjct: 64 RQAELEAKIKEYEAQQAQAKLERARVEAEERRKTLQEQ----------TQQEQQRAQYQD 113
Query: 208 EKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEK 267
E A + E E Q Q L + +VL+++ + + + E E + LE+
Sbjct: 114 ELARKRYQKELEQQRRQNEELLKMQEESVLRQEAMRRATE-EEILEMRRETIEEEAELER 172
Query: 268 TKNNLDLVHAE-MAQLKSEYEGKCQELNQLV 297
+N + AE + K E E + L
Sbjct: 173 -ENIRAKIEAEARGRAKEERENEDINREMLK 202
>gnl|CDD|148614 pfam07106, TBPIP, Tat binding protein 1(TBP-1)-interacting protein
(TBPIP). This family consists of several eukaryotic
TBP-1 interacting protein (TBPIP) sequences. TBP-1 has
been demonstrated to interact with the human
immunodeficiency virus type 1 (HIV-1) viral protein Tat,
then modulate the essential replication process of HIV.
In addition, TBP-1 has been shown to be a component of
the 26S proteasome, a basic multiprotein complex that
degrades ubiquitinated proteins in an ATP-dependent
fashion. Human TBPIP interacts with human TBP-1 then
modulates the inhibitory action of human TBP-1 on
HIV-Tat-mediated transactivation.
Length = 169
Score = 31.5 bits (72), Expect = 0.66
Identities = 19/89 (21%), Positives = 42/89 (47%), Gaps = 9/89 (10%)
Query: 213 MRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNL 272
+ K++ E +EL+ + L ++ + L+ + D T++ E +ELK + + + L
Sbjct: 74 LNKLDMEIEELREEVQLLKQDCSTLEIELKSLTSDLTTE-ELQEEIQELKKEVREIEEKL 132
Query: 273 DLVH--------AEMAQLKSEYEGKCQEL 293
+ + EM ++K EY+ +E
Sbjct: 133 ESLEEGWKPVTPEEMEKVKKEYKDLHKEW 161
>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 = 32.4 bits (74), Expect = 0.68
Identities = 41/186 (22%), Positives = 76/186 (40%), Gaps = 30/186 (16%)
Query: 399 GDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAG-------- 450
G+ VGKS + +G+ GV + K ++ + +++ D G
Sbjct: 1 GNPNVGKSTLFNALTGANQ--TVGNWPGVTVEKKEGKLGFQGEDIEIVDLPGIYSLTTFS 58
Query: 451 --QERFRSMTKNYFRRADGVMLLYDVTN-ERSFNSVKNWVEAVEEVTENSIPIVICANKV 507
+E R N + D V+ + D +N ER+ + ++ E IP+++ N V
Sbjct: 59 LEEEVARDYLLNE--KPDLVVNVVDASNLERN-------LYLTLQLLELGIPMILALNLV 109
Query: 508 DLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIALS-RHVYVFIPCV 566
D A+ KG++ ID EKL ++ G + TS+ G I A+ +
Sbjct: 110 DE---AEKKGIR-IDE---EKLEERLGVPVVPTSATEGRGIERLKDAIRKAIGLKELKKR 162
Query: 567 YLKDLP 572
++ +P
Sbjct: 163 AIEIVP 168
>gnl|CDD|132364 TIGR03321, alt_F1F0_F0_B, alternate F1F0 ATPase, F0 subunit B. A
small number of taxonomically diverse prokaryotic
species, including Methanosarcina barkeri, have what
appears to be a second ATP synthase, in addition to the
normal F1F0 ATPase in bacteria and A1A0 ATPase in
archaea. These enzymes use ion gradients to synthesize
ATP, CC and in principle may run in either direction.
This model represents the F0 subunit B of this apparent
second ATP synthase.
Length = 246
Score = 31.9 bits (73), Expect = 0.68
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 170 REREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRKMEHETQELQAHLN 228
RE E + EELD Q ++T+AKEEA+A E+ L+ + E E++
Sbjct: 53 REAEQERREYEEKNEELDQQREVLLTKAKEEAQA----ERQRLLDEAREEADEIREKWQ 107
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 32.4 bits (74), Expect = 0.74
Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 6/91 (6%)
Query: 134 SNCPEIVTHFEGALSSLLDDVKRLHEDNEKLEEMFNR-EREVHLERLKGLE-EELDVQVA 191
E V E S L +++ L + EKLE R REV + K E D ++
Sbjct: 425 KKLEETVERLEEENSELKRELEELKREIEKLESELERFRREVRDKVRKDREIRARDRRIE 484
Query: 192 KVVTQAKEEARAKYEQEKAIL----MRKMEH 218
++ + +E+ + E E+ + MRK+E
Sbjct: 485 RLEKELEEKKKRVEELERKLAELRKMRKLEL 515
Score = 29.3 bits (66), Expect = 6.3
Identities = 45/217 (20%), Positives = 92/217 (42%), Gaps = 32/217 (14%)
Query: 162 EKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRK---MEH 218
K++E E + EE ++ V + + EE + E+E + L R+ ++
Sbjct: 395 SKVKE----EERPREKEGTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEELKR 450
Query: 219 ETQELQAHLNLFQK--VNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNLDLVH 276
E ++L++ L F++ + V K+++I + E L+ LE+ K ++ +
Sbjct: 451 EIEKLESELERFRREVRDKVRKDREIRARDR---------RIERLEKELEEKKKRVEELE 501
Query: 277 AEMAQLKS----EYEGKCQELNQLVGDYLELDQGSDKQFAIQR----LMEDIDSGRSTMR 328
++A+L+ E GK + + LE + +++++ I+ L+ED SG
Sbjct: 502 RKLAELRKMRKLELSGKGTPVKVVEKLTLEAIEEAEEEYGIKEGDVILVED-PSGGGART 560
Query: 329 DCMDCSSDYKSNN---EENMSSLSEYDYNKRDYPELR 362
D K E MS + ++ K + P L
Sbjct: 561 AEELI--DKKPRAIIRGEEMSHAAAEEFFKNEIPVLP 595
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 32.3 bits (74), Expect = 0.83
Identities = 36/159 (22%), Positives = 70/159 (44%), Gaps = 38/159 (23%)
Query: 144 EGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARA 203
+G + SL ++++L E +KL E+ ++L LEEEL A+++ + +E
Sbjct: 538 KGEIKSLKKELEKLEELKKKLAEL--------EKKLDELEEEL----AELLKELEELGFE 585
Query: 204 KYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKI 263
E+ +E +EL+ N + ++ + KE + E+++
Sbjct: 586 SVEE--------LEERLKELEPFYNEYLELKDAEKELEREEKE----------------- 620
Query: 264 TLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDYLE 302
L+K + LD E+A+ + E +EL +L Y E
Sbjct: 621 -LKKLEEELDKAFEELAETEKRLEELRKELEELEKKYSE 658
>gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. This
model describes archaeal and eukaryotic orthologs of
bacterial IF-2. Like IF-2, it helps convey the initiator
tRNA to the ribosome, although the initiator is
N-formyl-Met in bacteria and Met here. This protein is
not closely related to the subunits of eIF-2 of
eukaryotes, which is also involved in the initiation of
translation. The aIF-2 of Methanococcus jannaschii
contains a large intein interrupting a region of very
strongly conserved sequence very near the amino end; the
alignment generated by This model does not correctly
align the sequences from Methanococcus jannaschii and
Pyrococcus horikoshii in this region [Protein synthesis,
Translation factors].
Length = 590
Score = 32.1 bits (73), Expect = 0.86
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 4/79 (5%)
Query: 431 MKTIRVDERNVALQLWDTAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAV 490
+K ++ + L DT G E F ++ K AD +L+ D+ NE F EA+
Sbjct: 59 LKKFKIRLKIPGLLFIDTPGHEAFTNLRKRGGALADLAILIVDI-NE-GFK--PQTQEAL 114
Query: 491 EEVTENSIPIVICANKVDL 509
+ P V+ ANK+D
Sbjct: 115 NILRMYKTPFVVAANKIDR 133
>gnl|CDD|205383 pfam13202, EF_hand_3, EF hand.
Length = 25
Score = 28.0 bits (64), Expect = 0.95
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 41 DAIFADLDHDGDGKVSLEDF 60
+F D +GDGK+S E+
Sbjct: 2 KDLFRQFDTNGDGKISKEEL 21
Score = 27.2 bits (62), Expect = 1.9
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 6 LEELFKTCDKKGTGQIGPEEFREL 29
L++LF+ D G G+I EE + L
Sbjct: 1 LKDLFRQFDTNGDGKISKEELKRL 24
>gnl|CDD|220417 pfam09812, MRP-L28, Mitochondrial ribosomal protein L28. Members
of this family are components of the mitochondrial large
ribosomal subunit. Mature mitochondrial ribosomes
consist of a small (37S) and a large (54S) subunit. The
37S subunit contains at least 33 different proteins and
1 molecule of RNA (15S). The 54S subunit contains at
least 45 different proteins and 1 molecule of RNA (21S).
Length = 146
Score = 30.8 bits (70), Expect = 0.96
Identities = 23/102 (22%), Positives = 42/102 (41%), Gaps = 9/102 (8%)
Query: 197 AKEEARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSF 256
+ E R + EK I RK + L+ + ++ L + +++Q S
Sbjct: 14 PQREQRKRKRLEKFI--RKRTKSARGLKP---VEDRIVPQLSVDEAKRRQRKLLKL--SP 66
Query: 257 ENEELKITLEK--TKNNLDLVHAEMAQLKSEYEGKCQELNQL 296
E+ E + +EK AE QL+ +YE + + L +L
Sbjct: 67 EDLERRALIEKCWALYQQQEREAENQQLRQQYEAQQEALEEL 108
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 31.9 bits (74), Expect = 0.98
Identities = 48/214 (22%), Positives = 72/214 (33%), Gaps = 56/214 (26%)
Query: 376 LLSLSNSLEPTGEPDRAFKIVFAGDAAVGKSCFIYRFSKE----VFLNKLGSTL-GVDFQ 430
+L E E D KI G VGKS I E V + G+T +D
Sbjct: 157 ILEELPEEEEEDEEDEPIKIAIIGRPNVGKSSLINALLGEERVIVS-DIAGTTRDSID-- 213
Query: 431 MKTIRVDERNVALQLWDTAG----------QERF------RSMTKNYFRRADGVMLLYDV 474
+ L DTAG E++ +++ RAD V+L+ D
Sbjct: 214 ---TPFERDGQKYTLIDTAGIRRKGKVTEGVEKYSVIRTLKAI-----ERADVVLLVIDA 265
Query: 475 TNERSFNSVKNWVEAVEE--------VTENSIPIVICANKVDLRADAQAKGVKCIDREVG 526
T E + E E +VI NK DL + + K +E+
Sbjct: 266 T------------EGITEQDLRIAGLALEAGRALVIVVNKWDLVDEKTMEEFK---KELR 310
Query: 527 EKLAQQYGAIFMETSSKSGDNILDALIALSRHVY 560
+L A + S+ +G + D L+ Y
Sbjct: 311 RRLPFLDYAPIVFISALTGQGV-DKLLEAIDEAY 343
>gnl|CDD|214568 smart00221, STYKc, Protein kinase; unclassified specificity.
Phosphotransferases. The specificity of this class of
kinases can not be predicted. Possible dual-specificity
Ser/Thr/Tyr kinase.
Length = 258
Score = 31.4 bits (72), Expect = 1.1
Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 173 EVHLERLKGLEEELDVQVA--KVVTQAKEEARAKYEQEKAILMRKMEHE 219
EV+ LKG + +V+VA + A E+ ++ +E A +MRK++H
Sbjct: 14 EVYKGTLKGKGDGKEVEVAVKTLKEDASEQQIEEFLRE-ARIMRKLDHP 61
>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 = 30.9 bits (71), Expect = 1.1
Identities = 25/127 (19%), Positives = 42/127 (33%), Gaps = 36/127 (28%)
Query: 440 NVALQLWDTAG------------QERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWV 487
+ ++L DTAG ER + AD V+L+ D +
Sbjct: 50 GIPVRLIDTAGLRETEDEIEKIGIER----AREAIEEADLVLLVVDASEGLDE------E 99
Query: 488 EAVEEVTENSIPIVICANKVDLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDN 547
+ P+++ NK DL +DA+ + S+K+G+
Sbjct: 100 DLEILELPAKKPVIVVLNKSDLLSDAEGISELNGKPIIA-------------ISAKTGEG 146
Query: 548 ILDALIA 554
I D L
Sbjct: 147 I-DELKE 152
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 31.9 bits (73), Expect = 1.1
Identities = 39/143 (27%), Positives = 60/143 (41%), Gaps = 32/143 (22%)
Query: 152 DDVKRLHEDNEKLEEMFNREREVHL----ERLKGLEEELDVQVAKVVTQAKEEARAKYEQ 207
D+++RL E E L E+ N ER L ER + LE E D EEAR E+
Sbjct: 606 DEIERLREKREALAEL-NDERRERLAEKRERKRELEAEFD-------EARIEEAREDKER 657
Query: 208 EKAILMRKMEHETQELQAHLNLFQK----VNNVLKEKKIEKQQDPTSDHNFSFENEELKI 263
+ L ++E + EL+ + Q V N L+E + + E +
Sbjct: 658 AEEYL-EQVEEKLDELREERDDLQAEIGAVENELEELEELR--------------ERRE- 701
Query: 264 TLEKTKNNLDLVHAEMAQLKSEY 286
LE L+ ++ E +L+S Y
Sbjct: 702 ALENRVEALEALYDEAEELESMY 724
Score = 30.8 bits (70), Expect = 2.8
Identities = 53/225 (23%), Positives = 91/225 (40%), Gaps = 32/225 (14%)
Query: 88 GPERRNSDVQNAWSLL---LAGIGEANVHKFLNTSGKKLADLYHEL-----------RTS 133
G ER SD + + L + E ++H+ LN +LA+L E+ T
Sbjct: 177 GVERVLSDQRGSLDQLKAQIEEKEEKDLHERLNGLESELAELDEEIERYEEQREQARETR 236
Query: 134 SNCPEIVTHFEG---ALSSLLDDVKRLHED---NEKLEEMFNREREVHLERLKGLEEELD 187
E++ E L +L +++ L E E+ E E ERL+ LEEE D
Sbjct: 237 DEADEVLEEHEERREELETLEAEIEDLRETIAETEREREELAEEVRDLRERLEELEEERD 296
Query: 188 VQVAKV-VTQAKEEA----RAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKI 242
+A+ + A EA R + E L ++E QAH + + +
Sbjct: 297 DLLAEAGLDDADAEAVEARREELEDRDEELRDRLEECRVAAQAHNE--EAESLREDADDL 354
Query: 243 EKQQDPTSDHNFSFENEELKITLEKTKNNLDLVHAEMAQLKSEYE 287
E++ + + E EL+ LE+ + ++ E+ +L+ E E
Sbjct: 355 EERAEELRE-----EAAELESELEEAREAVEDRREEIEELEEEIE 394
>gnl|CDD|198139 smart01071, CDC37_N, Cdc37 N terminal kinase binding. Cdc37 is a
molecular chaperone required for the activity of
numerous eukaryotic protein kinases. This domain
corresponds to the N terminal domain which binds
predominantly to protein kinases.and is found N terminal
to the Hsp (Heat shocked protein) 90-binding domain.
Expression of a construct consisting of only the
N-terminal domain of Saccharomyces pombe Cdc37 results
in cellular viability. This indicates that interactions
with the cochaperone Hsp90 may not be essential for
Cdc37 function.
Length = 154
Score = 30.5 bits (69), Expect = 1.3
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 121 KKLADLYHELRTSSNCPEIVTHFEGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLK 180
K++ L LR PE T+ E L+ L D +K+ E+ E E + H ++LK
Sbjct: 63 KRIDKLLKGLREEELSPETPTYNE-MLAELQDQLKKELEEANGDSEGLLEELKKHRDKLK 121
Query: 181 GLEEELD 187
++EL
Sbjct: 122 KEQKELR 128
>gnl|CDD|151528 pfam11083, Streptin-Immun, Lantibiotic streptin immunity protein.
Streptococcal species produce a lantibiotic, streptin,
in a similar manner to the production of nisin and
subtilin by other lactic acid bacteria, in order to
compete against competing bacteria within the
environment. The immunity protein protects the bacterium
from destruction by its own lantibiotic. In general,
there is little homology between the immunity proteins
of different genera of bacteria.
Length = 99
Score = 29.7 bits (67), Expect = 1.3
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 218 HETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNLDLVHA 277
+ETQE A LN +V LK +E ++ + ++FS N ITLE+ + + +
Sbjct: 9 NETQEKIATLNKMAEVLINLKSADVESRK--LARYDFSKLNLTESITLEQVEEEILKLQN 66
Query: 278 EMAQLKSEYEGKCQELNQLV 297
+++ EYE + L + V
Sbjct: 67 QLSLYLDEYEKLVRRLEKFV 86
>gnl|CDD|176809 cd08975, BaFpgNei_N_3, Uncharacterized bacterial subgroup of the
N-terminal domain of Fpg (formamidopyrimidine-DNA
glycosylase, MutM)_Nei (endonuclease VIII)
base-excision repair DNA glycosylases. This family is
an uncharacterized bacterial subgroup of the FpgNei_N
domain superfamily. DNA glycosylases maintain genome
integrity by recognizing base lesions created by
ionizing radiation, alkylating or oxidizing agents, and
endogenous reactive oxygen species. They initiate the
base-excision repair process, which is completed with
the help of enzymes such as phosphodiesterases, AP
endonucleases, DNA polymerases and DNA ligases. DNA
glycosylases cleave the N-glycosyl bond between the
sugar and the damaged base, creating an AP
(apurinic/apyrimidinic) site. Most FpgNei DNA
glycosylases use their N-terminal proline residue as the
key catalytic nucleophile, and the reaction proceeds via
a Schiff base intermediate. One exception is mouse
Nei-like glycosylase 3 (Neil3) which forms a Schiff base
intermediate via its N-terminal valine. In this family
the N-terminal proline is replaced by an isoleucine or
valine. Escherichia coli Fpg prefers
8-oxo-7,8-dihydroguanine (8-oxoG) and oxidized purines
and Escherichia coli Nei recognizes oxidized
pyrimidines. However, neither Escherichia coli Fpg or
Nei belong to this family. In addition to this
BaFpgNei_N_3 domain, enzymes belonging to this family
contain a helix-two turn-helix (H2TH) domain and a
zinc-finger motif.
Length = 117
Score = 30.0 bits (68), Expect = 1.3
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 222 ELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFEN 258
EL L +++N LK K+I TS H F++ N
Sbjct: 2 ELPESATLSKQLNETLKGKRITDVFPATSPHKFTWYN 38
>gnl|CDD|227644 COG5339, COG5339, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 479
Score = 31.3 bits (71), Expect = 1.4
Identities = 47/252 (18%), Positives = 78/252 (30%), Gaps = 51/252 (20%)
Query: 38 TDSDAIFADLDHDGDGKVSLEDFAYGFREFLNSDARRLKSNVNAGAMSSEGPERRNSDVQ 97
D A+ L D LN KS V + +G
Sbjct: 178 RDGGALSNSLSTDS--------LNSDAVNPLNQG----KSQVTLNNLKLDGSSTL----- 220
Query: 98 NAWSLLLAGIGEANVHKF-LNTSGKKLADL-YHELRTSSNCPEIVTHFEGALSSLLDDVK 155
+ G + + KF ++ G ++A L L+ SS+ + AL LDD
Sbjct: 221 -ESKGIPLGNQNSKLDKFRISNEGGEMAKLEGFNLKFSSDTVKDGAFINSALKYKLDD-- 277
Query: 156 RLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRK 215
L + L EL ++ + +A ++ +Y + +K
Sbjct: 278 -LKYGGQNLGSG-----------------ELTLKFEHLDGEALQQLSRQYNA----ISQK 315
Query: 216 MEHETQELQAHLNLFQKVNNVLKE--KKIEKQQDPTSDHNFSFENEELKITLEKTKNNLD 273
E Q ++V L + K+Q + S K + NLD
Sbjct: 316 QLTEDDIAQNLEAAQKQVAEALFADVPALLKKQPVLTLAPLS-----WKNDGGELALNLD 370
Query: 274 LVHAEMAQLKSE 285
L + A+LK E
Sbjct: 371 LFLPDPAKLKLE 382
>gnl|CDD|219530 pfam07714, Pkinase_Tyr, Protein tyrosine kinase.
Length = 258
Score = 30.9 bits (71), Expect = 1.5
Identities = 18/49 (36%), Positives = 29/49 (59%), Gaps = 3/49 (6%)
Query: 173 EVHLERLKGLEEELDVQVA-KVVTQ-AKEEARAKYEQEKAILMRKMEHE 219
EV+ LKG E + +VA K + + A EE R ++ +E A +M+K+ H
Sbjct: 14 EVYKGTLKGDGEGTETKVAVKTLKEGASEEEREEFLEE-ASIMKKLSHP 61
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 31.5 bits (72), Expect = 1.5
Identities = 21/83 (25%), Positives = 30/83 (36%), Gaps = 20/83 (24%)
Query: 434 IRVDERNVALQLWDTAGQERFRSMTKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEV 493
D N + L DT G F + R DG ++++D V V+
Sbjct: 66 TSCDWDNHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDA------------VTGVQPQ 113
Query: 494 TEN--------SIPIVICANKVD 508
TE IP +I NK+D
Sbjct: 114 TETVWRQADRYGIPRLIFINKMD 136
>gnl|CDD|219791 pfam08317, Spc7, Spc7 kinetochore protein. This domain is found in
cell division proteins which are required for
kinetochore-spindle association.
Length = 321
Score = 31.2 bits (71), Expect = 1.7
Identities = 21/111 (18%), Positives = 46/111 (41%), Gaps = 5/111 (4%)
Query: 141 THFEGALSSLLDDVKRLHEDNEKLEEMFNREREVH---LERLKGLEEELDV--QVAKVVT 195
EG L ++++ + D E L + N + ++L+ L+EE+ Q+A +
Sbjct: 143 QLLEGLKEGLEENLEGMKRDEELLNKDLNLINSIKPKLRKKLQALKEEIASLRQLADELN 202
Query: 196 QAKEEARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQ 246
K QE L K+ + ++L+ Q++ ++ +K +
Sbjct: 203 LCDPLELEKARQELRSLSVKISEKRKQLEELQQELQELTIAIEALTNKKSE 253
>gnl|CDD|236842 PRK11091, PRK11091, aerobic respiration control sensor protein
ArcB; Provisional.
Length = 779
Score = 31.4 bits (72), Expect = 1.7
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 12/68 (17%)
Query: 156 RLHEDNEKLEEMFNREREVHL-ERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMR 214
RL KLEEM RER++ L +LK +L+ ++ R K E+ +
Sbjct: 86 RLSRLVAKLEEM--RERDLELNVQLKDNIAQLNQEI---------AEREKAEEARQEAFE 134
Query: 215 KMEHETQE 222
++++E +E
Sbjct: 135 QLKNEIKE 142
>gnl|CDD|214710 smart00533, MUTSd, DNA-binding domain of DNA mismatch repair MUTS
family.
Length = 308
Score = 31.1 bits (71), Expect = 1.7
Identities = 33/180 (18%), Positives = 55/180 (30%), Gaps = 26/180 (14%)
Query: 119 SGKKLADLYHELRTSSNCPEIVTHFEGALSSLLDDVKR--LHEDNEKLEEM------FNR 170
DL + EI E LL + + L E LE + +
Sbjct: 74 GRASPRDLLRLYDSLEGLKEIRQLLESLDGPLLGLLLKVILEPLLELLELLLELLNDDDP 133
Query: 171 EREVHLERLK-GLEEELDV--QVAKVVTQAKEEARAKYEQEKAILMRKMEHETQELQAHL 227
+K G + ELD + + + + EE K +E I K+ + +
Sbjct: 134 LEVNDGGLIKDGFDPELDELREKLEELEEELEELLKKEREELGIDSLKLGYNKVH--GYY 191
Query: 228 NLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNLDLVHAEMAQLKSEYE 287
K K ++ + + F ELK L+ E+ + K E E
Sbjct: 192 IEVTKSEAKKVPKDFIRRS--SLKNTERFTTPELK--------ELE---NELLEAKEEIE 238
>gnl|CDD|239348 cd03050, GST_N_Theta, GST_N family, Class Theta subfamily; composed
of eukaryotic class Theta GSTs and bacterial
dichloromethane (DCM) dehalogenase. GSTs are cytosolic
dimeric proteins involved in cellular detoxification by
catalyzing the conjugation of glutathione (GSH) with a
wide range of endogenous and xenobiotic alkylating
agents, including carcinogens, therapeutic drugs,
environmental toxins and products of oxidative stress.
The GST fold contains an N-terminal TRX-fold domain and
a C-terminal alpha helical domain, with an active site
located in a cleft between the two domains. Mammalian
class Theta GSTs show poor GSH conjugating activity
towards the standard substrates, CDNB and ethacrynic
acid, differentiating them from other mammalian GSTs.
GSTT1-1 shows similar cataytic activity as bacterial DCM
dehalogenase, catalyzing the GSH-dependent hydrolytic
dehalogenation of dihalomethanes. This is an essential
process in methylotrophic bacteria to enable them to use
chloromethane and DCM as sole carbon and energy sources.
The presence of polymorphisms in human GSTT1-1 and its
relationship to the onset of diseases including cancer
is subject of many studies. Human GSTT2-2 exhibits a
highly specific sulfatase activity, catalyzing the
cleavage of sulfate ions from aralkyl sufate esters, but
not from aryl or alkyl sulfate esters.
Length = 76
Score = 28.7 bits (65), Expect = 1.7
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 207 QEKAILMRKMEHETQELQAHLNLFQKV 233
+E I +RK E T E + +N F KV
Sbjct: 27 EECPIDLRKGEQLTPEFKK-INPFGKV 52
>gnl|CDD|232848 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
Members of this protein were designated YjeQ and are now
designated RsgA (ribosome small subunit-dependent GTPase
A). The strongest motif in the alignment of these
proteins is GXSGVGKS[ST], a classic P-loop for
nucleotide binding. This protein has been shown to
cleave GTP and remain bound to GDP. A role as a
regulator of translation has been suggested. The Aquifex
aeolicus ortholog is split into consecutive open reading
frames. Consequently, this model was build in fragment
mode (-f option) [Protein synthesis, Translation
factors].
Length = 245
Score = 30.8 bits (70), Expect = 1.8
Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 7/69 (10%)
Query: 495 ENSIPIVICANKVDLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALIA 554
+I +I NK+DL D + +E + + M TSSK+ D + + + A
Sbjct: 65 AQNIEPIIVLNKIDLLDDEDME------KEQLDIYRNIGYQVLM-TSSKNQDGLKELIEA 117
Query: 555 LSRHVYVFI 563
L + VF
Sbjct: 118 LQNRISVFA 126
>gnl|CDD|217554 pfam03432, Relaxase, Relaxase/Mobilisation nuclease domain.
Relaxases/mobilisation proteins are required for the
horizontal transfer of genetic information contained on
plasmids that occurs during bacterial conjugation. The
relaxase, in conjunction with several auxiliary
proteins, forms the relaxation complex or relaxosome.
Relaxases nick duplex DNA in a specific manner by
catalyzing trans-esterification.
Length = 240
Score = 30.4 bits (69), Expect = 1.9
Identities = 24/129 (18%), Positives = 47/129 (36%), Gaps = 17/129 (13%)
Query: 155 KRLHEDN---EKLEEMFNR-EREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKA 210
K+ + KL + + E L +G + K K + K E +A
Sbjct: 117 KKFRPNYKAYRKLRKANDELELRHGLSIDEGNPRNRYTEAEKGK-AEKNKTSYKDEIRQA 175
Query: 211 ILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKI---TLEK 267
+ ++ QAH + F+ LKEK +E ++D + ++E K+ L +
Sbjct: 176 L---------KKAQAHASDFEDFKEALKEKGLEIRRDTGKFLTYKGDDENTKVRGSKLGR 226
Query: 268 TKNNLDLVH 276
+ +
Sbjct: 227 DYSKGKIEA 235
>gnl|CDD|220623 pfam10186, Atg14, UV radiation resistance protein and
autophagy-related subunit 14. The Atg14 or Apg14
proteins are hydrophilic proteins with a predicted
molecular mass of 40.5 kDa, and have a coiled-coil motif
at the N terminus region. Yeast cells with mutant Atg14
are defective not only in autophagy but also in sorting
of carboxypeptidase Y (CPY), a vacuolar-soluble
hydrolase, to the vacuole. Subcellular fractionation
indicate that Apg14p and Apg6p are peripherally
associated with a membrane structure(s). Apg14p was
co-immunoprecipitated with Apg6p, suggesting that they
form a stable protein complex. These results imply that
Apg6/Vps30p has two distinct functions: in the
autophagic process and in the vacuolar protein sorting
pathway. Apg14p may be a component specifically required
for the function of Apg6/Vps30p through the autophagic
pathway. There are 17 auto-phagosomal component proteins
which are categorized into six functional units, one of
which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The
AS-PI3K complex and the Atg2-Atg18 complex are essential
for nucleation, and the specific function of the AS-PI3K
apparently is to produce phosphatidylinositol
3-phosphate (PtdIns(3)P) at the pre-autophagosomal
structure (PAS). The localisation of this complex at the
PAS is controlled by Atg14. Autophagy mediates the
cellular response to nutrient deprivation, protein
aggregation, and pathogen invasion in humans, and
malfunction of autophagy has been implicated in multiple
human diseases including cancer. This effect seems to be
mediated through direct interaction of the human Atg14
with Beclin 1 in the human phosphatidylinositol 3-kinase
class III complex.
Length = 307
Score = 30.8 bits (70), Expect = 2.0
Identities = 24/136 (17%), Positives = 61/136 (44%), Gaps = 21/136 (15%)
Query: 176 LERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNN 235
L RL EEL +V + + A E + + + + +++A + ++
Sbjct: 29 LARLLLENEELKQKVEEALEGATNEDGKLAADLLKLEVARKKERLNQIRARI---SQLKE 85
Query: 236 VLKEKK--IEKQQD-------------PTSDHNFSFENEELKITLEKTKNNLDLVHAEMA 280
+++K+ IE+ + + + + E+L+ +++T++ L+ +H+ +A
Sbjct: 86 EIEQKRERIEELKRALAQRRSDLSSASYQLEKRRASQLEKLQDEIKRTRSKLNALHSLLA 145
Query: 281 QLKSEYEGKCQELNQL 296
+ +S C+EL +L
Sbjct: 146 EKRSF---LCRELAKL 158
>gnl|CDD|240157 cd05031, S-100A10_like, S-100A10_like: S-100A10 domain found in
proteins similar to S100A10. S100A10 is a member of the
S100 family of EF-hand superfamily of calcium-binding
proteins. Note that the S-100 hierarchy, to which this
S-100A1_like group belongs, contains only S-100 EF-hand
domains, other EF-hands have been modeled separately.
S100 proteins are expressed exclusively in vertebrates,
and are implicated in intracellular and extracellular
regulatory activities. A unique feature of S100A10 is
that it contains mutation in both of the calcium
binding sites, making it calcium insensitive. S100A10
has been detected in brain, heart, gastrointestinal
tract, kidney, liver, lung, spleen, testes, epidermis,
aorta, and thymus. Structural data supports the homo-
and hetero-dimeric as well as hetero-tetrameric nature
of the protein. S100A10 has multiple binding partners
in its calcium free state and is therefore involved in
many diverse biological functions.
Length = 94
Score = 28.9 bits (65), Expect = 2.1
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 37 PTDSDAIFADLDHDGDGKVSLEDF 60
P D I DLD + DGKV+ E+F
Sbjct: 50 PMAVDKIMKDLDQNRDGKVNFEEF 73
>gnl|CDD|206742 cd09915, Rag, Rag GTPase subfamily of Ras-related GTPases. Rag
GTPases (ras-related GTP-binding proteins) constitute a
unique subgroup of the Ras superfamily, playing 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. This subfamily consists of
RagA and RagB as well as RagC and RagD that are closely
related. Saccharomyces cerevisiae encodes single
orthologs of metazoan RagA/B and RagC/D, Gtr1 and Gtr2,
respectively. Dimer formation is important for their
cellular function; these domains form heterodimers, as
RagA or RagB dimerizes with RagC or RagD, and similarly,
Gtr1 dimerizes with Gtr2. 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 = 175
Score = 30.2 bits (68), Expect = 2.1
Identities = 24/98 (24%), Positives = 48/98 (48%), Gaps = 7/98 (7%)
Query: 440 NVALQLWDTAGQERFRSMTKNY---FRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTEN 496
N L LWD GQ+ F TK+ F+ ++ + DV +E ++ +A+++ +
Sbjct: 47 NXTLNLWDCPGQDVFFEPTKDKEHIFQXVGALIYVIDVQDE-YLKAITILAKALKQAYKV 105
Query: 497 S--IPIVICANKVD-LRADAQAKGVKCIDREVGEKLAQ 531
+ I + +KVD L D + + + I + + E L++
Sbjct: 106 NPDANIEVLIHKVDGLSLDKKEELQRDIXQRLSETLSE 143
>gnl|CDD|214922 smart00935, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 140
Score = 29.5 bits (67), Expect = 2.2
Identities = 20/87 (22%), Positives = 41/87 (47%), Gaps = 8/87 (9%)
Query: 161 NEKLEEMFNRER---EVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRKME 217
++LE+ F + + E + L+ L+E+L A + A+E+ + +++ RK +
Sbjct: 20 QKQLEKEFKKRQAELEKLEKELQKLKEKLQKDAATLSEAAREKKEKELQKKVQEFQRKQQ 79
Query: 218 HETQELQAHLN-----LFQKVNNVLKE 239
Q+LQ + K+N +KE
Sbjct: 80 KLQQDLQKRQQEELQKILDKINKAIKE 106
>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is
found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains
separated by a hinge in the middle. The eukaryotic SMC
proteins form two kind of heterodimers: the SMC1/SMC3
and the SMC2/SMC4 types. These heterodimers constitute
an essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family also
includes the RecF and RecN proteins that are involved in
DNA metabolism and recombination.
Length = 1162
Score = 31.1 bits (70), Expect = 2.3
Identities = 36/189 (19%), Positives = 67/189 (35%), Gaps = 21/189 (11%)
Query: 138 EIVTHFEGALSSLLDDVKR-----LHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAK 192
+ E A S K+ L E+ E L E+ E+ L+ LK E+
Sbjct: 155 RRLEIEEEAAGSREKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYY 214
Query: 193 VVTQAKEEARAK----------------YEQEKAILMRKMEHETQELQAHLNLFQKVNNV 236
+ + E ++ ++E QEL+ + +V
Sbjct: 215 QLKEKLELEEENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKE 274
Query: 237 LKEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQL 296
KE++ EK+ + E EELK L K + ++ + + E + +EL +
Sbjct: 275 NKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKE 334
Query: 297 VGDYLELDQ 305
+ EL++
Sbjct: 335 KEEIEELEK 343
Score = 29.6 bits (66), Expect = 5.9
Identities = 28/153 (18%), Positives = 54/153 (35%), Gaps = 14/153 (9%)
Query: 144 EGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARA 203
E + +K ++ +KLE+ +E+E E K L+E E R
Sbjct: 307 ERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKE-------------LEIKRE 353
Query: 204 KYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKI 263
E+E+ L + E Q + L + + L K+++ N + +L +
Sbjct: 354 AEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEE-LELKNEEEKEAKLLL 412
Query: 264 TLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQL 296
L + + +L + E + E Q
Sbjct: 413 ELSEQEEDLLKEEKKEELKIVEELEESLETKQG 445
>gnl|CDD|223783 COG0711, AtpF, F0F1-type ATP synthase, subunit b [Energy production
and conversion].
Length = 161
Score = 30.0 bits (68), Expect = 2.3
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 15/76 (19%)
Query: 151 LDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKA 210
L + +RL E+ + L + +E E E Q ++++ QAK+EA E+ KA
Sbjct: 46 LAEAERLKEEAQALLAEYEQELE-----------EAREQASEIIEQAKKEAEQIAEEIKA 94
Query: 211 ILMRKMEHETQELQAH 226
+ E E + ++
Sbjct: 95 ----EAEEELERIKEA 106
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are components
of TFIIH, a complex that is involved in nucleotide
excision repair and transcription initiation. Also known
as MAT1 (menage a trois 1). This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 309
Score = 30.5 bits (69), Expect = 2.3
Identities = 22/100 (22%), Positives = 41/100 (41%), Gaps = 14/100 (14%)
Query: 156 RLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRK 215
+ + E+LEE E+E +R L++E +EE + + K L+ +
Sbjct: 139 KSTREQEELEEALEFEKEEEEQRRLLLQKE------------EEEQQMNKRKNKQALLDE 186
Query: 216 MEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFS 255
+E T A + Q N +K + ++ P + FS
Sbjct: 187 LETSTLP--AAELIAQHKKNSVKLEMQVEKPKPEKPNTFS 224
>gnl|CDD|227061 COG4717, COG4717, Uncharacterized conserved protein [Function
unknown].
Length = 984
Score = 31.0 bits (70), Expect = 2.6
Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 5/87 (5%)
Query: 146 ALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVT----QAKEEA 201
+ L +++ E ++ + E+ ER++GL L+ Q + T Q A
Sbjct: 618 TMKDLKKLMQKKAELTHQVARL-REEQAAFEERVEGLLAVLEAQFIDLSTLFCVQRLRVA 676
Query: 202 RAKYEQEKAILMRKMEHETQELQAHLN 228
++E + + T+EL L
Sbjct: 677 AELQKEEARLALEGNIERTKELNDELR 703
Score = 30.2 bits (68), Expect = 3.5
Identities = 43/222 (19%), Positives = 81/222 (36%), Gaps = 23/222 (10%)
Query: 109 EANVHKFL---NTSGKKLADLYHELRTSSNCPEIVTHFEGALSSLLDDVKRLHED-NEKL 164
A HK L +LA+L ELR + + L L + K+L ++ +
Sbjct: 204 YATYHKLLESRRAEHARLAELRSELRADRDHIRALRD-AVELWPRLQEWKQLEQELTRRR 262
Query: 165 EE--MFNR----EREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRKMEH 218
EE F R E L+ E E+D + ++ ++ +E + H
Sbjct: 263 EELATFPRDGVLRLEKREAHLQKTEAEIDALLVRLAELKDLASQLIPAKEAVLQALVRLH 322
Query: 219 ETQELQAHLNLFQKVNNVLKEKKIE-KQQDPTSDHNFSFENEELKITLEKTKNNLDLVHA 277
Q+L ++ L + + + ++ + + F E +LE +
Sbjct: 323 --QQLSEIKASAFELTETLAGIEADLRDKEEAAGNGFEAERVHDLRSLECMLR----YQS 376
Query: 278 EMAQLKSEYEGKCQELNQLVGDYLELDQGSDKQFAIQRLMED 319
+LK C+ L++ L D+ ++ A QRL +D
Sbjct: 377 SQRELKQTEAAYCKRLDEKR---LFEDEAEEE--ARQRLADD 413
>gnl|CDD|225199 COG2317, COG2317, Zn-dependent carboxypeptidase [Amino acid
transport and metabolism].
Length = 497
Score = 30.3 bits (69), Expect = 2.9
Identities = 26/86 (30%), Positives = 41/86 (47%), Gaps = 17/86 (19%)
Query: 123 LADLYHELRTSSNCPEIVTHFEGALS-SLLDDVKRLHEDNEKLEEMFNREREVHLERLKG 181
L+ L HEL TS PE E A L +++ + E+ +RE E+ K
Sbjct: 50 LSVLRHELLTS---PEFAELLEKAEEEKDLSEIEA-----GVVREL---KREY--EKAKK 96
Query: 182 LEEELDVQVAKVVTQAK---EEARAK 204
+ EEL + +K+ ++A+ EAR K
Sbjct: 97 IPEELVKEYSKLTSKAEHAWREAREK 122
>gnl|CDD|184696 PRK14474, PRK14474, F0F1 ATP synthase subunit B; Provisional.
Length = 250
Score = 29.8 bits (67), Expect = 3.2
Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 155 KRLHEDNEKLEEMFNREREVH--LERLKGLEEELDVQVAKVVTQAKEEARAKYEQ 207
KR + ++ R++E ER + ++ L+ Q A + QA+E A + +
Sbjct: 36 KRQQRIANRWQDAEQRQQEAGQEAERYRQKQQSLEQQRASFMAQAQEAADEQRQH 90
>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 = 30.1 bits (69), Expect = 3.3
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 16/77 (20%)
Query: 487 VEAVEEVTE----NSIPIVICANKVDLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSS 542
+EAVE+V E IP ++ NK+DL + + A+F+ S+
Sbjct: 287 IEAVEKVLEELGAEDIPQLLVYNKIDLLDEP----------RIERLEEGYPEAVFV--SA 334
Query: 543 KSGDNILDALIALSRHV 559
K+G+ + L A++ +
Sbjct: 335 KTGEGLDLLLEAIAERL 351
>gnl|CDD|238009 cd00052, EH, Eps15 homology domain; found in proteins implicated
in endocytosis, vesicle transport, and signal
transduction. The alignment contains a pair of EF-hand
motifs, typically one of them is canonical and binds to
Ca2+, while the other may not bind to Ca2+. A
hydrophobic binding pocket is formed by residues from
both EF-hand motifs. The EH domain binds to proteins
containing NPF (class I), [WF]W or SWG (class II), or
H[TS]F (class III) sequence motifs.
Length = 67
Score = 27.6 bits (62), Expect = 3.4
Identities = 16/59 (27%), Positives = 27/59 (45%)
Query: 7 EELFKTCDKKGTGQIGPEEFRELCTGFDIQPTDSDAIFADLDHDGDGKVSLEDFAYGFR 65
+++F++ D G G I +E R + + I+ D D DGK+ E+FA
Sbjct: 2 DQIFRSLDPDGDGLISGDEARPFLGKSGLPRSVLAQIWDLADTDKDGKLDKEEFAIAMH 60
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 30.2 bits (69), Expect = 3.4
Identities = 48/194 (24%), Positives = 65/194 (33%), Gaps = 48/194 (24%)
Query: 388 EPDRAFKIVFAGDAAVGKSCFIYRFSKEVFL---NKLGSTLGVDFQMKTIRVDERNVALQ 444
E KI G VGKS I E + + G+T D D R
Sbjct: 174 EETDPIKIAIIGRPNVGKSSLINAILGEERVIVSDIAGTT--RDSIDIEFERDGRK--YV 229
Query: 445 LWDTAG----------QERFRSM-TKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEE- 492
L DTAG E++ T RAD V+L+ D T E + E
Sbjct: 230 LIDTAGIRRKGKITESVEKYSVARTLKAIERADVVLLVIDAT------------EGISEQ 277
Query: 493 -------VTENSIPIVICANKVDL---RADAQAKGVKCIDREVGEKLAQQYGAIFMETSS 542
+ E IVI NK DL + K + R KL A + S+
Sbjct: 278 DLRIAGLIEEAGRGIVIVVNKWDLVEEDEATMEEFKKKLRR----KLPFLDFAPIVFISA 333
Query: 543 KSG---DNILDALI 553
+G D + +A+
Sbjct: 334 LTGQGLDKLFEAIK 347
>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 = 29.4 bits (66), Expect = 3.4
Identities = 34/153 (22%), Positives = 64/153 (41%), Gaps = 15/153 (9%)
Query: 399 GDAAVGKSCFIYRFSKEVFLNKLGSTLGVDFQMKTIRVDERNVALQLWDTAGQERFRSMT 458
G+ GKS ++R+ ++ +L S G F+ K + VD ++ L + D G +
Sbjct: 7 GNLRSGKSALVHRYLTGSYV-QLESPEGGRFK-KEVLVDGQSHLLLIRDEGGAPDAQ--- 61
Query: 459 KNYFRRADGVMLLYDVTNERSFNSVKNWVEAVEEVTENS-IPIVICANKVDLRADA-QAK 516
+ D V+ ++ + +E SF +V + S IP+++ + DA A
Sbjct: 62 --FAGWVDAVIFVFSLEDEASFQTVYRLYHQLSSYRNISEIPLILVGTQ-----DAISAS 114
Query: 517 GVKCIDREVGEKLAQQYG-AIFMETSSKSGDNI 548
+ ID +L + ET + G N+
Sbjct: 115 NPRVIDDARARQLCADMKRCSYYETCATYGLNV 147
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 30.5 bits (68), Expect = 3.5
Identities = 44/223 (19%), Positives = 86/223 (38%), Gaps = 17/223 (7%)
Query: 138 EIVTHFEGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQA 197
E++ +E ++ K+ E K EE+ E E +E + + A+ + +A
Sbjct: 1596 EVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKA 1655
Query: 198 KEEARAKYEQE---------KAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDP 248
+EE + K +E KA +K E + ++ L + +E K ++ ++
Sbjct: 1656 EEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEK 1715
Query: 249 TSDHNFSFENEELKITLE--KTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDYLELDQG 306
EE KI E K + D AE A+ E + K L + E +
Sbjct: 1716 KKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAE-EIR 1774
Query: 307 SDKQFAIQRLMEDIDSGRS-----TMRDCMDCSSDYKSNNEEN 344
+K+ I+ +++ D R ++D D ++ +E
Sbjct: 1775 KEKEAVIEEELDEEDEKRRMEVDKKIKDIFDNFANIIEGGKEG 1817
Score = 29.7 bits (66), Expect = 6.5
Identities = 34/143 (23%), Positives = 52/143 (36%), Gaps = 17/143 (11%)
Query: 156 RLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAK---EEARAKYEQEKAIL 212
R ED K E E E E + E+ + K +AK EEA+ E+
Sbjct: 1194 RKAEDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEE 1253
Query: 213 MRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNL 272
+RK E A K K +++K ++ + +E K EK K
Sbjct: 1254 IRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKK-------KADEAKKAEEKKK--- 1303
Query: 273 DLVHAEMAQLKSEYEGKCQELNQ 295
A+ A+ K+E K E +
Sbjct: 1304 ----ADEAKKKAEEAKKADEAKK 1322
>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis). This nucleolar
family of proteins are involved in 60S ribosomal
biogenesis. They are specifically involved in the
processing beyond the 27S stage of 25S rRNA maturation.
This family contains sequences that bear similarity to
the glioma tumour suppressor candidate region gene 2
protein (p60). This protein has been found to interact
with herpes simplex type 1 regulatory proteins.
Length = 387
Score = 30.1 bits (68), Expect = 3.6
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 155 KRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMR 214
+R + E EE +++ L RLK + +E+ + +A+++ + K EK L R
Sbjct: 288 RRKELEREAKEEKQLKKKLAQLARLKEIAKEVAQKEKA---RARKKEQRKERGEKKKLKR 344
Query: 215 K 215
+
Sbjct: 345 R 345
>gnl|CDD|220368 pfam09730, BicD, Microtubule-associated protein Bicaudal-D. BicD
proteins consist of three coiled-coiled domains and are
involved in dynein-mediated minus end-directed transport
from the Golgi apparatus to the endoplasmic reticulum
(ER). For full functioning they bind with GSK-3beta
pfam05350 to maintain the anchoring of microtubules to
the centromere. It appears that amino-acid residues
437-617 of BicD and the kinase activity of GSK-3 are
necessary for the formation of a complex between BicD
and GSK-3beta in intact cells.
Length = 711
Score = 30.2 bits (68), Expect = 3.8
Identities = 32/158 (20%), Positives = 63/158 (39%), Gaps = 17/158 (10%)
Query: 173 EVHLERLKGLEEELDVQVAK---VVTQAKEEARAKYEQEKAILMRKMEHETQELQAHLNL 229
E++L ++ L+++L QV + + +E + + EQ + L + E + L
Sbjct: 255 ELNLSEIQKLKQQL-EQVEREKASLLANLQELQTQLEQSEGALSEQHEKVNR-------L 306
Query: 230 FQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNLDLVHAEMAQLKSEYEGK 289
+ +N + + ++QQD +E+ E N +++ + SE
Sbjct: 307 TEHLNALRNLQASKEQQDGLDSEKDRGSHEDGDY-YEVDINGPEILECKYRVAVSEVGEL 365
Query: 290 CQELNQLVGDYLELDQGSDKQFA-----IQRLMEDIDS 322
EL L Y EL + + + IQ L E + S
Sbjct: 366 KAELKALKARYNELQERYEDEKDRLRNEIQNLAEKLLS 403
>gnl|CDD|221232 pfam11802, CENP-K, Centromere-associated protein K. CENP-K is one
of seven new CENP-A-nucleosome distal (CAD) centromere
components (the others being CENP-L, CENP-O, CENP-P,
CENP-Q, CENP-R and CENP-S) that are identified as
assembling on the CENP-A nucleosome associated complex,
NAC. The CENP-A NAC is essential, as disruption of the
complex causes errors of chromosome alignment and
segregation that preclude cell survival despite
continued centromere-derived mitotic checkpoint
signalling. CENP-K is centromere-associated through its
interaction with one or more components of the CENP-A
NAC.
Length = 273
Score = 29.8 bits (67), Expect = 4.0
Identities = 29/138 (21%), Positives = 57/138 (41%), Gaps = 24/138 (17%)
Query: 185 ELDVQVAKVVTQAKEEARAKYEQ-------------EKAILMRKMEHET--QELQAHLNL 229
E D Q++ ++ Q K A+YEQ + + + K E + Q+L+ L+
Sbjct: 54 ESDAQLSLLIMQMKA-LTAEYEQWQKRTPEIISLNEDVLLTLGKEELQKLRQDLEMVLSS 112
Query: 230 FQKVNNVLKEKKIEKQQDPTSDH-----NFSFENEELKITLEKTKNNLDLVHAEMAQLKS 284
Q N LKE +E++Q + + + ELK + + + E+
Sbjct: 113 VQSKNEKLKED-LEREQQWLDEQQQILDSLNERQSELKNQVVTFSESR--IFQELKTKML 169
Query: 285 EYEGKCQELNQLVGDYLE 302
+ ++L +G++LE
Sbjct: 170 RIKEYKEKLLSALGEFLE 187
>gnl|CDD|200474 cd11335, AmyAc_MTase_N, Alpha amylase catalytic domain found in
maltosyltransferase. Maltosyltransferase (MTase), a
maltodextrin glycosyltransferase, acts on starch and
maltooligosaccharides. It catalyzes the transfer of
maltosyl units from alpha-1,4-linked glucans or
maltooligosaccharides to other alpha-1,4-linked
glucans, maltooligosaccharides or glucose. MTase is a
homodimer. The catalytic core domain has the
(beta/alpha) 8 barrel fold with the active-site cleft
formed at the C-terminal end of the barrel. Substrate
binding experiments have led to the location of two
distinct maltose-binding sites: one lies in the
active-site cleft and the other is located in a pocket
adjacent to the active-site cleft. It is a member of
the alpha-amylase family, but unlike typical
alpha-amylases, MTase does not require calcium for
activity and lacks two histidine residues which are
predicted to be critical for binding the glucose
residue adjacent to the scissile bond in the
substrates. The common reaction chemistry of the
alpha-amylase family of enzymes is based on a two-step
acid catalytic mechanism that requires two critical
carboxylates: one acting as a general acid/base (Glu)
and the other as a nucleophile (Asp). Both hydrolysis
and transglycosylation proceed via the nucleophilic
substitution reaction between the anomeric carbon, C1
and a nucleophile. The Alpha-amylase family comprises
the largest family of glycoside hydrolases (GH), with
the majority of enzymes acting on starch, glycogen, and
related oligo- and polysaccharides. These proteins
catalyze the transformation of alpha-1,4 and alpha-1,6
glucosidic linkages with retention of the anomeric
center. The protein is described as having 3 domains:
A, B, C. A is a (beta/alpha) 8-barrel; B is a loop
between the beta 3 strand and alpha 3 helix of A; C is
the C-terminal extension characterized by a Greek key.
The majority of the enzymes have an active site cleft
found between domains A and B where a triad of
catalytic residues (Asp, Glu and Asp) performs
catalysis. Other members of this family have lost the
catalytic activity as in the case of the human 4F2hc,
or only have 2 residues that serve as the catalytic
nucleophile and the acid/base, such as Thermus A4
beta-galactosidase with 2 Glu residues (GH42) and human
alpha-galactosidase with 2 Asp residues (GH31). The
family members are quite extensive and include: alpha
amylase, maltosyltransferase, cyclodextrin
glycotransferase, maltogenic amylase, neopullulanase,
isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 538
Score = 30.0 bits (68), Expect = 4.0
Identities = 14/26 (53%), Positives = 16/26 (61%), Gaps = 4/26 (15%)
Query: 48 DHDGDGKVSLEDFAYGFRE---FLNS 70
DHDGDG + E+ YGFRE FL
Sbjct: 60 DHDGDGALEPEN-LYGFRETGTFLKM 84
>gnl|CDD|240419 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
Provisional.
Length = 2722
Score = 30.2 bits (68), Expect = 4.1
Identities = 31/139 (22%), Positives = 59/139 (42%), Gaps = 13/139 (9%)
Query: 213 MRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFEN--EELKITLEKTKN 270
++++ E +++ L+ + + L EK + E + K LEKT N
Sbjct: 1267 LQQVIKENNKMENALHEIKNMYEFLISIDSEKILKEILNSTKKAEEFSNDAKKELEKTDN 1326
Query: 271 NLDLVHAEMAQLKSEYEGKCQELNQLVGDYLELDQGSDKQFAIQRLMEDIDSGRSTMRDC 330
+ V A++ Q K E++ K + LE Q D+ I+++ E+I + R +
Sbjct: 1327 LIKQVEAKIEQAK-EHKNK-------IYGSLEDKQIDDEIKKIEQIKEEISNKRKEI--- 1375
Query: 331 MDCSSDYKSNNEENMSSLS 349
S+ KSN E+ +
Sbjct: 1376 NKYLSNIKSNKEKCDLHVR 1394
>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 30.0 bits (68), Expect = 4.2
Identities = 19/87 (21%), Positives = 33/87 (37%), Gaps = 6/87 (6%)
Query: 239 EKKIEKQQDPTSDHNF------SFENEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQE 292
E KI+K P D S E +L+ + + + V + L+ E +
Sbjct: 44 ESKIKKLGIPLKDTGGKPDVPPSKEFLDLEEEILDLEAEIKEVEENLESLEKEINELEEW 103
Query: 293 LNQLVGDYLELDQGSDKQFAIQRLMED 319
LN L + LD+ ++ + L D
Sbjct: 104 LNVLDEEKSFLDENLEELSELSNLDID 130
>gnl|CDD|203593 pfam07200, Mod_r, Modifier of rudimentary (Mod(r)) protein. This
family represents a conserved region approximately 150
residues long within a number of eukaryotic proteins
that show homology with Drosophila melanogaster Modifier
of rudimentary (Mod(r)) proteins. The N-terminal half of
Mod(r) proteins is acidic, whereas the C-terminal half
is basic, and both of these regions are represented in
this family. Members of this family include the Vps37
subunit of the endosomal sorting complex ESCRT-I, a
complex involved in recruiting transport machinery for
protein sorting at the multivesicular body (MVB). The
yeast ESCRT-I complex consists of three proteins (Vps23,
Vps28 and Vps37). The mammalian homologue of Vps37
interacts with Tsg101 (Pfam: PF05743) through its mod(r)
domain and its function is essential for lysosomal
sorting of EGF receptors.
Length = 150
Score = 28.8 bits (65), Expect = 4.4
Identities = 16/44 (36%), Positives = 26/44 (59%)
Query: 257 ENEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDY 300
EN E + LE+ K L + E+ +L+ +YE K Q+L++L Y
Sbjct: 49 ENLEKEPQLEELKAQLRDKYEELKKLEEKYEEKKQQLDELSSSY 92
>gnl|CDD|232931 TIGR00344, alaS, alanine--tRNA ligase. The model describes
alanine--tRNA ligase. This enzyme catalyzes the reaction
(tRNAala + L-alanine + ATP = L-alanyl-tRNAala +
pyrophosphate + AMP) [Protein synthesis, tRNA
aminoacylation].
Length = 851
Score = 30.0 bits (68), Expect = 4.5
Identities = 19/103 (18%), Positives = 48/103 (46%), Gaps = 6/103 (5%)
Query: 114 KFLNTSGKKLADLYHELR-TSSNCPEIVTHFEGALSSLLDDVKRLHE--DNEKLEEMFNR 170
++LN KL +L L+ T + P+ + F +L +++ L ++K++E+ ++
Sbjct: 701 EYLNEQEDKLKELADILKVTPNELPKKIERFFEEWKALQKELESLKLKIADQKIDELKDK 760
Query: 171 EREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILM 213
++ +K L E +D + K + + ++K ++
Sbjct: 761 AETIN--GVKVLVEVVDAKDMKSLKTMADRLKSKLG-SAIYVL 800
>gnl|CDD|114219 pfam05483, SCP-1, Synaptonemal complex protein 1 (SCP-1).
Synaptonemal complex protein 1 (SCP-1) is the major
component of the transverse filaments of the
synaptonemal complex. Synaptonemal complexes are
structures that are formed between homologous
chromosomes during meiotic prophase.
Length = 787
Score = 30.1 bits (67), Expect = 4.6
Identities = 36/117 (30%), Positives = 54/117 (46%), Gaps = 22/117 (18%)
Query: 157 LHEDNEKLEEM--FNREREVHLERLKGL--EEELDVQVAKVVTQAKEEARAKYEQEKAIL 212
L + + +LEEM F +EV LE LK + E+E + K + EE + K EQE L
Sbjct: 386 LQKKSSELEEMTKFKNNKEVELEELKKILAEDEKLLDEKKQFEKIAEELKGK-EQELIFL 444
Query: 213 MRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEKTK 269
++ E E +L+ L + TS+ ++ E E+LK LEK K
Sbjct: 445 LQAREKEIHDLEIQLTAIK-----------------TSEEHYLKEVEDLKTELEKEK 484
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 29.9 bits (68), Expect = 4.8
Identities = 29/127 (22%), Positives = 57/127 (44%), Gaps = 9/127 (7%)
Query: 203 AKYEQEKAILMRKMEHETQELQAHLN-LFQKVNNVLKEKKIEKQQDPTSDHNFSFENEEL 261
K +Q R ++ +EL+ + LFQ + + + ++K ++Q + ++ E+E+
Sbjct: 508 KKSDQASRSSFRDLDESLKELKFEADELFQMLRSFVLKRKKQEQNGRLI-YRYNTESEKG 566
Query: 262 KI--TLEKTKNNL-----DLVHAEMAQLKSEYEGKCQELNQLVGDYLELDQGSDKQFAIQ 314
K+ + + N L DL+ AQ K E E L G+Y L +K +
Sbjct: 567 KLWDAITELANRLCYDLRDLLTLLEAQKKELQEKMESESAFLTGEYAHLIDLLEKMAQLL 626
Query: 315 RLMEDID 321
+L+ + D
Sbjct: 627 QLLFEED 633
>gnl|CDD|220664 pfam10267, Tmemb_cc2, Predicted transmembrane and coiled-coil 2
protein. This family of transmembrane coiled-coil
containing proteins is conserved from worms to humans.
Its function is unknown.
Length = 387
Score = 29.8 bits (67), Expect = 4.9
Identities = 29/109 (26%), Positives = 48/109 (44%), Gaps = 16/109 (14%)
Query: 141 THFEGALSSLLDDVKR--------LHEDN---EKLEEMFNREREVHLERLKGLEEELDVQ 189
+ E + L + ++R L E+ E+LEE N E+H + L++EL
Sbjct: 222 SRLEESYERLKEQLQRDYQYITQSLQEERYRYERLEEQLNDLTELHQNEIANLKQELASM 281
Query: 190 VAKVVTQAKEEARAKYEQEKAILMR--KMEHETQE---LQAHLNLFQKV 233
KV Q+ E AR E ++ R K+E + Q+ L+ N +V
Sbjct: 282 EEKVAYQSYERARDIQEAMESCQTRISKLEQQQQQVVQLEGMENSNARV 330
>gnl|CDD|222524 pfam14071, YlbD_coat, Putative coat protein. This is a family of
putative bacterial coat proteins. Proteins in this
family are approximately 140 amino acids in length.
Length = 122
Score = 28.5 bits (64), Expect = 5.0
Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 12/74 (16%)
Query: 195 TQAKEEARAKYEQEKAILMRKM-----EHETQELQAHLNLFQK----VNNVL---KEKKI 242
+ + E+ K + ++ + + +LQ HLN + V +VL +
Sbjct: 46 EPSSSSEEKEEEEGKNDFLSQLVSMVKKMDVNQLQNHLNNVSQAISSVQSVLQQFQGTGE 105
Query: 243 EKQQDPTSDHNFSF 256
+K Q + +H FSF
Sbjct: 106 KKSQQGSPEHPFSF 119
>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 = 28.9 bits (66), Expect = 5.0
Identities = 25/104 (24%), Positives = 43/104 (41%), Gaps = 24/104 (23%)
Query: 463 RRADGVMLLYDVTNERSFNSVKNWVEAVEE--------VTENSIPIVICANKVDLRADAQ 514
RAD V+L+ D + E + E + E ++I NK DL +
Sbjct: 83 ERADVVLLVLDAS------------EGITEQDLRIAGLILEEGKALIIVVNKWDLV-EKD 129
Query: 515 AKGVKCIDREVGEKLAQQYGAIFMETSSKSG---DNILDALIAL 555
K +K ++E+ KL A + S+ +G D + DA+ +
Sbjct: 130 EKTMKEFEKELRRKLPFLDYAPIVFISALTGQGVDKLFDAIKEV 173
>gnl|CDD|234575 PRK00016, PRK00016, metal-binding heat shock protein; Provisional.
Length = 159
Score = 28.7 bits (65), Expect = 5.1
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 158 HEDNEKLEEMFNREREVHLERLKGLEEELDVQ 189
H ++E+ EEMF E E+ L L GL +
Sbjct: 129 HIEDEEAEEMFGLEEEI-LAAL-GLPRPYIAE 158
>gnl|CDD|203820 pfam07956, DUF1690, Protein of Unknown function (DUF1690). Family
of uncharacterized fungal proteins.
Length = 142
Score = 28.6 bits (64), Expect = 5.2
Identities = 21/117 (17%), Positives = 41/117 (35%), Gaps = 7/117 (5%)
Query: 137 PEIVTHFEGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQ 196
P F L S L+ ++ E + +++ L LE E + K
Sbjct: 4 PSTPIEFSQKLVSQLESSTETDYSRQQYAEKYIQKKVA--AELSQLEVE---TLKKFEDT 58
Query: 197 AKEEARAKYEQ--EKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSD 251
+ + E + + + + L L F K+ K KK+++ +D S+
Sbjct: 59 LNSSLLSDDSKDNENGLSSNLLNEKIESLTEKLEEFSKLEEKEKSKKLKEVEDARSE 115
>gnl|CDD|221049 pfam11262, Tho2, Transcription factor/nuclear export subunit
protein 2. THO and TREX form a eukaryotic complex which
functions in messenger ribonucleoprotein metabolism and
plays a role in preventing the transcription-associated
genetic instability. Tho2, along with four other
subunits forms THO.
Length = 296
Score = 29.2 bits (66), Expect = 5.5
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 9/66 (13%)
Query: 176 LERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNN 235
+ERL+ +ELD + + + KE + + + L +EL+ H+ +K
Sbjct: 33 IERLEKQIKELDSSSSGIDKKKKE--KKRLKSLIKKLE-------EELKKHIEHNEKTKK 83
Query: 236 VLKEKK 241
L E+K
Sbjct: 84 RLSEEK 89
>gnl|CDD|223429 COG0352, ThiE, Thiamine monophosphate synthase [Coenzyme
metabolism].
Length = 211
Score = 29.1 bits (66), Expect = 5.5
Identities = 15/68 (22%), Positives = 23/68 (33%), Gaps = 6/68 (8%)
Query: 471 LYDVTNERSFNSVKNWVEAVEEVTENSIPIVICANKVDLRADAQAKGVKCIDREVGEKLA 530
LY VT+ + +E VE + + V K + A K L
Sbjct: 8 LYLVTDRPLIYDGVDLLEWVEAALKGGVTAVQLREKDLSDEEYLALAEKLRA------LC 61
Query: 531 QQYGAIFM 538
Q+YG +
Sbjct: 62 QKYGVPLI 69
>gnl|CDD|204632 pfam11365, DUF3166, Protein of unknown function (DUF3166). This
eukaryotic family of proteins has no known function.
Length = 97
Score = 27.9 bits (62), Expect = 5.6
Identities = 13/51 (25%), Positives = 27/51 (52%)
Query: 257 ENEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDYLELDQGS 307
++ +L+ L+ K L+ ++A+L+ E + EL + Y +LD G+
Sbjct: 2 DSADLRCQLQFVKEEAALMRKKLAKLEEEKDKVEGELQKYKSKYGDLDSGA 52
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 28.8 bits (65), Expect = 5.6
Identities = 24/92 (26%), Positives = 35/92 (38%), Gaps = 15/92 (16%)
Query: 438 ERNVALQLWDTAGQERFRSM-TKNYFRRADGVMLLYDVTNERSFNSVKNWVEAVE----- 491
+ L L D G E+ R + ++ + D +F KN + E
Sbjct: 44 SKGKKLTLVDVPGHEKLRDKLLEYLKASLKAIVFVVDSA---TFQ--KNIRDVAEFLYDI 98
Query: 492 ----EVTENSIPIVICANKVDLRADAQAKGVK 519
E +N IPI+I NK DL AK +K
Sbjct: 99 LTDLEKIKNKIPILIACNKQDLFTAKPAKKIK 130
>gnl|CDD|216865 pfam02074, Peptidase_M32, Carboxypeptidase Taq (M32)
metallopeptidase.
Length = 494
Score = 29.4 bits (66), Expect = 5.6
Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 14/85 (16%)
Query: 123 LADLYHELRTSSNCPEIVTHFEGALSSLLDDVKRLHEDNEKLEEMFNREREVHLERLKGL 182
L+ L HE T P I LL+ V+ ED + + R ER + +
Sbjct: 50 LSRLLHERLTD---PRIG--------ELLEKVEGSFEDLLEDAAVNVRVWRRAYERARAI 98
Query: 183 EEELDVQVAKVVTQAK---EEARAK 204
E L ++A+ ++A+ EEA+ K
Sbjct: 99 PERLAKELAQATSKAETAWEEAKPK 123
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 28.8 bits (65), Expect = 5.6
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 188 VQVAKVVTQAKE--EARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQ 245
V V KV++++ A+ + E+E L +++ + +ELQ QK L E+ + +
Sbjct: 21 VDVQKVLSESPAGKAAQKQLEKEFKKLQAELQKKEKELQKEEQKLQKQAATLSEEARKAK 80
Query: 246 QD 247
Q
Sbjct: 81 QQ 82
Score = 28.0 bits (63), Expect = 9.2
Identities = 20/90 (22%), Positives = 43/90 (47%), Gaps = 5/90 (5%)
Query: 155 KRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAILMR 214
K + EK + E + + L+ E++L Q A + +A++ + + +Q++ L +
Sbjct: 34 KAAQKQLEKEFKKLQAELQKKEKELQKEEQKLQKQAATLSEEARKAKQQELQQKQQELQQ 93
Query: 215 KMEHETQELQAHLN-----LFQKVNNVLKE 239
K + QELQ ++ K++ +KE
Sbjct: 94 KQQAAQQELQQKQQELLQPIYDKIDKAIKE 123
>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 = 29.3 bits (67), Expect = 5.7
Identities = 15/62 (24%), Positives = 31/62 (50%), Gaps = 9/62 (14%)
Query: 499 PIVICANKVDLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSSKSGDNILDALI-ALSR 557
P ++ NK+DL + + + E+ ++L + G S+ +G+ LD L+ AL+
Sbjct: 275 PRIVVLNKIDLLDEEELE-------ELLKELKEALGKPVFPISALTGEG-LDELLYALAE 326
Query: 558 HV 559
+
Sbjct: 327 LL 328
>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 = 29.3 bits (66), Expect = 6.4
Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 37/128 (28%)
Query: 447 DTAGQERFRSMTKNYFRRA-------------DGVMLLYDVTNERSFNSVKNWVEAVEEV 493
DT G E F SM R A DGVM +EA+
Sbjct: 141 DTPGHEAFTSMRA---RGAKVTDIVVLVVAADDGVM--------------PQTIEAISHA 183
Query: 494 TENSIPIVICANKVDLRADAQAKGVKCIDREVGEKLAQQYGA--IFMETSSKSGDNI--- 548
++PI++ NK+D + +A VK E G + + +G IF+ S+ +GD I
Sbjct: 184 KAANVPIIVAINKID-KPEANPDRVKQELSEYG-LVPEDWGGDTIFVPVSALTGDGIDEL 241
Query: 549 LDALIALS 556
LD ++ S
Sbjct: 242 LDMILLQS 249
>gnl|CDD|153337 cd07653, F-BAR_CIP4-like, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Cdc42-Interacting Protein
4 and similar proteins. F-BAR domains are dimerization
modules that bind and bend membranes and are found in
proteins involved in membrane dynamics and actin
reorganization. This subfamily is composed of
Cdc42-Interacting Protein 4 (CIP4), Formin Binding
Protein 17 (FBP17), FormiN Binding Protein 1-Like
(FNBP1L), and similar proteins. CIP4 and FNBP1L are
Cdc42 effectors that bind Wiskott-Aldrich syndrome
protein (WASP) and function in endocytosis. CIP4 and
FBP17 bind to the Fas ligand and may be implicated in
the inflammatory response. CIP4 may also play a role in
phagocytosis. Members of this subfamily typically
contain an N-terminal F-BAR domain and a C-terminal SH3
domain. In addition, some members such as FNBP1L contain
a central Cdc42-binding HR1 domain. F-BAR domains form
banana-shaped dimers with a positively-charged concave
surface that binds to negatively-charged lipid
membranes. They can induce membrane deformation in the
form of long tubules.
Length = 251
Score = 28.8 bits (65), Expect = 6.6
Identities = 26/117 (22%), Positives = 50/117 (42%), Gaps = 7/117 (5%)
Query: 199 EEARAKYEQEKAI--LMRKMEHETQELQAHLNLFQKVNNVLK--EKKIEKQQDPTSDHNF 254
E A+ L + QE + HL+ K+ L+ K++EK + + F
Sbjct: 81 HELIAENLNSNVCKELKTLISELRQERKKHLSEGSKLQQKLESSIKQLEKSKK-AYEKAF 139
Query: 255 SFENEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDY-LELDQGSDKQ 310
E E+ K EK +++L A++ + K+ K Q + +Y +L + + +Q
Sbjct: 140 -KEAEKAKQKYEKADADMNLTKADVEKAKANANLKTQAAEEAKNEYAAQLQKFNKEQ 195
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 29.5 bits (67), Expect = 6.7
Identities = 30/179 (16%), Positives = 59/179 (32%), Gaps = 22/179 (12%)
Query: 138 EIVTHFEGALSSLLDDVKRLHEDNEKLEEM---FNREREVHLERLKGLEEELD------- 187
E++ E L + ++K L E+ +LE +E E LE + +L
Sbjct: 86 ELIKDVEEELEKIEKEIKELEEEISELENEIKELEQEIER-LEPWGNFDLDLSLLLGFKY 144
Query: 188 --VQVAKVVTQAKEEARAKYEQEKAILMR-KMEHETQELQAHLNLFQKVNNVLKEKKIEK 244
V V V EE + + + E + + + L +V LK+ E+
Sbjct: 145 VSVFVGTVPEDKLEELKLESDVENVEYISTDKGYVYVVVVVLKELSDEVEEELKKLGFER 204
Query: 245 QQDPTSDHNFSFENEELKITLEKTKNNLDLVHAEMAQLKSEYEGKCQELNQLVGDYLEL 303
+ + + K L+ + E L E + ++ + + E
Sbjct: 205 LELEEE--------GTPSELIREIKEELEEIEKERESLLEELKELAKKYLEELLALYEY 255
>gnl|CDD|114015 pfam05266, DUF724, Protein of unknown function (DUF724). This
family contains several uncharacterized proteins found
in Arabidopsis thaliana and other plants. This region is
often found associated with Agenet domains and may
contain coiled-coil.
Length = 190
Score = 28.6 bits (64), Expect = 6.7
Identities = 25/109 (22%), Positives = 46/109 (42%), Gaps = 15/109 (13%)
Query: 153 DVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAIL 212
+V+ L KL + + + + LE KGLE+E KE +R + + E
Sbjct: 87 NVQALQSRLNKLLSLKDDQTKK-LEERKGLEKE---------IAEKEISRQELDSE---- 132
Query: 213 MRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEEL 261
+ ++E + ELQ L ++ +K+I + + S + EL
Sbjct: 133 IAELERKILELQRQAALLKEKKEAE-DKEIARLKSEASKIKQELVDAEL 180
>gnl|CDD|220614 pfam10174, Cast, RIM-binding protein of the cytomatrix active zone.
This is a family of proteins that form part of the CAZ
(cytomatrix at the active zone) complex which is
involved in determining the site of synaptic vesicle
fusion. The C-terminus is a PDZ-binding motif that binds
directly to RIM (a small G protein Rab-3A effector). The
family also contains four coiled-coil domains.
Length = 774
Score = 29.2 bits (65), Expect = 7.0
Identities = 32/173 (18%), Positives = 65/173 (37%), Gaps = 5/173 (2%)
Query: 154 VKRLHEDNEKLEEMFNREREVHLERLKG-LEEELDVQVAKVVTQAKEEARAKYEQEKAIL 212
++ L + E L+E F R +E L+ K L + E+A A+ E+ L
Sbjct: 394 LRVLQKKIENLQETF-RRKERRLKEEKERLRSLQTDTNTDTALEKLEKALAEKERIIERL 452
Query: 213 MRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNL 272
+ + + + Q ++K LKE +++ Q S+ E LK + K +N
Sbjct: 453 KEQRDRDERYEQEEFETYKKEFEDLKE-EVQNLQLKLSERELQL--ELLKEEVSKLASNQ 509
Query: 273 DLVHAEMAQLKSEYEGKCQELNQLVGDYLELDQGSDKQFAIQRLMEDIDSGRS 325
+++ + E E ++ +L + L + + R+
Sbjct: 510 LKQRSDLERAHIELEKIREKHEKLEKELKRLRANPESADRGSAVDAGTSRSRA 562
>gnl|CDD|216295 pfam01093, Clusterin, Clusterin.
Length = 434
Score = 29.3 bits (66), Expect = 7.3
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 177 ERLKGLEEE----LDVQVAKVVTQAKE--EARAKYEQEKAILMRKMEHETQELQAHLNLF 230
LK L EE +D +V + K+ + E+E LM +E +E + L L
Sbjct: 1 NELKQLSEEGEKYVDEEVKNALIGVKQMKTLMERTEEEHKNLMSTLEKTKKEKEEALKLA 60
Query: 231 QKVNNVLKEKK 241
+V L+E++
Sbjct: 61 NEVEEKLEEEE 71
>gnl|CDD|215507 PLN02939, PLN02939, transferase, transferring glycosyl groups.
Length = 977
Score = 29.1 bits (65), Expect = 7.6
Identities = 25/149 (16%), Positives = 58/149 (38%), Gaps = 27/149 (18%)
Query: 148 SSLLDDVKRLHEDNEKLEEMFNR-----------EREVHLERLKGLEEELDVQVAKVVTQ 196
++ L V L + + ++ NR K E+ D Q+ +V
Sbjct: 77 NTSLRTVMELPQKSTSSDDDHNRASMQRDEAIAAIDNEQQTNSKDGEQLSDFQLEDLVGM 136
Query: 197 AKEEARAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSF 256
+ EK IL+ QA L + + +L EK+ + + + S
Sbjct: 137 IQN-------AEKNILLLN--------QARLQALEDLEKILTEKEALQGKINILEMRLSE 181
Query: 257 ENEELKITLEKTKNNLDLVHAEMAQLKSE 285
+ +K+ ++ K +++++ ++ +L++E
Sbjct: 182 TDARIKLAAQE-KIHVEILEEQLEKLRNE 209
>gnl|CDD|132868 cd07230, Pat_TGL4-5_like, Triacylglycerol lipase 4 and 5. TGL4 and
TGL5 are triacylglycerol lipases that are involved in
triacylglycerol mobilization and degradation; they are
found in lipid particles. Tgl4 is a functional ortholog
of mammalian adipose TG lipase (ATGL) and is
phosphorylated and activated by cyclin-dependent kinase
1 (Cdk1/Cdc28). TGL4 is 30% homologus to TGL3, whereas
TGL5 is 26% homologus to TGL3. This family includes TGL4
(STC1) and TGL5 (STC2) from Saccharomyces cerevisiae.
Length = 421
Score = 29.1 bits (66), Expect = 7.8
Identities = 15/77 (19%), Positives = 29/77 (37%), Gaps = 12/77 (15%)
Query: 96 VQNAWSLLLAGIGEANVHKFLNTSGKKLADLYHELRTSSNCPEIVTHFEGALSSLLDDVK 155
++ S L +G N+++ + KKL + Y + + L L+DD +
Sbjct: 5 IRTTLSRDLGNMGNVNLYRHSHVGTKKLIERY--ITEALLT----------LEYLVDDDE 52
Query: 156 RLHEDNEKLEEMFNRER 172
ED L + +
Sbjct: 53 DGLEDRYLLGMLLQTRK 69
>gnl|CDD|224914 COG2003, RadC, DNA repair proteins [DNA replication, recombination,
and repair].
Length = 224
Score = 28.7 bits (65), Expect = 8.1
Identities = 24/132 (18%), Positives = 44/132 (33%), Gaps = 14/132 (10%)
Query: 155 KRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAI--- 211
K L ++ L E+ E L +KG+ +Q+ + K + + I
Sbjct: 48 KELLQEFGSLAELLKASVE-ELSSVKGIGLAKAIQIKAAIELGKRILAERLREGVVITSP 106
Query: 212 ------LMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKITL 265
L ++ E +E L L + N ++ E T + + E K L
Sbjct: 107 EAVAEYLRAELGGEEREHFVVLYLDSQ-NRLIAT---ETLFIGTLNVSEVHPREIFKEAL 162
Query: 266 EKTKNNLDLVHA 277
+ + L H
Sbjct: 163 KYNAAAVILAHN 174
>gnl|CDD|150420 pfam09744, Jnk-SapK_ap_N, JNK_SAPK-associated protein-1. This is
the N-terminal 200 residues of a set of proteins
conserved from yeasts to humans. Most of the proteins in
this entry have an RhoGEF pfam00621 domain at their
C-terminal end.
Length = 158
Score = 28.2 bits (63), Expect = 8.5
Identities = 29/138 (21%), Positives = 57/138 (41%), Gaps = 20/138 (14%)
Query: 149 SLLDDVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQE 208
+L+++ L +N++LE RE + E E +E R + EQ+
Sbjct: 33 RVLENLDSLASENQELEVELELLREDNERLSTQYERE-------------KELRKQAEQK 79
Query: 209 KAILMRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEKT 268
++E E +ELQ + ++ +++E + SD E E + L+K
Sbjct: 80 LLEFEDELEQEKKELQKKIEDLEENV-----RQLELKAKNLSDQVSRLEERETE--LKKE 132
Query: 269 KNNLDLVHAEMAQLKSEY 286
N+L + ++ + EY
Sbjct: 133 YNSLHERYTKLLKNYVEY 150
Score = 27.8 bits (62), Expect = 9.9
Identities = 26/108 (24%), Positives = 54/108 (50%), Gaps = 15/108 (13%)
Query: 153 DVKRLHEDNEKLEEMFNRERE---------VHLE-RLKGLEEELDVQVAKVVTQAKE-EA 201
+++ L EDNE+L + RE+E + E L+ ++EL ++ + ++ E
Sbjct: 51 ELELLREDNERLSTQYEREKELRKQAEQKLLEFEDELEQEKKELQKKIEDLEENVRQLEL 110
Query: 202 RAKYEQEKAILMRKMEHETQELQAHLNLFQKVNNVLKEKK--IEKQQD 247
+AK ++ R E ET+ + + +L ++ +LK +E+Q+D
Sbjct: 111 KAKNLSDQVS--RLEERETELKKEYNSLHERYTKLLKNYVEYVERQKD 156
>gnl|CDD|226039 COG3508, HmgA, Homogentisate 1,2-dioxygenase [Secondary metabolites
biosynthesis, transport, and catabolism].
Length = 427
Score = 29.0 bits (65), Expect = 8.7
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 455 RSMTKNYFRRADGVMLLY 472
SMTK +FR ADG +L+
Sbjct: 134 ESMTKRFFRNADGELLIV 151
>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 = 28.2 bits (64), Expect = 9.0
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 16/73 (21%)
Query: 487 VEAVEEVTE----NSIPIVICANKVDLRADAQAKGVKCIDREVGEKLAQQYGAIFMETSS 542
+E VEEV + + IPI++ NK+DL +D E E+ + + S+
Sbjct: 139 IETVEEVLKELGADDIPIILVLNKIDL-----------LDDEELEERLRAGRPDAVFISA 187
Query: 543 KSGDNILDALIAL 555
K+G+ LD L
Sbjct: 188 KTGEG-LDLLKEA 199
>gnl|CDD|180871 PRK07191, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 456
Score = 28.6 bits (64), Expect = 9.4
Identities = 16/96 (16%), Positives = 38/96 (39%), Gaps = 5/96 (5%)
Query: 421 LGSTLGVDFQMKTIRVDERNVALQLWDTAGQERFRSMTKNYFRRADGVMLLYDVTNERSF 480
+ + GV+ R+ ++ V +Q W Q+ + + YF + V+ +
Sbjct: 51 VNAGNGVNVD-GIRRLSQQYVVMQEWQANSQQGYYDAGEQYFNALELVVGNKSTSLATGL 109
Query: 481 NSVKNWVEAVEEVTENSIPIVICANKVDLRADAQAK 516
N+ + + A ++ ++ +V A+A A
Sbjct: 110 NNFFSALSAATQLPDSP----PMRQQVIESANAMAL 141
>gnl|CDD|226809 COG4372, COG4372, Uncharacterized protein conserved in bacteria
with the myosin-like domain [Function unknown].
Length = 499
Score = 28.8 bits (64), Expect = 9.8
Identities = 26/156 (16%), Positives = 53/156 (33%), Gaps = 13/156 (8%)
Query: 161 NEKLEEMFNREREVHLERLKGLEEELDVQVAKV-VTQAKEEARAKYEQEKAILMRKMEHE 219
+ + + +++ L+ +L QV + + A+ E A+ +A + E
Sbjct: 164 EAQAQSLQASQKQ-----LQASATQLKSQVLDLKLRSAQIEQEAQNLATRANAAQARTEE 218
Query: 220 TQELQAHLNLFQKVNNVLKEKKIEKQQDPTSDHNFSFENEELKITLEKTKNNLDLVHAEM 279
A + + +K Q + E E L++ + + E+
Sbjct: 219 LARRAAAAQQTAQAIQQRDAQISQKAQQIAARAEQIRERER---QLQRLETAQARLEQEV 275
Query: 280 AQLKSEYEGKCQELNQLVGDYLELDQGSDKQFAIQR 315
AQL++ Y Q +L +G A QR
Sbjct: 276 AQLEAYY----QAYVRLRQQAAATQRGQVLAGAAQR 307
>gnl|CDD|236966 PRK11747, dinG, ATP-dependent DNA helicase DinG; Provisional.
Length = 697
Score = 29.0 bits (66), Expect = 9.8
Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 175 HLERLKGLEEELDVQVAKVVTQAKEEARAKYE-----QEKAILMRKMEHETQELQAHLNL 229
H E L+ L L+ + + EEAR ++E +E L ++ T++L L L
Sbjct: 307 HCEELRELLASLNQILNLFLPAGGEEARYRFEMGELPEELLELAERLAKLTEKL---LGL 363
Query: 230 FQKVNNVLKEKKIEKQQDP 248
+K+ N L E + D
Sbjct: 364 LEKLLNDLSEAMKTGKIDI 382
>gnl|CDD|236410 PRK09202, nusA, transcription elongation factor NusA; Validated.
Length = 470
Score = 28.7 bits (65), Expect = 10.0
Identities = 20/99 (20%), Positives = 41/99 (41%), Gaps = 7/99 (7%)
Query: 153 DVKRLHEDNEKLEEMFNREREVHLERLKGLEEELDVQVAKVVTQAKEEARAKYEQEKAIL 212
D+ E +EK + F+ ++ +E L EE + V + + +E A E+ I
Sbjct: 336 DIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIE 395
Query: 213 MRKMEHETQELQAHLNLFQKVNNVLKEKKIEKQQDPTSD 251
+ ET E L ++ L+ + + +++ D
Sbjct: 396 --GFDEETVE-----ELRERAKEALETEALAQEEKLADD 427
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
0.315 0.132 0.371
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,941,182
Number of extensions: 2965414
Number of successful extensions: 4514
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4117
Number of HSP's successfully gapped: 517
Length of query: 593
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 491
Effective length of database: 6,413,494
Effective search space: 3149025554
Effective search space used: 3149025554
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 (21.6 bits)
S2: 62 (27.8 bits)