RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11510
(171 letters)
>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 = 172 bits (439), Expect = 9e-56
Identities = 75/118 (63%), Positives = 86/118 (72%), Gaps = 16/118 (13%)
Query: 48 NGGETLILKK----------------KKMIMTFRFKLNIWDVGGQKSLRSYWRNYFESTD 91
N G+T ILKK K + +KLNIWDVGGQKSLRSYWRNYFESTD
Sbjct: 24 NAGKTTILKKFNGEDISTISPTLGFNIKTLEYNGYKLNIWDVGGQKSLRSYWRNYFESTD 83
Query: 92 GLIWVVDSADKRRLEDCARELHELLQEERLAGATLLVFANKQDIEGALTPEDIKNVSE 149
LIWVVDS+D+ RLEDC REL +LL EERLAGATLL+FANKQD+ GAL+PE+I+ V E
Sbjct: 84 ALIWVVDSSDRARLEDCKRELQKLLVEERLAGATLLIFANKQDLPGALSPEEIREVLE 141
Score = 43.5 bits (103), Expect = 8e-06
Identities = 16/17 (94%), Positives = 17/17 (100%)
Query: 5 FKLNIWDVGGQKSLRSY 21
+KLNIWDVGGQKSLRSY
Sbjct: 58 YKLNIWDVGGQKSLRSY 74
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 137 bits (348), Expect = 7e-42
Identities = 56/115 (48%), Positives = 71/115 (61%), Gaps = 16/115 (13%)
Query: 48 NGGETLILKKKK------MIMTFRF----------KLNIWDVGGQKSLRSYWRNYFESTD 91
N G+T IL K K I T F K +WDVGGQ+SLR WRNYF +TD
Sbjct: 24 NAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTD 83
Query: 92 GLIWVVDSADKRRLEDCARELHELLQEERLAGATLLVFANKQDIEGALTPEDIKN 146
+I+VVDSAD+ R+E+ ELH LL EE LA A LL+ ANKQD+ GA++ +I+
Sbjct: 84 AVIFVVDSADRDRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIRE 138
Score = 36.8 bits (86), Expect = 0.002
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 5 FKLNIWDVGGQKSLRSY--SYY 24
K +WDVGGQ+SLR +Y+
Sbjct: 58 VKFTVWDVGGQESLRPLWRNYF 79
>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 = 129 bits (326), Expect = 9e-39
Identities = 44/81 (54%), Positives = 60/81 (74%)
Query: 66 FKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGAT 125
K +WDVGGQ +R W++Y+E+TDGLI+VVDS+D+ R+E+ ELH+LL EE L GA
Sbjct: 43 VKFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEEELKGAP 102
Query: 126 LLVFANKQDIEGALTPEDIKN 146
LL+ ANKQD+ GALT ++
Sbjct: 103 LLILANKQDLPGALTESELIE 123
Score = 37.2 bits (87), Expect = 0.001
Identities = 10/22 (45%), Positives = 12/22 (54%), Gaps = 2/22 (9%)
Query: 5 FKLNIWDVGGQKSLRSY--SYY 24
K +WDVGGQ +R YY
Sbjct: 43 VKFTVWDVGGQDKIRPLWKHYY 64
>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 = 127 bits (320), Expect = 1e-37
Identities = 58/134 (43%), Positives = 82/134 (61%), Gaps = 16/134 (11%)
Query: 27 GMLRHRPQVSNVAVVSLLRNKNGGETLILKKK----------------KMIMTFRFKLNI 70
+ + +P + LL N G+T ILK+ K + FKLN+
Sbjct: 4 ILRKLKPSSRQEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQADGFKLNV 63
Query: 71 WDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATLLVFA 130
WD+GGQ+ +R YWRNYFE+TD LI+V+DSAD++R E+ +EL ELL+EE+LAG +LVFA
Sbjct: 64 WDIGGQRKIRPYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLVFA 123
Query: 131 NKQDIEGALTPEDI 144
NKQD+ A E++
Sbjct: 124 NKQDLLTAAPAEEV 137
Score = 38.5 bits (90), Expect = 4e-04
Identities = 12/22 (54%), Positives = 18/22 (81%), Gaps = 2/22 (9%)
Query: 5 FKLNIWDVGGQKSLRSY--SYY 24
FKLN+WD+GGQ+ +R Y +Y+
Sbjct: 59 FKLNVWDIGGQRKIRPYWRNYF 80
>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 = 110 bits (278), Expect = 1e-31
Identities = 42/78 (53%), Positives = 56/78 (71%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATL 126
K +WD+GGQ S+R YWR Y+ +TD +I+VVDS D+ RL ELH +L+EE L A L
Sbjct: 44 KFQVWDLGGQTSIRPYWRCYYSNTDAIIYVVDSTDRDRLGISKSELHAMLEEEELKDAVL 103
Query: 127 LVFANKQDIEGALTPEDI 144
LVFANKQD+ GAL+ ++
Sbjct: 104 LVFANKQDMPGALSEAEV 121
Score = 31.2 bits (71), Expect = 0.16
Identities = 11/21 (52%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 6 KLNIWDVGGQKSLRSY--SYY 24
K +WD+GGQ S+R Y YY
Sbjct: 44 KFQVWDLGGQTSIRPYWRCYY 64
>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 = 105 bits (263), Expect = 3e-29
Identities = 42/96 (43%), Positives = 64/96 (66%), Gaps = 7/96 (7%)
Query: 51 ETLILKKKKMIMTFRFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCAR 110
E L L+K L +WDVGGQ+ +R+ W+ Y E+TDGL++VVDS+D+ RL++ +
Sbjct: 36 EMLQLEKH-------LSLTVWDVGGQEKMRTVWKCYLENTDGLVYVVDSSDEARLDESQK 88
Query: 111 ELHELLQEERLAGATLLVFANKQDIEGALTPEDIKN 146
EL +L+ E + G +++ ANKQD+ GALT E+I
Sbjct: 89 ELKHILKNEHIKGVPVVLLANKQDLPGALTAEEITR 124
Score = 27.8 bits (62), Expect = 2.4
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 5 FKLNIWDVGGQKSLRS 20
L +WDVGGQ+ +R+
Sbjct: 44 LSLTVWDVGGQEKMRT 59
>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 = 104 bits (261), Expect = 5e-29
Identities = 46/111 (41%), Positives = 64/111 (57%), Gaps = 16/111 (14%)
Query: 50 GETLILKKKKM------IMTFRF----------KLNIWDVGGQKSLRSYWRNYFESTDGL 93
G+T IL K K+ I T F +WDVGGQ +R WR+YF++T GL
Sbjct: 12 GKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGL 71
Query: 94 IWVVDSADKRRLEDCARELHELLQEERLAGATLLVFANKQDIEGALTPEDI 144
I+VVDS D+ R+ + EL +L E+ L A LLVFANKQD+ A++ ++
Sbjct: 72 IFVVDSNDRERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNAMSAAEV 122
>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 = 102 bits (256), Expect = 3e-28
Identities = 48/113 (42%), Positives = 67/113 (59%), Gaps = 16/113 (14%)
Query: 48 NGGETLILKKKKM------IMTFRF----------KLNIWDVGGQKSLRSYWRNYFESTD 91
G+T IL K K+ I T F K N+WDVGGQ +R WR+Y+ T
Sbjct: 19 AAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQ 78
Query: 92 GLIWVVDSADKRRLEDCARELHELLQEERLAGATLLVFANKQDIEGALTPEDI 144
GLI+VVDSAD+ R+++ +ELH ++ + + A LLVFANKQD+ A+ P +I
Sbjct: 79 GLIFVVDSADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPDAMKPHEI 131
Score = 28.6 bits (64), Expect = 1.2
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 6 KLNIWDVGGQKSLR 19
K N+WDVGGQ +R
Sbjct: 54 KFNVWDVGGQDKIR 67
>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 = 102 bits (255), Expect = 6e-28
Identities = 39/75 (52%), Positives = 54/75 (72%)
Query: 70 IWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATLLVF 129
+WD+GGQ+SLRS W Y+ +TD +I V+DS D+ RL EL+++L E L A LLV
Sbjct: 63 MWDIGGQESLRSSWNTYYTNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVL 122
Query: 130 ANKQDIEGALTPEDI 144
ANKQD++GA+TP +I
Sbjct: 123 ANKQDLKGAMTPAEI 137
Score = 28.9 bits (65), Expect = 0.85
Identities = 11/18 (61%), Positives = 15/18 (83%), Gaps = 2/18 (11%)
Query: 9 IWDVGGQKSLRSY--SYY 24
+WD+GGQ+SLRS +YY
Sbjct: 63 MWDIGGQESLRSSWNTYY 80
>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 = 98.6 bits (246), Expect = 1e-26
Identities = 34/86 (39%), Positives = 51/86 (59%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATL 126
+L WD+GGQ+ LRS W Y+ + G+I+V+DS D+ R + +++ E L G L
Sbjct: 52 RLMFWDLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPL 111
Query: 127 LVFANKQDIEGALTPEDIKNVSEKAT 152
LV ANKQD+ AL+ +IK V +
Sbjct: 112 LVLANKQDLPDALSVAEIKEVFDDCI 137
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 98.0 bits (244), Expect = 3e-26
Identities = 51/117 (43%), Positives = 69/117 (58%), Gaps = 19/117 (16%)
Query: 50 GETLILKKKKM------IMTFRF----------KLNIWDVGGQKSLRSYWRNYFESTDGL 93
G+T IL K K+ I T F K +WDVGGQ LR WR+Y+++T+GL
Sbjct: 29 GKTTILYKLKLGEVVTTIPTIGFNVETVEYKNLKFTMWDVGGQDKLRPLWRHYYQNTNGL 88
Query: 94 IWVVDSADKRRLEDCARELHELLQEERLAGATLLVFANKQDIEGALTPEDIKNVSEK 150
I+VVDS D+ R+ D EL +L E+ L A LLVFANKQD+ A++ + V+EK
Sbjct: 89 IFVVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMSTTE---VTEK 142
>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 = 92.3 bits (229), Expect = 3e-24
Identities = 37/78 (47%), Positives = 53/78 (67%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATL 126
+WDVGGQ +R WR+Y+ +T GLI+VVDS D+ R+++ ELH +L E+ L A +
Sbjct: 58 SFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVI 117
Query: 127 LVFANKQDIEGALTPEDI 144
LVFANKQD+ A+ +I
Sbjct: 118 LVFANKQDLPDAMKAAEI 135
Score = 26.0 bits (57), Expect = 8.5
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 6 KLNIWDVGGQKSLRS 20
+WDVGGQ +R
Sbjct: 58 SFTVWDVGGQDKIRP 72
>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 = 91.3 bits (227), Expect = 8e-24
Identities = 33/80 (41%), Positives = 52/80 (65%)
Query: 65 RFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGA 124
++++ I+D+GG + R W NY+ GL++VVDS+D R+++ L ELLQ R++G
Sbjct: 42 KYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGK 101
Query: 125 TLLVFANKQDIEGALTPEDI 144
+LV ANKQD + AL D+
Sbjct: 102 PILVLANKQDKKNALLGADV 121
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 90.8 bits (225), Expect = 2e-23
Identities = 47/111 (42%), Positives = 65/111 (58%), Gaps = 16/111 (14%)
Query: 50 GETLILKKKKM-------------IMTFRFK---LNIWDVGGQKSLRSYWRNYFESTDGL 93
G+T IL K K+ + T +K +WDVGGQ +R WR+YF++T GL
Sbjct: 29 GKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGL 88
Query: 94 IWVVDSADKRRLEDCARELHELLQEERLAGATLLVFANKQDIEGALTPEDI 144
I+VVDS D+ R+ + ELH +L E+ L A LLVFANKQD+ A+ +I
Sbjct: 89 IFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEI 139
>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 = 86.3 bits (214), Expect = 5e-22
Identities = 35/87 (40%), Positives = 51/87 (58%), Gaps = 2/87 (2%)
Query: 59 KMIMTFRFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQE 118
I T + + ++GG ++LR YW+ Y + GLI+VVDSAD RL +ELH+LLQ
Sbjct: 37 VAIPTQDAIMELLEIGGSQNLRKYWKRYLSGSQGLIFVVDSADSERLPLARQELHQLLQH 96
Query: 119 ERLAGATLLVFANKQDIEGALTPEDIK 145
L+V ANKQD+ A + ++I
Sbjct: 97 P--PDLPLVVLANKQDLPAARSVQEIH 121
>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 = 82.0 bits (203), Expect = 2e-20
Identities = 32/77 (41%), Positives = 50/77 (64%)
Query: 68 LNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATLL 127
+ +WD+GGQ RS W Y + +++VVD+AD+ +LE ELH+LL++ L G LL
Sbjct: 46 IKVWDLGGQPRFRSMWERYCRGVNAIVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLL 105
Query: 128 VFANKQDIEGALTPEDI 144
V NK D+ GAL+ +++
Sbjct: 106 VLGNKNDLPGALSVDEL 122
>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 = 80.8 bits (199), Expect = 1e-19
Identities = 35/79 (44%), Positives = 55/79 (69%)
Query: 66 FKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGAT 125
K IWDVGG+ LR W++Y+ +T +++V+DS+ + R+ + EL +LL E+ L A
Sbjct: 43 LKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHRDRVSEAHSELAKLLTEKELRDAL 102
Query: 126 LLVFANKQDIEGALTPEDI 144
LL+FANKQD+ GAL+ E++
Sbjct: 103 LLIFANKQDVAGALSVEEM 121
>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 = 80.8 bits (200), Expect = 1e-19
Identities = 29/79 (36%), Positives = 49/79 (62%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATL 126
K +D+GG + R W++YF DG++++VD+AD R ++ EL LL +E LA +
Sbjct: 64 KFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDAADPERFQESKEELDSLLNDEELANVPI 123
Query: 127 LVFANKQDIEGALTPEDIK 145
L+ NK D GA++ E+++
Sbjct: 124 LILGNKIDKPGAVSEEELR 142
>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 = 79.8 bits (197), Expect = 3e-19
Identities = 36/86 (41%), Positives = 54/86 (62%), Gaps = 4/86 (4%)
Query: 62 MTFRFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERL 121
+TF F WDVGGQ+ LR W++Y TDG+++VVDS D R+E+ ELH++ +
Sbjct: 52 VTFHF----WDVGGQEKLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFSEN 107
Query: 122 AGATLLVFANKQDIEGALTPEDIKNV 147
G +LV ANKQD+ AL +++ +
Sbjct: 108 QGVPVLVLANKQDLPNALPVSEVEKL 133
>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 = 74.0 bits (182), Expect = 3e-17
Identities = 26/84 (30%), Positives = 42/84 (50%), Gaps = 2/84 (2%)
Query: 63 TFRFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLA 122
+D+ GQ R W +Y+++ G+I+V+DS+D+ R+ EL LL +
Sbjct: 42 KGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPDIK 101
Query: 123 GATL--LVFANKQDIEGALTPEDI 144
+ L +ANK D+ ALT I
Sbjct: 102 HRRIPILFYANKMDLPDALTAVKI 125
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 69.2 bits (169), Expect = 5e-15
Identities = 23/90 (25%), Positives = 36/90 (40%)
Query: 49 GGETLILKKKKMIMTFRFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDC 108
L K KL +WD GQ+ RS Y+ +G++ V DS + ++
Sbjct: 37 TIGNLDPAKTIEPYRRNIKLQLWDTAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDEL 96
Query: 109 ARELHELLQEERLAGATLLVFANKQDIEGA 138
E E L+E +L+ NK D+
Sbjct: 97 TEEWLEELRELAPDDVPILLVGNKIDLFDE 126
>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 = 65.7 bits (160), Expect = 6e-14
Identities = 27/79 (34%), Positives = 46/79 (58%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATL 126
K +D+GG + R W++YF +G++++VD+ DK R + REL LL +E LA
Sbjct: 62 KFTTFDLGGHQQARRLWKDYFPEVNGIVYLVDAYDKERFAESKRELDALLSDEELATVPF 121
Query: 127 LVFANKQDIEGALTPEDIK 145
L+ NK D A + ++++
Sbjct: 122 LILGNKIDAPYAASEDELR 140
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 55.9 bits (135), Expect = 3e-10
Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 4/88 (4%)
Query: 66 FKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGAT 125
++++ GQ+ + W G I +VDS+ A E+ + L
Sbjct: 68 TGVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFH--AEEIIDFLTSR--NPIP 123
Query: 126 LLVFANKQDIEGALTPEDIKNVSEKATK 153
++V NKQD+ AL PE I+ +
Sbjct: 124 VVVAINKQDLFDALPPEKIREALKLELL 151
>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 = 50.5 bits (121), Expect = 2e-08
Identities = 27/121 (22%), Positives = 44/121 (36%), Gaps = 11/121 (9%)
Query: 36 SNVAVVSLLRNKNGGETLILKKKKMIMTFRFKLNIWDVGGQ-----KSLRSYWRNYFEST 90
V VS + G K + + KL + D G R
Sbjct: 20 GEVGEVS---DVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEFGGLGREELARLLLRGA 76
Query: 91 DGLIWVVDSADKRRLEDCARELHELLQEERLAGATLLVFANKQDIEGALTPEDIKNVSEK 150
D ++ VVDS D+ ED + L++E G +++ NK D+ E++ + E
Sbjct: 77 DLILLVVDSTDRESEEDAKLLILRRLRKE---GIPIILVGNKIDLLEEREVEELLRLEEL 133
Query: 151 A 151
A
Sbjct: 134 A 134
>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 = 45.4 bits (108), Expect = 2e-06
Identities = 27/89 (30%), Positives = 44/89 (49%), Gaps = 4/89 (4%)
Query: 66 FKLNIWDVGGQKSLRS-YWRNYFESTDGLIWVVDSAD-KRRLEDCARELHELLQEERL-- 121
KL + DV G + LR S +++VVDSA ++ + D A L+++L +
Sbjct: 47 KKLTLVDVPGHEKLRDKLLEYLKASLKAIVFVVDSATFQKNIRDVAEFLYDILTDLEKIK 106
Query: 122 AGATLLVFANKQDIEGALTPEDIKNVSEK 150
+L+ NKQD+ A + IK + EK
Sbjct: 107 NKIPILIACNKQDLFTAKPAKKIKELLEK 135
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 44.7 bits (106), Expect = 4e-06
Identities = 28/91 (30%), Positives = 42/91 (46%), Gaps = 6/91 (6%)
Query: 66 FKLNIWDVGGQKSLRSYWRNYFESTD---GLIWVVDS-ADKRRLEDCARELHELLQEERL 121
F + D G LR + + G+++VVDS A + + D A L+E+L L
Sbjct: 49 FSFTLIDFPGHVKLRQKLLETIKDSSSLRGIVFVVDSTAFPKEVTDTAEFLYEILSITEL 108
Query: 122 A--GATLLVFANKQDIEGALTPEDIKNVSEK 150
G +L+ NKQ+ A P+ IK EK
Sbjct: 109 LKNGIDILIACNKQESFTARPPKKIKQALEK 139
>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 = 42.7 bits (101), Expect = 1e-05
Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 5/83 (6%)
Query: 66 FKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQE---ERLA 122
+K N+ D GQ+ + R Y+ + + + V D + D L + +E +
Sbjct: 51 YKFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIV--ILVLDVEEILEKQTKEIIHHAES 108
Query: 123 GATLLVFANKQDIEGALTPEDIK 145
G +++ NK D+ A +
Sbjct: 109 GVPIILVGNKIDLRDAKLKTHVA 131
>gnl|CDD|215955 pfam00503, G-alpha, G-protein alpha subunit. G proteins couple
receptors of extracellular signals to intracellular
signaling pathways. The G protein alpha subunit binds
guanyl nucleotide and is a weak GTPase. A set of
residues that are unique to G-alpha as compared to its
ancestor the Arf-like family form a ring of residues
centered on the nucleotide binding site. A Ggamma is
found fused to an inactive Galpha in the Dictyostelium
protein gbqA.
Length = 329
Score = 42.2 bits (100), Expect = 4e-05
Identities = 24/87 (27%), Positives = 38/87 (43%), Gaps = 13/87 (14%)
Query: 62 MTFRFKLNIW---DVGGQKSLRSYWRNYFESTDGLIWVVDSAD----------KRRLEDC 108
F FK + DVGGQ+S R W + FE +I+VV ++ RLE+
Sbjct: 161 TKFDFKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVVSLSEYDQVLYEDDSTNRLEES 220
Query: 109 ARELHELLQEERLAGATLLVFANKQDI 135
E+ +++F NK+D+
Sbjct: 221 LNLFEEICNSPWFKNTPIILFLNKKDL 247
>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 = 40.5 bits (95), Expect = 8e-05
Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATL 126
KL IWD GQ+S RS R+Y+ G + V D + L + Q + T+
Sbjct: 54 KLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSN-SNMTI 112
Query: 127 LVFANKQDIE 136
++ NK D+E
Sbjct: 113 MLIGNKCDLE 122
Score = 30.9 bits (70), Expect = 0.17
Identities = 13/21 (61%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 6 KLNIWDVGGQKSLRSY--SYY 24
KL IWD GQ+S RS SYY
Sbjct: 54 KLQIWDTAGQESFRSITRSYY 74
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 41.1 bits (96), Expect = 8e-05
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATL 126
KL IWD GQ+S RS R+Y+ G + V D + A L + Q A T+
Sbjct: 56 KLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHAN-ANMTI 114
Query: 127 LVFANKQDI 135
++ NK D+
Sbjct: 115 MLIGNKCDL 123
Score = 30.3 bits (68), Expect = 0.34
Identities = 13/21 (61%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 6 KLNIWDVGGQKSLRSY--SYY 24
KL IWD GQ+S RS SYY
Sbjct: 56 KLQIWDTAGQESFRSITRSYY 76
>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 = 40.4 bits (94), Expect = 1e-04
Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 7/86 (8%)
Query: 51 ETLILKKKKMIMTFRFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCAR 110
+T+ L+ KK+ +L IWD GQ+ S Y+ S G+I V D K +D +
Sbjct: 40 KTVELRGKKI------RLQIWDTAGQERFNSITSAYYRSAKGIILVYDITKKETFDDLPK 93
Query: 111 ELHELLQEERLAGATLLVFANKQDIE 136
+ +++ + A LL+ NK D E
Sbjct: 94 WM-KMIDKYASEDAELLLVGNKLDCE 118
>gnl|CDD|214595 smart00275, G_alpha, G protein alpha subunit. Subunit of G
proteins that contains the guanine nucleotide binding
site.
Length = 342
Score = 40.6 bits (96), Expect = 1e-04
Identities = 35/126 (27%), Positives = 52/126 (41%), Gaps = 30/126 (23%)
Query: 45 RNKNGG--ETLILKKKKMIMTFRFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSA-- 100
R G ET + KK + FR +DVGGQ+S R W + F++ +I+ V +
Sbjct: 168 RVPTTGIQETAFIVKK---LFFRM----FDVGGQRSERKKWIHCFDNVTAIIFCVALSEY 220
Query: 101 DKRRLED-CARELHELLQ------EER-LAGATLLVFANKQDIEGALTPEDIKNVSEKAT 152
D+ ED + E L R A ++++F NK D+ EK
Sbjct: 221 DQVLEEDESTNRMQESLNLFESICNSRWFANTSIILFLNKIDLF-----------EEKIK 269
Query: 153 KVKLNK 158
KV L
Sbjct: 270 KVPLVD 275
>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 = 39.3 bits (92), Expect = 2e-04
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 65 RFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGA 124
R KL IWD GQ+ R+ ++Y+ S +G I D + E + E+ E+ +
Sbjct: 51 RVKLQIWDTAGQERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEV---EKYGAS 107
Query: 125 T--LLVFANKQDIE 136
LL+ NK D+E
Sbjct: 108 NVVLLLIGNKCDLE 121
Score = 27.8 bits (62), Expect = 2.0
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 4 RFKLNIWDVGGQKSLRSY--SYY 24
R KL IWD GQ+ R+ SYY
Sbjct: 51 RVKLQIWDTAGQERFRTITQSYY 73
>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 = 38.7 bits (90), Expect = 6e-04
Identities = 18/51 (35%), Positives = 25/51 (49%)
Query: 65 RFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHEL 115
R KL IWD GQ+ R+ Y+ T G+I V D + + R L E+
Sbjct: 54 RVKLQIWDTAGQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEI 104
Score = 26.0 bits (57), Expect = 9.0
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 4 RFKLNIWDVGGQKSLRSY--SYY 24
R KL IWD GQ+ R+ +YY
Sbjct: 54 RVKLQIWDTAGQERFRTITSTYY 76
>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 = 38.1 bits (89), Expect = 6e-04
Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 9/88 (10%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGAT- 125
KL IWD GQ+ R+ +Y+ G+I V D D+ + + L E+ +R A
Sbjct: 52 KLQIWDTAGQERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEI---DRYASENV 108
Query: 126 --LLVFANKQDI--EGALTPEDIKNVSE 149
LLV NK D+ + + + K ++
Sbjct: 109 NKLLV-GNKCDLTDKKVVDYTEAKEFAD 135
Score = 26.9 bits (60), Expect = 5.0
Identities = 11/21 (52%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 6 KLNIWDVGGQKSLRSY--SYY 24
KL IWD GQ+ R+ SYY
Sbjct: 52 KLQIWDTAGQERFRTITSSYY 72
>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 = 37.8 bits (89), Expect = 8e-04
Identities = 22/88 (25%), Positives = 42/88 (47%), Gaps = 3/88 (3%)
Query: 65 RFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGA 124
+ KL IWD GQ+ RS +Y+ G I V D ++ E+ + L+E
Sbjct: 48 KVKLQIWDTAGQERFRSITSSYYRGAHGAILVYDVTNRESFENL-DKWLNELKEYAPPNI 106
Query: 125 TLLVFANKQDIEG--ALTPEDIKNVSEK 150
+++ NK D+E ++ E+ + +++
Sbjct: 107 PIILVGNKSDLEDERQVSTEEAQQFAKE 134
Score = 27.8 bits (63), Expect = 2.1
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 4 RFKLNIWDVGGQKSLRS--YSYY 24
+ KL IWD GQ+ RS SYY
Sbjct: 48 KVKLQIWDTAGQERFRSITSSYY 70
>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 = 37.8 bits (88), Expect = 0.001
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 4/57 (7%)
Query: 65 RFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERL 121
R KL +WD GQ+ RS R+Y+ ++ G++ V D ++ E +H+ L+E R
Sbjct: 51 RIKLQLWDTAGQERFRSITRSYYRNSVGVLLVFDITNRESFE----HVHDWLEEARS 103
Score = 29.7 bits (67), Expect = 0.57
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 4 RFKLNIWDVGGQKSLRSY--SYY 24
R KL +WD GQ+ RS SYY
Sbjct: 51 RIKLQLWDTAGQERFRSITRSYY 73
>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 = 36.4 bits (84), Expect = 0.002
Identities = 22/97 (22%), Positives = 42/97 (43%), Gaps = 3/97 (3%)
Query: 66 FKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGAT 125
F L +WD GQ+ + Y+ +I V D D LE + L + L+E +
Sbjct: 49 FSLQLWDTAGQERFKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVL 108
Query: 126 LLVFANKQDIEGALTPEDIKNVSEKATKVKLNKQSKF 162
L + K+D+ +P + + A K+ ++++
Sbjct: 109 LFLVGTKKDL---SSPAQYALMEQDAIKLAREMKAEY 142
>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 = 35.9 bits (83), Expect = 0.003
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATL 126
KL IWD GQ+ RS R+Y+ G + V D + L + LA +
Sbjct: 50 KLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLTDA---RTLASPDI 106
Query: 127 LVF--ANKQDIE 136
++ NK+D+E
Sbjct: 107 VIILVGNKKDLE 118
Score = 28.2 bits (63), Expect = 1.7
Identities = 12/21 (57%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 6 KLNIWDVGGQKSLRSY--SYY 24
KL IWD GQ+ RS SYY
Sbjct: 50 KLQIWDTAGQERFRSVTRSYY 70
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 35.9 bits (84), Expect = 0.004
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 65 RFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGA 124
R KL IWD GQ+ RS +Y+ G + V D ++ E+ L E L+E
Sbjct: 48 RVKLQIWDTAGQERFRSITSSYYRGAVGALLVYDITNRESFENLENWLKE-LREYASPNV 106
Query: 125 TLLVFANKQDIE 136
+++ NK D+E
Sbjct: 107 VIMLVGNKSDLE 118
Score = 26.7 bits (60), Expect = 5.2
Identities = 13/23 (56%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 4 RFKLNIWDVGGQKSLRSY--SYY 24
R KL IWD GQ+ RS SYY
Sbjct: 48 RVKLQIWDTAGQERFRSITSSYY 70
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 36.1 bits (83), Expect = 0.004
Identities = 27/113 (23%), Positives = 51/113 (45%), Gaps = 11/113 (9%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATL 126
K IWD GQ+ R+ Y+ G + V D ++ ++ R L E L++ + +
Sbjct: 62 KAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRE-LRDHADSNIVI 120
Query: 127 LVFANKQDIEG--ALTPEDIKNVSEK--------ATKVKLNKQSKFQVLLNEV 169
++ NK D+ ++ ED + ++EK + N + FQ +L E+
Sbjct: 121 MMAGNKSDLNHLRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFQTILLEI 173
>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 = 35.6 bits (82), Expect = 0.004
Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 65 RFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQE 118
+ KL IWD GQ+ RS ++Y+ S + LI D E+ R L E L+E
Sbjct: 55 KIKLQIWDTAGQERFRSITQSYYRSANALILTYDIT----CEESFRCLPEWLRE 104
Score = 27.9 bits (62), Expect = 1.9
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 4 RFKLNIWDVGGQKSLRSY--SYY 24
+ KL IWD GQ+ RS SYY
Sbjct: 55 KIKLQIWDTAGQERFRSITQSYY 77
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 35.8 bits (82), Expect = 0.006
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 65 RFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVD 98
R KL IWD GQ+ R+ +Y+ + G+I V D
Sbjct: 61 RLKLTIWDTAGQERFRTLTSSYYRNAQGIILVYD 94
Score = 28.1 bits (62), Expect = 1.9
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 4 RFKLNIWDVGGQKSLRSY--SYY 24
R KL IWD GQ+ R+ SYY
Sbjct: 61 RLKLTIWDTAGQERFRTLTSSYY 83
>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 = 35.2 bits (81), Expect = 0.007
Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 7/76 (9%)
Query: 65 RFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCAR---ELHELLQEERL 121
+ KL IWD GQ+ RS Y+ L+ + D +K ++ E+ E Q +
Sbjct: 49 KVKLQIWDTAGQERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSD-- 106
Query: 122 AGATLLVFANKQDIEG 137
+++ NK D+ G
Sbjct: 107 --VVIMLLGNKADMSG 120
Score = 28.7 bits (64), Expect = 1.2
Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 4 RFKLNIWDVGGQKSLRS--YSYY 24
+ KL IWD GQ+ RS ++YY
Sbjct: 49 KVKLQIWDTAGQERFRSVTHAYY 71
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 35.1 bits (80), Expect = 0.008
Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATL 126
+L +WD GQ+ RS +Y + I V D +++ E+ + + ++L ER +
Sbjct: 30 RLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILN-ERGKDVII 88
Query: 127 LVFANKQDI 135
+ NK D+
Sbjct: 89 ALVGNKTDL 97
>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 = 34.9 bits (81), Expect = 0.009
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 65 RFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGA 124
+ KL IWD GQ+ R+ +Y+ G+I V D D++ E+ + + E
Sbjct: 51 KIKLQIWDTAGQERFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRN-IDEHASEDV 109
Query: 125 TLLVFANKQDIE 136
++ NK D+E
Sbjct: 110 ERMLVGNKCDME 121
Score = 27.2 bits (61), Expect = 3.5
Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 4/30 (13%)
Query: 4 RFKLNIWDVGGQKSLRSY--SYY--GMGML 29
+ KL IWD GQ+ R+ SYY MG++
Sbjct: 51 KIKLQIWDTAGQERFRTITTSYYRGAMGII 80
>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 = 33.9 bits (78), Expect = 0.012
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGAT- 125
LNIWD GG++ L+ + + D ++ V D D+ L + +R + L +L G
Sbjct: 49 LLNIWDFGGREELKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIP 108
Query: 126 LLVFANKQ 133
+++ NK
Sbjct: 109 VILVGNKL 116
>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 = 34.4 bits (79), Expect = 0.012
Identities = 14/71 (19%), Positives = 29/71 (40%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATL 126
+L I+D GQ+ N +E + V D ++ +C+R ++ +
Sbjct: 54 ELFIFDSAGQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPG 113
Query: 127 LVFANKQDIEG 137
++ NK D+
Sbjct: 114 VLVGNKCDLTD 124
>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 = 34.2 bits (79), Expect = 0.013
Identities = 21/79 (26%), Positives = 34/79 (43%)
Query: 65 RFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGA 124
+ KL IWD GQ+ R+ +Y+ G+I V D + ++ L+EL A
Sbjct: 48 KVKLAIWDTAGQERFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDA 107
Query: 125 TLLVFANKQDIEGALTPED 143
++ NK D E +
Sbjct: 108 VKMLVGNKIDKENREVTRE 126
Score = 27.7 bits (62), Expect = 2.1
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 4 RFKLNIWDVGGQKSLRSY--SYY 24
+ KL IWD GQ+ R+ SYY
Sbjct: 48 KVKLAIWDTAGQERFRTLTSSYY 70
>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 = 34.0 bits (78), Expect = 0.014
Identities = 27/91 (29%), Positives = 42/91 (46%), Gaps = 9/91 (9%)
Query: 65 RFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEER-LAG 123
+ KL IWD GQ+ R+ R+Y+ G + V D RR L L + R L
Sbjct: 50 KIKLQIWDTAGQERFRAVTRSYYRGAAGALMVYDIT--RRS--TYNHLSSWLTDARNLTN 105
Query: 124 ATLLVF--ANKQDIEGA--LTPEDIKNVSEK 150
++F NK D+E +T E+ K +++
Sbjct: 106 PNTVIFLIGNKADLEAQRDVTYEEAKQFADE 136
Score = 26.7 bits (59), Expect = 4.7
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 4 RFKLNIWDVGGQKSLRSY--SYY 24
+ KL IWD GQ+ R+ SYY
Sbjct: 50 KIKLQIWDTAGQERFRAVTRSYY 72
>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 = 34.0 bits (78), Expect = 0.018
Identities = 20/91 (21%), Positives = 37/91 (40%), Gaps = 6/91 (6%)
Query: 63 TFRFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLA 122
FR L +WD GQ+ RS +F G + + D ++ + + +L
Sbjct: 60 AFRVHLQLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCE 119
Query: 123 GATLLVFANKQDIEGALTPEDIKNVSEKATK 153
+++ NK D+ D + VSE+ +
Sbjct: 120 NPDIVLIGNKADL------PDQREVSERQAR 144
>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 = 33.9 bits (78), Expect = 0.020
Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 4/82 (4%)
Query: 57 KKKMIMTFRFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELL 116
KK + ++N +D+ G +++ T G++ V D D++ E L E+
Sbjct: 40 KKVSVRNKEVRVNFFDLSGHPEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMK 99
Query: 117 QEERLAG----ATLLVFANKQD 134
QE G ++V ANK D
Sbjct: 100 QEGGPHGNMENIVVVVCANKID 121
>gnl|CDD|206744 cd11384, RagA_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins A and B. RagA
and RagB are closely related Rag GTPases (ras-related
GTP-binding protein A and B) that constitute a unique
subgroup of the Ras superfamily, and are functional
homologs of Saccharomyces cerevisiae Gtr1. These domains
function by forming heterodimers with RagC or RagD, and
similarly, Gtr1 dimerizes with Gtr2, through the
carboxy-terminal segments. They play an essential role
in regulating amino acid-induced target of rapamycin
complex 1 (TORC1) kinase signaling, exocytic cargo
sorting at endosomes, and epigenetic control of gene
expression. In response to amino acids, the Rag GTPases
guide the TORC1 complex to activate the platform
containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 286
Score = 33.0 bits (76), Expect = 0.061
Identities = 29/106 (27%), Positives = 44/106 (41%), Gaps = 18/106 (16%)
Query: 66 FKLNIWDVGGQKSLRSYWRNYFES--------TDGLIWVVDSADKRRLEDCARELHELLQ 117
LN+WD GGQ ++ NYF S + LI+V D + R LE L+
Sbjct: 48 LVLNLWDCGGQD---AFMENYFTSQRDHIFRNVEVLIYVFD-VESRELEKDLTYFRSCLE 103
Query: 118 EER--LAGATLLVFANKQDIEGALTPEDIKNVSEKATKVKLNKQSK 161
R A + V +K D L ED + + + +L + S+
Sbjct: 104 ALRQNSPDAKVFVLIHKMD----LVQEDEREAVFERKEKELRRLSE 145
>gnl|CDD|206639 cd00066, G-alpha, Alpha subunit of G proteins (guanine nucleotide
binding). The alpha subunit of G proteins contains the
guanine nucleotide binding site. The heterotrimeric
GNP-binding proteins are signal transducers that
communicate signals from many hormones,
neurotransmitters, chemokines, and autocrine and
paracrine factors. Extracellular signals are received by
receptors, which activate the G proteins, which in turn
route the signals to several distinct intracellular
signaling pathways. The alpha subunit of G proteins is a
weak GTPase. In the resting state, heterotrimeric G
proteins are associated at the cytosolic face of the
plasma membrane and the alpha subunit binds to GDP. Upon
activation by a receptor GDP is replaced with GTP, and
the G-alpha/GTP complex dissociates from the beta and
gamma subunits. This results in activation of downstream
signaling pathways, such as cAMP synthesis by adenylyl
cyclase, which is terminated when GTP is hydrolized and
the heterotrimers reconstitute.
Length = 315
Score = 32.9 bits (76), Expect = 0.064
Identities = 26/88 (29%), Positives = 43/88 (48%), Gaps = 15/88 (17%)
Query: 62 MTFRFK---LNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSA--DKRRLEDC--ARELHE 114
F K ++DVGGQ+S R W + FE +I+VV + D+ +ED R + E
Sbjct: 154 TDFSIKNLKFRMFDVGGQRSERKKWIHCFEDVTAIIFVVALSEYDQVLVEDESVNR-MQE 212
Query: 115 LLQEER-------LAGATLLVFANKQDI 135
L+ A ++++F NK+D+
Sbjct: 213 SLKLFDSICNSRWFANTSIILFLNKKDL 240
>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 = 32.6 bits (74), Expect = 0.066
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 65 RFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGA 124
R KL +WD GQ + +R+Y G+I V D ++ + R + E+ +E G
Sbjct: 54 RVKLQLWDTSGQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEI--DEHAPGV 111
Query: 125 TLLVFANK 132
++ N+
Sbjct: 112 PKILVGNR 119
>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 = 31.8 bits (73), Expect = 0.12
Identities = 22/78 (28%), Positives = 33/78 (42%), Gaps = 12/78 (15%)
Query: 66 FKLNIWDVGGQKSL-RSYWR----NYFESTDGLIWVVDSADKRRLEDCARELHELLQEER 120
LN+WD GQ +Y + F + LI+V D + ED A L +++ E
Sbjct: 48 LTLNLWDCPGQDDFMENYLTRQKEHIFSNVGVLIYVFDVESREYEEDLAT-LVKII--EA 104
Query: 121 LA----GATLLVFANKQD 134
L A + V +K D
Sbjct: 105 LYQYSPNAKVFVLIHKMD 122
>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 = 31.2 bits (71), Expect = 0.16
Identities = 21/70 (30%), Positives = 31/70 (44%)
Query: 68 LNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATLL 127
LNI D GQ+ + NYF S +G + V D A ++L+ + LL
Sbjct: 50 LNILDTAGQEDYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLL 109
Query: 128 VFANKQDIEG 137
+ NK D+E
Sbjct: 110 LVGNKCDLED 119
>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 = 30.7 bits (70), Expect = 0.20
Identities = 24/87 (27%), Positives = 38/87 (43%), Gaps = 15/87 (17%)
Query: 57 KKKMIMTFRFKLNIWDVGGQKSLRS----YWRNYFESTDGLIWVVDSADKR---RLEDCA 109
K I R L IWD GQ+ + Y+R+ DG I V D D +++
Sbjct: 40 KTVNIGGKRIDLAIWDTAGQERYHALGPIYYRD----ADGAILVYDITDADSFQKVKKWI 95
Query: 110 RELHELLQEERLAGATLLVFANKQDIE 136
+EL ++ +L++ NK D+E
Sbjct: 96 KELKQMRGNN----ISLVIVGNKIDLE 118
>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 = 30.6 bits (70), Expect = 0.21
Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 3/86 (3%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATL 126
KL IWD GQ+ R+ Y+ G + V D + E+ + L E+L+ +
Sbjct: 49 KLQIWDTAGQERFRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADENVPIV 108
Query: 127 LVFANKQDIEG--ALTPEDIKNVSEK 150
LV NK D+E ++ E+ + ++++
Sbjct: 109 LV-GNKCDLEDQRVVSTEEGEALAKE 133
>gnl|CDD|238928 cd01966, Nitrogenase_NifN_1, Nitrogenase_nifN1: A subgroup of the
NifN subunit of the NifEN complex: NifN forms an
alpha2beta2 tetramer with NifE. NifN and nifE are
structurally homologous to nitrogenase MoFe protein beta
and alpha subunits respectively. NifEN participates in
the synthesis of the iron-molybdenum cofactor (FeMoco)
of the MoFe protein. NifB-co (an iron and sulfur
containing precursor of the FeMoco) from NifB is
transferred to the NifEN complex where it is further
processed to FeMoco. The nifEN bound precursor of FeMoco
has been identified as a molybdenum-free, iron- and
sulfur- containing analog of FeMoco. It has been
suggested that this nifEN bound precursor also acts as a
cofactor precursor in nitrogenase systems which require
a cofactor other than FeMoco: i.e. iron-vanadium
cofactor (FeVco) or iron only cofactor (FeFeco).
Length = 417
Score = 30.7 bits (70), Expect = 0.38
Identities = 10/34 (29%), Positives = 15/34 (44%)
Query: 106 EDCARELHELLQEERLAGATLLVFANKQDIEGAL 139
ED A L + E +V+ + D EG+L
Sbjct: 98 EDIAGALKQFRAEHPELADVPVVYVSTPDFEGSL 131
>gnl|CDD|204739 pfam11768, DUF3312, Protein of unknown function (DUF3312). This is
a eukaryotic family of uncharacterized proteins. This
family shows similarity to WD40 repeat proteins.
Length = 544
Score = 30.5 bits (69), Expect = 0.39
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 84 RNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLA 122
R Y ES W + + +L D +EL ELLQ+ R
Sbjct: 2 RQYAESRGYP-WTLKNKRPEKLRDNLKELEELLQQSRCV 39
>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 = 29.9 bits (68), Expect = 0.41
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 7/65 (10%)
Query: 72 DVGGQKSLRSY-WRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATLLVFA 130
+ GG R R + D ++ VVDS D +E+ A+ L R G +L+
Sbjct: 58 EEGGLGRERVEEARQVADRADLVLLVVDS-DLTPVEEEAK-----LGLLRERGKPVLLVL 111
Query: 131 NKQDI 135
NK D+
Sbjct: 112 NKIDL 116
>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 = 29.8 bits (67), Expect = 0.45
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 68 LNIWDVGGQKSLRSYWRNY---FESTDGLIWVVDSAD 101
LN+WD GQ ++ F+ LI+V+D D
Sbjct: 50 LNLWDCPGQDVFFEPTKDKEHIFQXVGALIYVIDVQD 86
>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 = 29.9 bits (67), Expect = 0.48
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 65 RFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRR---LEDCARELHELLQEERL 121
R KL IWD GQ+ R+ Y+ G I + D ++ ++D + ++ +
Sbjct: 49 RIKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDN-- 106
Query: 122 AGATLLVFANKQDIE 136
A +++ NK D+E
Sbjct: 107 --AQVILVGNKCDME 119
Score = 26.4 bits (58), Expect = 5.7
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 4/30 (13%)
Query: 4 RFKLNIWDVGGQKSLRSYS--YY--GMGML 29
R KL IWD GQ+ R+ + YY MG +
Sbjct: 49 RIKLQIWDTAGQERYRTITTAYYRGAMGFI 78
>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 = 29.4 bits (66), Expect = 0.65
Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 2/71 (2%)
Query: 68 LNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCA--RELHELLQEERLAGAT 125
L +WD+GGQ+ Y + V D + + E+ + + + EE
Sbjct: 52 LQVWDIGGQQIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPK 111
Query: 126 LLVFANKQDIE 136
+++ NK D+E
Sbjct: 112 MVLVGNKTDLE 122
>gnl|CDD|143418 cd07100, ALDH_SSADH1_GabD1, Mycobacterium tuberculosis
succinate-semialdehyde dehydrogenase 1-like.
Succinate-semialdehyde dehydrogenase 1 (SSADH1, GabD1,
EC=1.2.1.16) catalyzes the NADP(+)-dependent oxidation
of succinate semialdehyde (SSA) to succinate. SSADH
activity in Mycobacterium tuberculosis (Mtb) is encoded
by both gabD1 (Rv0234c) and gabD2 (Rv1731). The Mtb
GabD1 SSADH1 reportedly is an enzyme of the
gamma-aminobutyrate shunt, which forms a functional link
between two TCA half-cycles by converting
alpha-ketoglutarate to succinate.
Length = 429
Score = 29.0 bits (66), Expect = 1.1
Identities = 15/33 (45%), Positives = 20/33 (60%)
Query: 106 EDCARELHELLQEERLAGATLLVFANKQDIEGA 138
+D ELHE ++E AGATLL+ + D GA
Sbjct: 283 KDLRDELHEQVEEAVAAGATLLLGGKRPDGPGA 315
>gnl|CDD|235976 PRK07232, PRK07232, bifunctional malic enzyme
oxidoreductase/phosphotransacetylase; Reviewed.
Length = 752
Score = 29.3 bits (67), Expect = 1.1
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 96 VVDSADKRRLEDCARELHELLQ 117
+V+ D R E+ + +ELLQ
Sbjct: 495 IVNPEDDPRYEEYWQYYYELLQ 516
>gnl|CDD|227204 COG4867, COG4867, Uncharacterized protein with a von Willebrand
factor type A (vWA) domain [General function prediction
only].
Length = 652
Score = 29.2 bits (65), Expect = 1.2
Identities = 14/49 (28%), Positives = 23/49 (46%)
Query: 101 DKRRLEDCARELHELLQEERLAGATLLVFANKQDIEGALTPEDIKNVSE 149
D+RR+ + +L++LL + T F G PE+ +NV E
Sbjct: 179 DRRRVTEMLDDLNDLLDKHARGEDTQRDFDEFMTKHGEFFPENPRNVEE 227
>gnl|CDD|240633 cd12156, HPPR, Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific
2-hydroxyacid-related dehydrogenase.
Hydroxy(phenyl)pyruvate reductase (HPPR) catalyzes the
NADP-dependent reduction of hydroxyphenylpyruvates,
hydroxypyruvate, or pyruvate to its respective lactate.
HPPR acts as a dimer and is related to D-isomer-specific
2-hydroxyacid dehydrogenases, a superfamily that
includes groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 301
Score = 28.6 bits (65), Expect = 1.4
Identities = 16/36 (44%), Positives = 17/36 (47%), Gaps = 10/36 (27%)
Query: 96 VVDSADKRRLEDCARELHELLQEERLAGATLLVFAN 131
VVD A L LQE R+AGA L VF N
Sbjct: 232 VVDEA----------ALIAALQEGRIAGAGLDVFEN 257
>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 = 28.4 bits (64), Expect = 1.5
Identities = 23/88 (26%), Positives = 34/88 (38%), Gaps = 9/88 (10%)
Query: 68 LNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGA--- 124
L +WD+ GQ+ R Y++ G I V D E + +L + L
Sbjct: 52 LQLWDIAGQERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPI 111
Query: 125 -TLLVFANKQDIEGALTPEDIKNVSEKA 151
LL+ ANK D L E + E+
Sbjct: 112 PALLL-ANKCD----LKKERLAKDPEQM 134
>gnl|CDD|203394 pfam06133, DUF964, Protein of unknown function (DUF964). This
family consists of several relatively short bacterial
and archaeal hypothetical sequences. The function of
this family is unknown.
Length = 108
Score = 27.5 bits (62), Expect = 1.7
Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 8/48 (16%)
Query: 131 NKQDIEGALTPEDIKNVSEKATKVKLN--------KQSKFQVLLNEVS 170
KQ + E + + E ++ LN + Q LL EV+
Sbjct: 51 EKQMFGKEIPKEVQQKIQELKREIDLNPLVAEFKEAEQALQDLLQEVN 98
>gnl|CDD|223146 COG0068, HypF, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 750
Score = 28.5 bits (64), Expect = 1.8
Identities = 8/37 (21%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 49 GGETLILKKKKMIMTFRFKLNIWDVGGQKSLRSYWRN 85
GGE L++ K+ + + GG +++ R
Sbjct: 518 GGEFLVIDYKEYERLAHLE-YVDLPGGDLAIKYPLRM 553
>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 = 28.2 bits (64), Expect = 2.0
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 10/56 (17%)
Query: 87 FEST-------DGLIWVVDSADKRRLEDCARELHELLQE-ERLAGATLLVFANKQD 134
F +T D L+ VVD++D R E + ++L+E LLV+ NK D
Sbjct: 259 FRATLEEVREADLLLHVVDASDPDREEQ-IEAVEKVLEELGAEDIPQLLVY-NKID 312
>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 = 27.6 bits (62), Expect = 2.2
Identities = 15/70 (21%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATL 126
+L +WD GQ+ RS +Y + + V D +++ ++ + + +++ER +
Sbjct: 50 RLQLWDTAGQERFRSLIPSYIRDSSVAVVVYDITNRQSFDN-TDKWIDDVRDERGNDVII 108
Query: 127 LVFANKQDIE 136
++ NK D+
Sbjct: 109 VLVGNKTDLS 118
>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 = 27.6 bits (61), Expect = 2.3
Identities = 10/39 (25%), Positives = 21/39 (53%)
Query: 65 RFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKR 103
+ ++ IWD GQ+ ++ + Y+ G+ V D + +R
Sbjct: 48 KVRIQIWDTAGQERYQTITKQYYRRAQGIFLVYDISSER 86
>gnl|CDD|223358 COG0281, SfcA, Malic enzyme [Energy production and conversion].
Length = 432
Score = 27.9 bits (63), Expect = 2.9
Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 15/70 (21%)
Query: 94 IWVVDS----ADKR--------RLEDCARELHELLQEERLAGATLLVFANKQDIEGALTP 141
I+VVD D R + + E + LAGA +L+ + GA T
Sbjct: 228 IFVVDRKGLLYDGREDLTMNQKKYAKAIEDTGERTLDLALAGADVLIGVSGV---GAFTE 284
Query: 142 EDIKNVSEKA 151
E +K +++
Sbjct: 285 EMVKEMAKHP 294
>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 = 27.1 bits (60), Expect = 3.4
Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 8/78 (10%)
Query: 66 FKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADK---RRLEDCARELHELLQEERLA 122
++ WD GQ+ ++ +Y+ I V D K + L EL E E
Sbjct: 49 ILVDFWDTAGQERFQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYRPE---- 104
Query: 123 GATLLVFANKQDIEGALT 140
+V ANK D++ ++T
Sbjct: 105 -IPCIVVANKIDLDPSVT 121
>gnl|CDD|131313 TIGR02260, benz_CoA_red_B, benzoyl-CoA reductase, bcr type, subunit
B. This model describes B, or beta, subunit of the bcr
type of benzoyl-CoA reductase, a 4-subunit enzyme. Many
aromatic compounds are metabolized by way of
benzoyl-CoA.
Length = 413
Score = 27.7 bits (61), Expect = 3.9
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 79 LRSYWRNYFESTDGLIWVVDSADKR 103
LR Y + ++ D +WV++SA +
Sbjct: 184 LREYLKKSAKAEDDHVWVLESAKHK 208
>gnl|CDD|235611 PRK05793, PRK05793, amidophosphoribosyltransferase; Provisional.
Length = 469
Score = 27.3 bits (61), Expect = 4.1
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 20 SYSYYGMGMLRHRPQVSNVAVVSLLRNKNGGETLILK 56
S +YYG+ L+HR Q S VS +G + + K
Sbjct: 30 SLTYYGLYALQHRGQESAGIAVS-----DGEKIKVHK 61
>gnl|CDD|187659 cd08956, KR_3_FAS_SDR_x, beta-ketoacyl reductase (KR) domain of
fatty acid synthase (FAS), subgroup 3, complex (x).
Ketoreductase, a module of the multidomain polyketide
synthase (PKS), has 2 subdomains, each corresponding to
a SDR family monomer. The C-terminal subdomain catalyzes
the NADPH-dependent reduction of the beta-carbonyl of a
polyketide to a hydroxyl group, a step in the
biosynthesis of polyketides, such as erythromycin. The
N-terminal subdomain, an interdomain linker, is a
truncated Rossmann fold which acts to stabilizes the
catalytic subdomain. Unlike typical SDRs, the isolated
domain does not oligomerize but is composed of 2
subdomains, each resembling an SDR monomer. The active
site resembles that of typical SDRs, except that the
usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. In some instances, such as
porcine FAS, an enoyl reductase (ER) module is inserted
between the sub-domains. Fatty acid synthesis occurs via
the stepwise elongation of a chain (which is attached to
acyl carrier protein, ACP) with 2-carbon units.
Eukaryotic systems consists of large, multifunctional
synthases (type I) while bacterial, type II systems, use
single function proteins. Fungal fatty acid synthesis
uses a dodecamer of 6 alpha and 6 beta subunits. In
mammalian type FAS cycles, ketoacyl synthase forms
acetoacetyl-ACP which is reduced by the NADP-dependent
beta-KR, forming beta-hydroxyacyl-ACP, which is in turn
dehydrated by dehydratase to a beta-enoyl intermediate,
which is reduced by NADP-dependent beta- ER. Polyketide
synthesis also proceeds via the addition of 2-carbon
units as in fatty acid synthesis. The complex SDR
NADP-binding motif, GGXGXXG, is often present, but is
not strictly conserved in each instance of the module.
This subfamily includes KR domains found in many
multidomain PKSs, including six of seven Sorangium
cellulosum PKSs (encoded by spiDEFGHIJ) which
participate in the synthesis of the polyketide scaffold
of the cytotoxic spiroketal polyketide spirangien. These
seven PKSs have either a single PKS module (SpiF), two
PKR modules (SpiD,-E,-I,-J), or three PKS modules
(SpiG,-H). This subfamily includes the second KR domains
of SpiE,-G, I, and -J, both KR domains of SpiD, and the
third KR domain of SpiH. The single KR domain of SpiF,
the first and second KR domains of SpiH, the first KR
domains of SpiE,-G,- I, and -J, and the third KR domain
of SpiG, belong to a different KR_FAS_SDR subfamily.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes catalyze a wide range of activities including
the metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
prostaglandin dehydrogenase (PGDH) numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107,
PGDH numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type KRs have
a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 448
Score = 27.2 bits (61), Expect = 4.2
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 8/46 (17%)
Query: 91 DGLIWVVDSADKRRLEDCARE--------LHELLQEERLAGATLLV 128
D ++ +A L A L L + RLA + L+V
Sbjct: 54 DVVVVPCPAAAGGDLAAAAHAAAARALALLQAWLADPRLADSRLVV 99
>gnl|CDD|182383 PRK10331, PRK10331, L-fuculokinase; Provisional.
Length = 470
Score = 27.3 bits (61), Expect = 4.2
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 5/52 (9%)
Query: 88 ESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATLLVFANKQDIEGAL 139
E++D W +D A +R DC R+++ L E + G T+ F ++GAL
Sbjct: 40 ENSDWHQWSLD-AILQRFADCCRQINSELTECHIRGITVTTFG----VDGAL 86
>gnl|CDD|233342 TIGR01285, nifN, nitrogenase molybdenum-iron cofactor biosynthesis
protein NifN. This protein forms a complex with NifE,
and appears as a NifEN in some species. NifEN is a
required for producing the molybdenum-iron cofactor of
molybdenum-requiring nitrogenases. NifN is closely
related to the nitrogenase molybdenum-iron protein beta
chain NifK. This model describes most examples of NifN
but excludes some cases, such as the putative NifN of
Chlorobium tepidum, for which a separate model may be
created [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other, Central intermediary metabolism,
Nitrogen fixation].
Length = 432
Score = 27.4 bits (61), Expect = 4.2
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 104 RLEDCARELHELLQE-ERLAGATLLVFANKQDIEGAL 139
R ED AR + + ++ + G T +V N D +G+L
Sbjct: 106 RGEDIARVVRQFREKHPQHKG-TAVVTVNTPDFKGSL 141
>gnl|CDD|237001 PRK11856, PRK11856, branched-chain alpha-keto acid dehydrogenase
subunit E2; Reviewed.
Length = 411
Score = 27.4 bits (62), Expect = 4.2
Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 9/44 (20%)
Query: 91 DGLIW-VVDSADKRRLEDCARELHEL--------LQEERLAGAT 125
GLI V+ ADK+ L + ARE+ +L L+ E L G T
Sbjct: 284 GGLIVPVIRDADKKSLFELAREIKDLAEKAREGKLKPEELQGGT 327
>gnl|CDD|225265 COG2401, COG2401, ABC-type ATPase fused to a predicted
acetyltransferase domain [General function prediction
only].
Length = 593
Score = 27.5 bits (61), Expect = 4.7
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 6/47 (12%)
Query: 96 VVDSADKRRLEDCARELHELLQEERLAGATLLVFANKQDIEGALTPE 142
+D R+ AR++ EL +E AG TL+V ++ ++ AL P+
Sbjct: 537 HLDELTAVRV---ARKISELARE---AGITLIVVTHRPEVGNALRPD 577
>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 = 26.8 bits (60), Expect = 4.9
Identities = 24/113 (21%), Positives = 50/113 (44%), Gaps = 12/113 (10%)
Query: 68 LNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQE-ERLAGATL 126
L+I D GQ+ + Y + +G + V D++ E+ A+ E + + +
Sbjct: 52 LDILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAK-FREQILRVKDRDDVPI 110
Query: 127 LVFANKQDIEG--ALTPEDIKNVS--------EKATKVKLNKQSKFQVLLNEV 169
++ NK D+E ++ E+ K ++ E + K ++N F L+ E+
Sbjct: 111 VLVGNKCDLENERVVSTEEGKELARQWGCPFLETSAKERINVDEAFYDLVREI 163
>gnl|CDD|236522 PRK09450, cyaA, adenylate cyclase; Provisional.
Length = 830
Score = 27.2 bits (61), Expect = 5.1
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 16/61 (26%)
Query: 110 RELH-ELLQEERLAGATLLVFANKQDIEGALTPEDIKNV---------SEKATKV-KLNK 158
EL L+Q R L+ FA + ++ +++P+DI + KV LN
Sbjct: 385 NELVDALMQSYR----NLIRFARRNNLSSSISPQDI-GILTRKLYAAFERLPGKVTLLNP 439
Query: 159 Q 159
Q
Sbjct: 440 Q 440
>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 = 26.8 bits (60), Expect = 5.3
Identities = 18/88 (20%), Positives = 40/88 (45%), Gaps = 8/88 (9%)
Query: 68 LNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGAT-- 125
L+I D GQ+ + Y + +G + V D++ E+ + E + R+
Sbjct: 50 LDILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKK-FREQIL--RVKDRDDV 106
Query: 126 -LLVFANKQDIEG--ALTPEDIKNVSEK 150
+++ NK D+E ++ E+ K ++ +
Sbjct: 107 PIVLVGNKCDLESERVVSTEEGKELARQ 134
>gnl|CDD|233931 TIGR02565, cas_Csy2, CRISPR type I-F/YPEST-associated protein Csy2.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) is a widespread family of
prokaryotic direct repeats with spacers of unique
sequence between consecutive repeats. This protein
family, typified by YPO2464 of Yersinia pestis, is a
CRISPR-associated (Cas) family strictly associated with
the Ypest subtype of CRISPR/Cas locus. This family is
designated Csy2, for CRISPR/Cas Subtype Ypest protein 2
[Mobile and extrachromosomal element functions, Other].
Length = 296
Score = 26.7 bits (59), Expect = 6.3
Identities = 30/127 (23%), Positives = 48/127 (37%), Gaps = 31/127 (24%)
Query: 30 RHRPQVSNVAVVSLLRN---KNGGETLILKKKKMIMTFRFKLNIWDVGGQKSLRSYWRNY 86
+ V L RN KNG I+++ + +T SL
Sbjct: 62 TYGSAQRWDRVFILTRNPVTKNGKTAAIIEEGRCHLTV-------------SL------V 102
Query: 87 FESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATLLVFANKQDIEGALTPEDIKN 146
+ I D A + LE + LL+++RLAG T++ F + ++ PE N
Sbjct: 103 IGVSGSDIAPTDDALQALLEHLKQ----LLKQQRLAGGTVIEFIERVQVQ--TLPE---N 153
Query: 147 VSEKATK 153
E AT+
Sbjct: 154 EDEAATR 160
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 27.0 bits (60), Expect = 6.3
Identities = 15/58 (25%), Positives = 25/58 (43%)
Query: 96 VVDSADKRRLEDCARELHELLQEERLAGATLLVFANKQDIEGALTPEDIKNVSEKATK 153
+VD A KR ++D L+ E L A F +D+ P+D +S + +
Sbjct: 446 IVDRAKKRAIKDHITGGQVGLRAEHLLAAVEDEFRENEDLPNTTNPDDWARISGRKGE 503
>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 = 26.6 bits (59), Expect = 6.4
Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 65 RFKLNIWDVGGQKSLR-SYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAG 123
R K+ +WD GQ+ R S ++Y+ + +++V D + + E Q
Sbjct: 50 RIKVQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNE 109
Query: 124 ATLLVFANKQDIE 136
++ NK D+
Sbjct: 110 VPRILVGNKCDLR 122
>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 = 26.4 bits (59), Expect = 7.0
Identities = 17/49 (34%), Positives = 22/49 (44%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHEL 115
K IWD GQ+ R+ Y+ G + V D K E+ R L EL
Sbjct: 53 KAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKEL 101
>gnl|CDD|225701 COG3159, COG3159, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 218
Score = 26.6 bits (59), Expect = 7.2
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 95 WVVDSADKRRLEDCARELHELLQEE-RLAGATLLVF 129
+D D R L+D R + + LA A+L +F
Sbjct: 81 LQLDLLDARSLDDLLRRVDRSWARDFGLAAASLRLF 116
>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 = 26.0 bits (58), Expect = 8.3
Identities = 9/22 (40%), Positives = 10/22 (45%), Gaps = 3/22 (13%)
Query: 5 FKLNIWDVGGQ---KSLRSYSY 23
L +WD GQ LR SY
Sbjct: 48 VNLGLWDTAGQEEYDRLRPLSY 69
>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 = 26.0 bits (58), Expect = 8.7
Identities = 10/23 (43%), Positives = 12/23 (52%), Gaps = 4/23 (17%)
Query: 67 KLNIWDVGGQKSLRS----YWRN 85
K IWD GQ+ RS Y+R
Sbjct: 51 KFEIWDTAGQERYRSLAPMYYRG 73
>gnl|CDD|233943 TIGR02590, cas_Csh2, CRISPR-associated protein Cas7/Csh2, subtype
I-B/HMARI. This model represents one of two closely
related CRISPR-associated proteins that belong to the
larger family of TIGR01595. Members are the Csh2 protein
of the Hmari subtype of CRISPR/cas system. CRISPR stands
for Clustered Regularly Interspaced Short Palindromic
Repeats. The related model is TIGR02589, the Csd3
protein of the Dvulg CRISPR subtype [Mobile and
extrachromosomal element functions, Other].
Length = 286
Score = 26.0 bits (57), Expect = 9.7
Identities = 16/89 (17%), Positives = 36/89 (40%), Gaps = 9/89 (10%)
Query: 67 KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADKRRLEDCARELHELLQEERLAGATL 126
+L + DV ++ +R + G++ ++ RL+ + +++ +E +
Sbjct: 33 QLIVTDVRLKRYVRDQLD---DDGHGVLIRTVQEEEDRLKSVDYDSYDVDDDEEVKEFRE 89
Query: 127 LVFA---NKQ-DIE--GALTPEDIKNVSE 149
VF K D+ GA+ D +V
Sbjct: 90 DVFGEYLRKSIDVRLFGAVISVDKDDVLP 118
>gnl|CDD|185053 PRK15098, PRK15098, beta-D-glucoside glucohydrolase; Provisional.
Length = 765
Score = 26.6 bits (59), Expect = 9.8
Identities = 15/31 (48%), Positives = 17/31 (54%)
Query: 31 HRPQVSNVAVVSLLRNKNGGETLILKKKKMI 61
HR + VA SL+ KN ETL LKK I
Sbjct: 383 HRKEAREVARESLVLLKNRLETLPLKKSGTI 413
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
0.319 0.134 0.390
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,551,407
Number of extensions: 776471
Number of successful extensions: 1125
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1115
Number of HSP's successfully gapped: 164
Length of query: 171
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 81
Effective length of database: 6,945,742
Effective search space: 562605102
Effective search space used: 562605102
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (24.8 bits)