RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3651
(334 letters)
>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 = 343 bits (882), Expect = e-118
Identities = 122/285 (42%), Positives = 166/285 (58%), Gaps = 16/285 (5%)
Query: 44 GMKVLIDARSKLLHDNKFGIPWQNDMNAIHAEKIFQFDNNTCIDSRLFSTYVDELKSLWD 103
MK L+ A L IP+ + N A+KI + L + +K LW
Sbjct: 47 SMKALLRAMETL------NIPYGDPENEKDAKKILSLAPRA-EEGPLPPELAEAIKRLWK 99
Query: 104 DVAIRQAFERRSEYQLGDSIQYFFDNWDRISRRVNSPLFQDYIPSNKDILHARKATKGIT 163
D I+ ++RR+EYQL DS +YF DN DRIS DYIP+ +DIL +R T GI
Sbjct: 100 DPGIQACYDRRNEYQLNDSAKYFLDNLDRISDP-------DYIPTEQDILRSRVKTTGII 152
Query: 164 EFTIVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRTNRLHE 223
E I N+ F DVGGQRS+R+KW CF+ VT+I+F+V+ SEYDQ LVED NR+ E
Sbjct: 153 ETDFSIKNLKFRMFDVGGQRSERKKWIHCFEDVTAIIFVVALSEYDQVLVEDESVNRMQE 212
Query: 224 SRNIFDTIINNVIFRNVSFILFLNKTDLLAEKLRTSKTSIAEHFPEFEGDPQDMQAVQTF 283
S +FD+I N+ F N S ILFLNK DL EK++ S + ++FP++ G P D + +
Sbjct: 213 SLKLFDSICNSRWFANTSIILFLNKKDLFEEKIKKS--PLTDYFPDYTGPPNDYEEAAKY 270
Query: 284 LLNYFKAVKRDEKKPLFHHFTTAVDTENIKIVFNAVKNTILHRNL 328
+ F + R+ K ++ HFT A DTENI+ VF+AVK+ IL NL
Sbjct: 271 IKKKFLDLNRNPNKEIYPHFTCATDTENIRFVFDAVKDIILQNNL 315
>gnl|CDD|214595 smart00275, G_alpha, G protein alpha subunit. Subunit of G
proteins that contains the guanine nucleotide binding
site.
Length = 342
Score = 324 bits (832), Expect = e-110
Identities = 118/291 (40%), Positives = 170/291 (58%), Gaps = 18/291 (6%)
Query: 44 GMKVLIDARSKLLHDNKFGIPWQNDMNAIHAEKIFQFDN-NTCIDSRLFSTYVDELKSLW 102
MK L+DA + IP+++ + + I + N ++ L +K+LW
Sbjct: 68 SMKALVDAM------EELNIPFEDPESILDIRIITEQFNKTDETENVLPKEIAKAIKALW 121
Query: 103 DDVAIRQAFERRSEYQLGDSIQYFFDNWDRISRRVNSPLFQDYIPSNKDILHARKATKGI 162
D I++ + RR+E+QL DS YF DN DRI DY+P+ +DIL +R T GI
Sbjct: 122 KDEGIQECYRRRNEFQLNDSASYFLDNIDRIGDP-------DYVPTEQDILRSRVPTTGI 174
Query: 163 TEFTIVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRTNRLH 222
E ++ + F DVGGQRS+R+KW CFD+VT+I+F V+ SEYDQ L ED TNR+
Sbjct: 175 QETAFIVKKLFFRMFDVGGQRSERKKWIHCFDNVTAIIFCVALSEYDQVLEEDESTNRMQ 234
Query: 223 ESRNIFDTIINNVIFRNVSFILFLNKTDLLAEKLRTSKTSIAEHFPEFEGDPQDMQAVQT 282
ES N+F++I N+ F N S ILFLNK DL EK++ FP+++G P D +A
Sbjct: 235 ESLNLFESICNSRWFANTSIILFLNKIDLFEEKIKKVPLVDY--FPDYKG-PNDYEAAAK 291
Query: 283 FLLNYF-KAVKRDEKKPLFHHFTTAVDTENIKIVFNAVKNTILHRNLRDLM 332
F+ F + + +K ++HHFT A DT NI++VF+AVK+ IL RNL+D
Sbjct: 292 FIKQKFLRLNRNSSRKSIYHHFTCATDTRNIRVVFDAVKDIILQRNLKDAG 342
>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 = 301 bits (774), Expect = e-101
Identities = 117/293 (39%), Positives = 175/293 (59%), Gaps = 16/293 (5%)
Query: 45 MKVLIDARSKLLHDNKFGIPWQNDMNAIHAEKIFQFDNNTC--IDSRLFSTYVDELKSLW 102
+K L++A L + N A+K+ ++ ++R +++K LW
Sbjct: 50 LKTLLEALENL----EIESSNSKPENEEIAKKLKSILDSLLDVDETRFSEELAEDIKELW 105
Query: 103 DDVAIRQAFERRSEYQLGDSIQYFFDNWDRISRRVNSPLFQDYIPSNKDILHARKATKGI 162
+D I++ + R +E+QL DS +YF DN DRI+ DY+P+++DIL AR T GI
Sbjct: 106 NDPGIQEVYNRSNEFQLSDSAKYFLDNLDRIASP-------DYVPTDQDILRARVKTTGI 158
Query: 163 TEFTIVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRTNRLH 222
E + F DVGGQRS+R+KW CF+ VT+I+F+VS SEYDQ L ED TNRL
Sbjct: 159 IETKFDFKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVVSLSEYDQVLYEDDSTNRLE 218
Query: 223 ESRNIFDTIINNVIFRNVSFILFLNKTDLLAEKLRTSKTSIAEHFPEFEGDPQDMQAVQT 282
ES N+F+ I N+ F+N ILFLNK DL EKL+ K ++++FPE+EGDP D ++
Sbjct: 219 ESLNLFEEICNSPWFKNTPIILFLNKKDLFEEKLK--KGPLSDYFPEYEGDPNDYESASK 276
Query: 283 FLLNYFKAVKRDE-KKPLFHHFTTAVDTENIKIVFNAVKNTILHRNLRDLMLQ 334
++ N F + ++ ++ ++ HFT A DTEN++ VF AVK+ IL NL++ L
Sbjct: 277 YIRNKFLELNKNNSERKIYTHFTNATDTENVRFVFEAVKDIILQNNLKESGLL 329
>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 = 60.7 bits (148), Expect = 3e-11
Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 10/88 (11%)
Query: 166 TIVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRTNRLHESR 225
T+ N+ F DVGGQ R W +++ ++F+V SS DR R+ E++
Sbjct: 37 TVEYKNVKFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSS--------DRE--RIEEAK 86
Query: 226 NIFDTIINNVIFRNVSFILFLNKTDLLA 253
N ++N + ++ NK DL
Sbjct: 87 NELHKLLNEEELKGAPLLILANKQDLPG 114
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 56.8 bits (138), Expect = 9e-10
Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 10/93 (10%)
Query: 159 TKGITEFTIVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRT 218
T G T+ N+ F DVGGQ S R W F + +++F+V S+ DR
Sbjct: 45 TIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSA--------DR-- 94
Query: 219 NRLHESRNIFDTIINNVIFRNVSFILFLNKTDL 251
+R+ E++ ++N + ++ NK DL
Sbjct: 95 DRIEEAKEELHALLNEEELADAPLLILANKQDL 127
>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 = 55.0 bits (133), Expect = 3e-09
Identities = 25/94 (26%), Positives = 45/94 (47%), Gaps = 10/94 (10%)
Query: 158 ATKGITEFTIVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRR 217
T G+ TI + +F D+GGQ R W + + +++++ S+ D+
Sbjct: 37 PTVGLNIGTIEVGKARLMFWDLGGQEELRSLWDKYYAESHGVIYVIDST--DRE------ 88
Query: 218 TNRLHESRNIFDTIINNVIFRNVSFILFLNKTDL 251
R +ES++ F+ +INN V ++ NK DL
Sbjct: 89 --RFNESKSAFEKVINNEALEGVPLLVLANKQDL 120
>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 = 49.6 bits (119), Expect = 3e-07
Identities = 25/85 (29%), Positives = 39/85 (45%), Gaps = 10/85 (11%)
Query: 167 IVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRTNRLHESRN 226
+ I N+ F D+GG RR W F V I+FLV +++ R ES+
Sbjct: 58 LTIGNVKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDAADP----------ERFQESKE 107
Query: 227 IFDTIINNVIFRNVSFILFLNKTDL 251
D+++N+ NV ++ NK D
Sbjct: 108 ELDSLLNDEELANVPILILGNKIDK 132
>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 = 47.8 bits (114), Expect = 1e-06
Identities = 25/105 (23%), Positives = 45/105 (42%), Gaps = 11/105 (10%)
Query: 148 SNKDILHARKATKGITEFTIVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSE 207
+++DI H T+G + D+GGQR R W F++ +++++ S+
Sbjct: 36 ASEDISHI-TPTQGFNIKNVQADGFKLNVWDIGGQRKIRPYWRNYFENTDVLIYVIDSA- 93
Query: 208 YDQTLVEDRRTNRLHESRNIFDTIINNVIFRNVSFILFLNKTDLL 252
DR+ R E+ ++ V ++F NK DLL
Sbjct: 94 -------DRK--RFEEAGQELVELLEEEKLAGVPVLVFANKQDLL 129
>gnl|CDD|206716 cd04149, Arf6, ADP ribosylation factor 6 (Arf6). Arf6 subfamily.
Arf6 (ADP ribosylation factor 6) proteins localize to
the plasma membrane, where they perform a wide variety
of functions. In its active, GTP-bound form, Arf6 is
involved in cell spreading, Rac-induced formation of
plasma membrane ruffles, cell migration, wound healing,
and Fc-mediated phagocytosis. Arf6 appears to change the
actin structure at the plasma membrane by activating
Rac, a Rho family protein involved in membrane ruffling.
Arf6 is required for and enhances Rac formation of
ruffles. Arf6 can regulate dendritic branching in
hippocampal neurons, and in yeast it localizes to the
growing bud, where it plays a role in polarized growth
and bud site selection. In leukocytes, Arf6 is required
for chemokine-stimulated migration across endothelial
cells. Arf6 also plays a role in down-regulation of
beta2-adrenergic receptors and luteinizing hormone
receptors by facilitating the release of sequestered
arrestin to allow endocytosis. Arf6 is believed to
function at multiple sites on the plasma membrane
through interaction with a specific set of GEFs, GAPs,
and effectors. Arf6 has been implicated in breast cancer
and melanoma cell invasion, and in actin remodelling at
the invasion site of Chlamydia infection.
Length = 168
Score = 46.7 bits (111), Expect = 3e-06
Identities = 29/93 (31%), Positives = 43/93 (46%), Gaps = 10/93 (10%)
Query: 159 TKGITEFTIVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRT 218
T G T+ N+ F DVGGQ R W + ++F+V S+ DR
Sbjct: 40 TVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDSA--------DR-- 89
Query: 219 NRLHESRNIFDTIINNVIFRNVSFILFLNKTDL 251
+R+ E+R IIN+ R+ ++F NK DL
Sbjct: 90 DRIDEARQELHRIINDREMRDALLLVFANKQDL 122
>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 = 45.9 bits (109), Expect = 4e-06
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 10/74 (13%)
Query: 178 DVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRTNRLHESRNIFDTIINNVIF 237
DVGGQ R W ++ ++++V SS+ RL ES+ I+ N
Sbjct: 50 DVGGQEKMRTVWKCYLENTDGLVYVVDSSDEA----------RLDESQKELKHILKNEHI 99
Query: 238 RNVSFILFLNKTDL 251
+ V +L NK DL
Sbjct: 100 KGVPVVLLANKQDL 113
>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 = 45.3 bits (107), Expect = 8e-06
Identities = 28/100 (28%), Positives = 45/100 (45%), Gaps = 10/100 (10%)
Query: 151 DILHARKATKGITEFTIVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQ 210
D L + T+ T + I NI F D+GG + RR W F V I++LV + + +
Sbjct: 40 DRLAQHQPTQHPTSEELAIGNIKFTTFDLGGHQQARRLWKDYFPEVNGIVYLVDAYDKE- 98
Query: 211 TLVEDRRTNRLHESRNIFDTIINNVIFRNVSFILFLNKTD 250
R ES+ D ++++ V F++ NK D
Sbjct: 99 ---------RFAESKRELDALLSDEELATVPFLILGNKID 129
>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 = 45.3 bits (107), Expect = 9e-06
Identities = 27/93 (29%), Positives = 42/93 (45%), Gaps = 10/93 (10%)
Query: 159 TKGITEFTIVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRT 218
T G T+ NI F DVGGQ R W + + ++F+V S++ D
Sbjct: 44 TIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDSNDRD--------- 94
Query: 219 NRLHESRNIFDTIINNVIFRNVSFILFLNKTDL 251
R+ E+R ++N R+ ++F NK DL
Sbjct: 95 -RIDEAREELHRMLNEDELRDAVILVFANKQDL 126
>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 = 43.9 bits (104), Expect = 2e-05
Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 10/86 (11%)
Query: 166 TIVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRTNRLHESR 225
T+ NI F DVGGQ R W F + ++F+V S++ + R+ E+R
Sbjct: 38 TVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRE----------RIGEAR 87
Query: 226 NIFDTIINNVIFRNVSFILFLNKTDL 251
++N R+ ++F NK DL
Sbjct: 88 EELQRMLNEDELRDAVLLVFANKQDL 113
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 43.0 bits (101), Expect = 5e-05
Identities = 28/93 (30%), Positives = 43/93 (46%), Gaps = 10/93 (10%)
Query: 159 TKGITEFTIVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRT 218
T G T+ NI F DVGGQ R W F + ++F+V S++ D
Sbjct: 48 TIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRD--------- 98
Query: 219 NRLHESRNIFDTIINNVIFRNVSFILFLNKTDL 251
R+ E+R+ ++N R+ ++F NK DL
Sbjct: 99 -RVVEARDELHRMLNEDELRDAVLLVFANKQDL 130
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 42.1 bits (99), Expect = 1e-04
Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 10/93 (10%)
Query: 159 TKGITEFTIVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRT 218
T G T+ N+ F DVGGQ R W + + ++F+V S++ +
Sbjct: 48 TIGFNVETVEYKNLKFTMWDVGGQDKLRPLWRHYYQNTNGLIFVVDSNDRE--------- 98
Query: 219 NRLHESRNIFDTIINNVIFRNVSFILFLNKTDL 251
R+ ++R + +++ R+ ++F NK DL
Sbjct: 99 -RIGDAREELERMLSEDELRDAVLLVFANKQDL 130
>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 = 41.6 bits (98), Expect = 1e-04
Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 10/85 (11%)
Query: 167 IVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRTNRLHESRN 226
IV NI FL D+GGQ S R W + + +++ ++ S+ DR RL ++
Sbjct: 54 IVYKNIRFLMWDIGGQESLRSSWNTYYTNTDAVILVIDST--------DR--ERLPLTKE 103
Query: 227 IFDTIINNVIFRNVSFILFLNKTDL 251
++ + R ++ NK DL
Sbjct: 104 ELYKMLAHEDLRKAVLLVLANKQDL 128
>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 = 40.0 bits (94), Expect = 5e-04
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 10/74 (13%)
Query: 178 DVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRTNRLHESRNIFDTIINNVIF 237
DVGGQ+S R W F+S +++++V SS DR RL + + ++
Sbjct: 64 DVGGQKSLRSYWRNYFESTDALIWVVDSS--------DRA--RLEDCKRELQKLLVEERL 113
Query: 238 RNVSFILFLNKTDL 251
+ ++F NK DL
Sbjct: 114 AGATLLIFANKQDL 127
>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 = 36.9 bits (85), Expect = 0.006
Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 10/93 (10%)
Query: 159 TKGITEFTIVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRT 218
T G T+ N+ F DVGG+ R W + + +++F++ SS D
Sbjct: 30 TIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHRD--------- 80
Query: 219 NRLHESRNIFDTIINNVIFRNVSFILFLNKTDL 251
R+ E+ + ++ R+ ++F NK D+
Sbjct: 81 -RVSEAHSELAKLLTEKELRDALLLIFANKQDV 112
>gnl|CDD|206718 cd04151, Arl1, ADP ribosylation factor 1 (Arf1). Arl1 subfamily.
Arl1 (Arf-like 1) localizes to the Golgi complex, where
it is believed to recruit effector proteins to the
trans-Golgi network. Like most members of the Arf
family, Arl1 is myristoylated at its N-terminal helix
and mutation of the myristoylation site disrupts Golgi
targeting. In humans, the Golgi-localized proteins
golgin-97 and golgin-245 have been identified as Arl1
effectors. Golgins are large coiled-coil proteins found
in the Golgi, and these golgins contain a C-terminal
GRIP domain, which is the site of Arl1 binding.
Additional Arl1 effectors include the GARP
(Golgi-associated retrograde protein)/VFT (Vps53)
vesicle-tethering complex and Arfaptin 2. Arl1 is not
required for exocytosis, but appears necessary for
trafficking from the endosomes to the Golgi. In
Drosophila zygotes, mutation of Arl1 is lethal, and in
the host-bloodstream form of Trypanosoma brucei, Arl1 is
essential for viability.
Length = 158
Score = 36.2 bits (84), Expect = 0.007
Identities = 24/87 (27%), Positives = 43/87 (49%), Gaps = 12/87 (13%)
Query: 166 TIVISNIPFLFVDVGGQRSQRRKWFQCFDSVTS-ILFLVSSSEYDQTLVEDRRTNRLHES 224
T+ N+ F D+GGQ S R W +C+ S T I+++V S++ D RL S
Sbjct: 37 TVTYKNLKFQVWDLGGQTSIRPYW-RCYYSNTDAIIYVVDSTDRD----------RLGIS 85
Query: 225 RNIFDTIINNVIFRNVSFILFLNKTDL 251
++ ++ ++ ++F NK D+
Sbjct: 86 KSELHAMLEEEELKDAVLLVFANKQDM 112
>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 = 34.3 bits (79), Expect = 0.040
Identities = 31/138 (22%), Positives = 46/138 (33%), Gaps = 16/138 (11%)
Query: 149 NKDILHARKATKGIT--EFTIVISNIPFLF--VDVGGQRSQRRKWFQCFDSVTSILFLVS 204
NK + K I + F +D GQ + +V S L +
Sbjct: 24 NKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQEDYDAIRRLYYRAVESSLRVFD 83
Query: 205 SSEYDQTLVEDRRTNRLHESRNIFDTIINNVIFRNVSFILFLNKTDLLAEKLRTSKTSIA 264
LV D +++ I + V IL NK DL KL KT +A
Sbjct: 84 IV----ILVLDVEEILEKQTK-----EIIHHAESGVPIILVGNKIDLRDAKL---KTHVA 131
Query: 265 EHFPEFEGDPQDMQAVQT 282
F + G+P + +T
Sbjct: 132 FLFAKLNGEPIIPLSAET 149
>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 = 33.9 bits (78), Expect = 0.043
Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 12/85 (14%)
Query: 169 ISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRTNRLHESRNIF 228
N+ F D+ GQ R W + ++ I+F++ SS DR R+ +++
Sbjct: 42 KGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSS--------DRL--RMVVAKDEL 91
Query: 229 DTIIN--NVIFRNVSFILFLNKTDL 251
+ ++N ++ R + + + NK DL
Sbjct: 92 ELLLNHPDIKHRRIPILFYANKMDL 116
>gnl|CDD|221152 pfam11635, Med16, Mediator complex subunit 16. Mediator is a large
complex of up to 33 proteins that is conserved from
plants through fungi to humans - the number and
representation of individual subunits varying with
species. It is arranged into four different sections, a
core, a head, a tail and a kinase-activity part, and the
number of subunits within each of these is what varies
with species. Overall, Mediator regulates the
transcriptional activity of RNA polymerase II but it
would appear that each of the four different sections
has a slightly different function. Med16 is one of the
subunits of the Tail portion of the Mediator complex and
is required for lipopolysaccharide gene-expression.
Several members including a human protein have one or
more WD40 domains on them, pfam00400.
Length = 744
Score = 34.8 bits (80), Expect = 0.066
Identities = 22/99 (22%), Positives = 36/99 (36%), Gaps = 9/99 (9%)
Query: 221 LHESRNIFDTIINNVIFRNVSFILFLNKTDLLAEKLRTSKTSIAEHFPEFEGD-----PQ 275
L+ES + +N+ R F FL++ D KL ++ + E E P
Sbjct: 570 LNESSTPLYSALNDSPVRLELFEKFLSELDSKVTKLAGNEQAPRNK-REPELLVKGEIPP 628
Query: 276 DMQAVQTFLLNYFKAVKRDEKKPLFHHFTTAVDTENIKI 314
+ + FLL + E +F DT + I
Sbjct: 629 QLLKIVKFLLQRTNSALASEIDRAALYFA---DTSWLGI 664
>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 = 33.6 bits (77), Expect = 0.067
Identities = 17/104 (16%), Positives = 30/104 (28%), Gaps = 20/104 (19%)
Query: 159 TKGIT--EFTIVISNIPFLFVDVGGQRSQRRKW-----FQCFDSVTSILFLVSSSEYDQT 211
T+ + + + VD G IL +V S++ +
Sbjct: 32 TRDPDVYVKELDKGKVKLVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRE-- 89
Query: 212 LVEDRRTNRLHESRNIFDTIINNVIFRNVSFILFLNKTDLLAEK 255
+ I+ + + IL NK DLL E+
Sbjct: 90 -----------SEEDAKLLILRRLRKEGIPIILVGNKIDLLEER 122
>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 = 32.6 bits (75), Expect = 0.15
Identities = 22/107 (20%), Positives = 36/107 (33%), Gaps = 24/107 (22%)
Query: 159 TKGITEFTIVIS-NIPFLFVDVGG-------QRSQRRKWFQCFDSVTSILFLVSSSEYDQ 210
T+ + P + +D G R + + Q D +L +V S D
Sbjct: 32 TRDPVRKEWELLPLGPVVLIDTPGLDEEGGLGRERVEEARQVADRADLVLLVVDS---DL 88
Query: 211 TLVEDRRTNRLHESRNIFDTIINNVIFRNVSFILFLNKTDLLAEKLR 257
T VE+ + + + R +L LNK DL+ E
Sbjct: 89 TPVEE-------------EAKLGLLRERGKPVLLVLNKIDLVPESEE 122
>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 = 31.1 bits (71), Expect = 0.38
Identities = 16/74 (21%), Positives = 34/74 (45%), Gaps = 10/74 (13%)
Query: 178 DVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRTNRLHESRNIFDTIINNVIF 237
D+GGQ R W + V +I+++V +++ ++ + N LH+ ++
Sbjct: 50 DLGGQPRFRSMWERYCRGVNAIVYVVDAADREKL---EVAKNELHD-------LLEKPSL 99
Query: 238 RNVSFILFLNKTDL 251
+ ++ NK DL
Sbjct: 100 EGIPLLVLGNKNDL 113
>gnl|CDD|219161 pfam06755, DUF1219, Protein of unknown function (DUF1219). This
family consists of several hypothetical proteins which
seem to be specific to the Enterobacteria Escherichia
coli and Shigella flexneri. Family members are often
known as YeeV proteins and are around 125 residues in
length. The function of this family is unknown.
Length = 109
Score = 30.2 bits (68), Expect = 0.54
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 103 DDVAIRQAFERRSEYQLGDSIQYFFDNWD--RISRRVNSPLFQDYIPSNKDILHARKAT 159
D+ I++ E + L D++ + + + RI RR S Q + DIL AR+AT
Sbjct: 45 DETVIQEHIE--AGISLCDAVNFLVEKYALVRIDRRGFSAQEQSPFITAIDILRARRAT 101
>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 = 30.9 bits (70), Expect = 0.61
Identities = 29/101 (28%), Positives = 45/101 (44%), Gaps = 21/101 (20%)
Query: 159 TKGITEFTIVISN-----IPFLFVDVGGQRSQRRKW---FQCFDSVTSILFLVSSSEYDQ 210
TKG I +S + F F DVGGQ R W +C D I+F+V S + ++
Sbjct: 34 TKGFNTEKIKVSLGNAKGVTFHFWDVGGQEKLRPLWKSYTRCTD---GIVFVVDSVDVER 90
Query: 211 TLVEDRRTNRLHESRNIFDTIINNVIFRNVSFILFLNKTDL 251
+E+ +T LH+ + + V ++ NK DL
Sbjct: 91 --MEEAKT-ELHKITKFSEN-------QGVPVLVLANKQDL 121
>gnl|CDD|185710 cd07900, Adenylation_DNA_ligase_I_Euk, Adenylation domain of
eukaryotic DNA Ligase I. ATP-dependent polynucleotide
ligases catalyze phosphodiester bond formation using
nicked nucleic acid substrates with the high energy
nucleotide of ATP as a cofactor in a three step reaction
mechanism. DNA ligases play a vital role in the diverse
processes of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms such
as viruses, bacteriophages, eukarya, archaea and
bacteria. Some organisms express a variety of different
ligases which appear to be targeted to specific
functions. There are three classes of ATP-dependent DNA
ligases in eukaryotic cells (I, III and IV). DNA ligase
I is required for the ligation of Okazaki fragments
during lagging-strand DNA synthesis and for base
excision repair (BER). DNA ligases have a highly modular
architecture consisting of a unique arrangement of two
or more discrete domains. The adenylation and C-terminal
oligonucleotide/oligosaccharide binding (OB)-fold
domains comprise a catalytic core unit that is common to
most members of the ATP-dependent DNA ligase family. The
adenylation domain binds ATP and contains many of the
active-site residues. DNA ligase I is the main
replicative ligase in eukaryotes. The common catalytic
core unit comprises six conserved sequence motifs (I,
III, IIIa, IV, V and VI) that define this family of
related nucleotidyltransferases.
Length = 219
Score = 30.6 bits (70), Expect = 0.87
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 8/56 (14%)
Query: 243 ILFLNKTDLLAEKLRTSKTSIAEHFPEFEG--------DPQDMQAVQTFLLNYFKA 290
+L+LN LL + LR + + F E G D +D + +Q FL K
Sbjct: 132 LLYLNGESLLKKPLRERRELLHSLFKEVPGRFQFATSKDSEDTEEIQEFLEEAVKN 187
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 29.9 bits (67), Expect = 1.6
Identities = 20/98 (20%), Positives = 30/98 (30%), Gaps = 10/98 (10%)
Query: 163 TEFTIVISNIPFLFVDVGGQRSQRRKWFQCFDSVTSILFLVSSSEYDQTLVEDRRTNRLH 222
NI D GQ R + + IL + YD TL E
Sbjct: 45 KTIEPYRRNIKLQLWDTAGQEEYRSLRPEYYRGANGILIV-----YDSTLRESSDELTEE 99
Query: 223 ESRNIFDTIINNVIFRNVSFILFLNKTDLLAEKLRTSK 260
+ + +V +L NK DL E+ + +
Sbjct: 100 W-----LEELRELAPDDVPILLVGNKIDLFDEQSSSEE 132
>gnl|CDD|227369 COG5036, COG5036, SPX domain-containing protein involved in
vacuolar polyphosphate accumulation [Inorganic ion
transport and metabolism].
Length = 509
Score = 29.4 bits (66), Expect = 3.2
Identities = 30/124 (24%), Positives = 50/124 (40%), Gaps = 18/124 (14%)
Query: 224 SRNIFDTIINNVIFRNVSFILFLNKTDLL--AEKLR---TSKTSIAEHFPE---FEGDPQ 275
++ D I ++ F N +F L+ + + L AE LR K S + F E D
Sbjct: 227 DKDSHDPAITSLYFDNENFDLYNGRLEKLEGAEALRLRWYGKLSPKDIFVERKTHREDWT 286
Query: 276 DMQAVQT-------FLLNYFKA---VKRDEKKPLFHHFTTAVDTENIKIVFNAVKNTILH 325
+ + F+ + K + K TTA D E ++ +F V+N I+
Sbjct: 287 GESSFKARFQLKEKFVNKFIKGDYTFEEQFAKVRKEGGTTAEDLERLERLFEEVQNFIVK 346
Query: 326 RNLR 329
R L+
Sbjct: 347 RGLQ 350
>gnl|CDD|223199 COG0121, COG0121, Predicted glutamine amidotransferase [General
function prediction only].
Length = 252
Score = 28.1 bits (63), Expect = 6.2
Identities = 10/47 (21%), Positives = 16/47 (34%), Gaps = 1/47 (2%)
Query: 120 GDSIQYFFDNWDRISRRVNSPLFQDYIPSNKDILHARKATKGITEFT 166
G + + + + I S I H RKAT+G +
Sbjct: 43 GRGPRLYKSP-LPAWEDIALLVLAYPIKSELVIAHVRKATQGEVSLS 88
>gnl|CDD|223073 PHA03394, lef-8, DNA-directed RNA polymerase subunit beta-like
protein; Provisional.
Length = 865
Score = 28.3 bits (64), Expect = 7.0
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 223 ESRNIFDTIINNVIFRNVS 241
ES+ I DTI+N + +VS
Sbjct: 267 ESKKIVDTIVNGKLIYSVS 285
>gnl|CDD|216981 pfam02338, OTU, OTU-like cysteine protease. This family is
comprised of a group of predicted cysteine proteases,
homologous to the Ovarian Tumour (OTU) gene in
Drosophila. Members include proteins from eukaryotes,
viruses and pathogenic bacterium. The conserved cysteine
and histidine, and possibly the aspartate, represent the
catalytic residues in this putative group of proteases.
Length = 123
Score = 27.1 bits (60), Expect = 7.0
Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 233 NNVIFRNVSFILFLNKTDLLAEKLR-TSKTSIAEHFPEFEGDPQD 276
N +F VS L L ++LR + E+ +FE ++
Sbjct: 4 GNCLFHAVSDQLGDAGRQELHDELREAVVEYLRENREDFEKFLEE 48
>gnl|CDD|234061 TIGR02923, AhaC, ATP synthase A1, C subunit. The A1/A0 ATP
synthase is homologous to the V-type (V1/V0, vacuolar)
ATPase, but functions in the ATP synthetic direction as
does the F1/F0 ATPase of bacteria. The C subunit is part
of the hydrophilic A1 "stalk" complex (AhaABCDEFG) which
is the site of ATP generation and is coupled to the
membrane-embedded proton translocating A0 complex.
Length = 343
Score = 27.8 bits (62), Expect = 9.5
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 284 LLNYFKAVKRDEKKPLFHHFT-TAVDTENIKIVFNA 318
LL Y + DE K LF F T VD N+K +
Sbjct: 183 LLKYVGSPSDDETK-LFTEFIKTEVDIRNLKTLLRL 217
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 27.1 bits (61), Expect = 9.9
Identities = 23/114 (20%), Positives = 38/114 (33%), Gaps = 27/114 (23%)
Query: 164 EFTIVISNIPFLFVDVGGQRS---------QRRKWFQCFDSVTSILFLVSSSEYDQTLVE 214
E I + IP +D G R R + + +L +V +SE E
Sbjct: 43 EEEIDLGGIPVRLIDTAGLRETEDEIEKIGIERAR-EAIEEADLVLLVVDASE--GLDEE 99
Query: 215 DRRTNRLHESRNIFDTIINNVIFRNVSFILFLNKTDLLAEKLRTSKTSIAEHFP 268
D L + + I+ LNK+DLL++ S+ +
Sbjct: 100 DLEILELPAKKPV---------------IVVLNKSDLLSDAEGISELNGKPIIA 138
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
0.325 0.137 0.415
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: 16,833,478
Number of extensions: 1606767
Number of successful extensions: 1956
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1925
Number of HSP's successfully gapped: 52
Length of query: 334
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 237
Effective length of database: 6,635,264
Effective search space: 1572557568
Effective search space used: 1572557568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 59 (26.4 bits)