RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14891
(359 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 = 433 bits (1117), Expect = e-153
Identities = 159/318 (50%), Positives = 214/318 (67%), Gaps = 3/318 (0%)
Query: 36 IKILLLGAGESGKSTLVKQMKIIHNDGFTREELESFKPTVMDNLLSSMKYVLGGMGILRI 95
+K+LLLGAGESGKST++KQMKI+H +GF+ EE F+P + N+L SMK +L M L I
Sbjct: 1 VKLLLLGAGESGKSTILKQMKILHGNGFSDEERREFRPVIYSNILQSMKALLRAMETLNI 60
Query: 96 NLQSAKNKNYAKTILSTMCCFDEEFQMLPDVSTAMLALWQDRGVRLAVARGYEYELNDSA 155
+N+ AK ILS + EE + P+++ A+ LW+D G++ R EY+LNDSA
Sbjct: 61 PYGDPENEKDAKKILS-LAPRAEEGPLPPELAEAIKRLWKDPGIQACYDRRNEYQLNDSA 119
Query: 156 LYLFENMERICDLKYVPNATDVLRARVRTNGIIETNFRLGESIVNMVDVGGQRSQRRKWI 215
Y +N++RI D Y+P D+LR+RV+T GIIET+F + M DVGGQRS+R+KWI
Sbjct: 120 KYFLDNLDRISDPDYIPTEQDILRSRVKTTGIIETDFSIKNLKFRMFDVGGQRSERKKWI 179
Query: 216 YCFDDVKAVLYVVALSGYDMTLLEDSSVNRLDESLNLFEQVVNNRYFREASFILFLNKFD 275
+CF+DV A+++VVALS YD L+ED SVNR+ ESL LF+ + N+R+F S ILFLNK D
Sbjct: 180 HCFEDVTAIIFVVALSEYDQVLVEDESVNRMQESLKLFDSICNSRWFANTSIILFLNKKD 239
Query: 276 LFREKILYSGRHLRYYLSDFKGPDFDVDSGALFIQHKFALRNHNSAKVIYPHFTTATDTS 335
LF EKI S L Y D+ GP D + A +I+ KF N N K IYPHFT ATDT
Sbjct: 240 LFEEKIKKS--PLTDYFPDYTGPPNDYEEAAKYIKKKFLDLNRNPNKEIYPHFTCATDTE 297
Query: 336 NVQTVFHAVMDLVIKINL 353
N++ VF AV D++++ NL
Sbjct: 298 NIRFVFDAVKDIILQNNL 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 = 408 bits (1050), Expect = e-143
Identities = 161/342 (47%), Positives = 225/342 (65%), Gaps = 5/342 (1%)
Query: 16 RRSDEIDKQLTQLSLQEKHVIKILLLGAGESGKSTLVKQMKIIHNDGFTREELESFKPTV 75
RR+ EI+KQL + ++K +K+LLLGAGESGKST++KQM+I+H DGF++EE ++P +
Sbjct: 2 RRNKEIEKQLEEERKKKKREVKLLLLGAGESGKSTILKQMRILHGDGFSQEERREYRPLI 61
Query: 76 MDNLLSSMKYVLGGMGILRINLQSAKNKNYAKTILSTMCCFDE-EFQMLPDVSTAMLALW 134
N+L SMK ++ M L I + ++ + I DE E + +++ A+ ALW
Sbjct: 62 YSNILESMKALVDAMEELNIPFEDPESILDIRIITEQFNKTDETENVLPKEIAKAIKALW 121
Query: 135 QDRGVRLAVARGYEYELNDSALYLFENMERICDLKYVPNATDVLRARVRTNGIIETNFRL 194
+D G++ R E++LNDSA Y +N++RI D YVP D+LR+RV T GI ET F +
Sbjct: 122 KDEGIQECYRRRNEFQLNDSASYFLDNIDRIGDPDYVPTEQDILRSRVPTTGIQETAFIV 181
Query: 195 GESIVNMVDVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSSVNRLDESLNLFE 254
+ M DVGGQRS+R+KWI+CFD+V A+++ VALS YD L ED S NR+ ESLNLFE
Sbjct: 182 KKLFFRMFDVGGQRSERKKWIHCFDNVTAIIFCVALSEYDQVLEEDESTNRMQESLNLFE 241
Query: 255 QVVNNRYFREASFILFLNKFDLFREKILYSGRHLRYYLSDFKGPDFDVDSGALFIQHKFA 314
+ N+R+F S ILFLNK DLF EKI L Y D+KGP+ D ++ A FI+ KF
Sbjct: 242 SICNSRWFANTSIILFLNKIDLFEEKIKKV--PLVDYFPDYKGPN-DYEAAAKFIKQKFL 298
Query: 315 LRNHNSA-KVIYPHFTTATDTSNVQTVFHAVMDLVIKINLQQ 355
N NS+ K IY HFT ATDT N++ VF AV D++++ NL+
Sbjct: 299 RLNRNSSRKSIYHHFTCATDTRNIRVVFDAVKDIILQRNLKD 340
>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 = 370 bits (953), Expect = e-128
Identities = 147/329 (44%), Positives = 213/329 (64%), Gaps = 7/329 (2%)
Query: 36 IKILLLGAGESGKSTLVKQMKIIHNDGFTREELESFKPTVMDNLLSSMKYVLGGMGILRI 95
IK+LLLGAGESGKST++KQMKI+H GF+ EE E ++ + N++ S+K +L + L I
Sbjct: 3 IKLLLLGAGESGKSTILKQMKILHGGGFSDEEREQYRAVIYSNIIRSLKTLLEALENLEI 62
Query: 96 NLQSAK--NKNYAKTILS--TMCCFDEEFQMLPDVSTAMLALWQDRGVRLAVARGYEYEL 151
++K N+ AK + S +E + +++ + LW D G++ R E++L
Sbjct: 63 ESSNSKPENEEIAKKLKSILDSLLDVDETRFSEELAEDIKELWNDPGIQEVYNRSNEFQL 122
Query: 152 NDSALYLFENMERICDLKYVPNATDVLRARVRTNGIIETNFRLGESIVNMVDVGGQRSQR 211
+DSA Y +N++RI YVP D+LRARV+T GIIET F + DVGGQRS+R
Sbjct: 123 SDSAKYFLDNLDRIASPDYVPTDQDILRARVKTTGIIETKFDFKGLKFRLFDVGGQRSER 182
Query: 212 RKWIYCFDDVKAVLYVVALSGYDMTLLEDSSVNRLDESLNLFEQVVNNRYFREASFILFL 271
+KWI+CF+DV A+++VV+LS YD L ED S NRL+ESLNLFE++ N+ +F+ ILFL
Sbjct: 183 KKWIHCFEDVTAIIFVVSLSEYDQVLYEDDSTNRLEESLNLFEEICNSPWFKNTPIILFL 242
Query: 272 NKFDLFREKILYSGRHLRYYLSDFKGPDFDVDSGALFIQHKF-ALRNHNSAKVIYPHFTT 330
NK DLF EK+ L Y +++G D +S + +I++KF L +NS + IY HFT
Sbjct: 243 NKKDLFEEKLKKG--PLSDYFPEYEGDPNDYESASKYIRNKFLELNKNNSERKIYTHFTN 300
Query: 331 ATDTSNVQTVFHAVMDLVIKINLQQVTLL 359
ATDT NV+ VF AV D++++ NL++ LL
Sbjct: 301 ATDTENVRFVFEAVKDIILQNNLKESGLL 329
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 48.4 bits (116), Expect = 8e-07
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 12/78 (15%)
Query: 200 NMVDVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSS-VNRLDESLNLFEQVVN 258
+ DVGGQ S R W F + AV++VV DS+ +R++E+ ++N
Sbjct: 61 TVWDVGGQESLRPLWRNYFPNTDAVIFVV-----------DSADRDRIEEAKEELHALLN 109
Query: 259 NRYFREASFILFLNKFDL 276
+A ++ NK DL
Sbjct: 110 EEELADAPLLILANKQDL 127
Score = 32.2 bits (74), Expect = 0.22
Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 18/78 (23%)
Query: 25 LTQLSLQEKHVIKILLLGAGESGKSTLVKQMK------IIHNDGFTREELES--FKPTVM 76
L +L K ++IL+LG +GK+T++ ++K I GF E + K TV
Sbjct: 5 LAKLFGWNKE-MRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVW 63
Query: 77 DNLLSSMKYVLGGMGILR 94
D +GG LR
Sbjct: 64 D---------VGGQESLR 72
>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 = 47.4 bits (113), Expect = 1e-06
Identities = 24/75 (32%), Positives = 34/75 (45%), Gaps = 12/75 (16%)
Query: 203 DVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSS-VNRLDESLNLFEQVVNNRY 261
DVGGQ R W ++ ++YVV DSS RLDES + ++ N +
Sbjct: 50 DVGGQEKMRTVWKCYLENTDGLVYVV-----------DSSDEARLDESQKELKHILKNEH 98
Query: 262 FREASFILFLNKFDL 276
+ +L NK DL
Sbjct: 99 IKGVPVVLLANKQDL 113
>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 = 47.2 bits (113), Expect = 1e-06
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 12/80 (15%)
Query: 198 IVNMVDVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSS-VNRLDESLNLFEQV 256
+ DVGGQ R W + +++ +++VV DSS R++E+ N ++
Sbjct: 44 KFTVWDVGGQDKIRPLWKHYYENTDGLIFVV-----------DSSDRERIEEAKNELHKL 92
Query: 257 VNNRYFREASFILFLNKFDL 276
+N + A ++ NK DL
Sbjct: 93 LNEEELKGAPLLILANKQDL 112
Score = 29.9 bits (68), Expect = 1.0
Identities = 11/39 (28%), Positives = 22/39 (56%), Gaps = 8/39 (20%)
Query: 37 KILLLGAGESGKSTLVKQMKIIHNDGFTREELESFKPTV 75
+IL+LG +GK+T++ ++K E+ + PT+
Sbjct: 1 RILMLGLDGAGKTTILYKLK--------LGEVVTTIPTI 31
>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 = 45.0 bits (107), Expect = 1e-05
Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 12/84 (14%)
Query: 194 LGESIVNMVDVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSS-VNRLDESLNL 252
+G++ + D+GGQ R W + + V+YV+ DS+ R +ES +
Sbjct: 48 VGKARLMFWDLGGQEELRSLWDKYYAESHGVIYVI-----------DSTDRERFNESKSA 96
Query: 253 FEQVVNNRYFREASFILFLNKFDL 276
FE+V+NN ++ NK DL
Sbjct: 97 FEKVINNEALEGVPLLVLANKQDL 120
Score = 28.5 bits (64), Expect = 4.0
Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 13/64 (20%)
Query: 38 ILLLGAGESGKSTLVKQMKIIHNDGFTREELESFKPTVMDNLLSSMKYVLGGMGILRINL 97
+L+LG +GK+T ++Q K + + PTV G+ I I +
Sbjct: 2 VLILGLDNAGKTTFLEQTKTKFSKNYKGLNPSKITPTV-------------GLNIGTIEV 48
Query: 98 QSAK 101
A+
Sbjct: 49 GKAR 52
>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 = 42.8 bits (101), Expect = 6e-05
Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 12/78 (15%)
Query: 200 NMVDVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSSV-NRLDESLNLFEQVVN 258
N+ DVGGQ R W + + + +++VV DS+ +R+DE+ +++N
Sbjct: 56 NVWDVGGQDKIRPLWRHYYTGTQGLIFVV-----------DSADRDRIDEARQELHRIIN 104
Query: 259 NRYFREASFILFLNKFDL 276
+R R+A ++F NK DL
Sbjct: 105 DREMRDALLLVFANKQDL 122
>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 = 39.1 bits (91), Expect = 0.001
Identities = 26/102 (25%), Positives = 49/102 (48%), Gaps = 19/102 (18%)
Query: 200 NMVDVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSSVNRLDESLNLFEQVVNN 259
+ DVGGQ R W + + + + +++VV + + +R+DE+ +++N
Sbjct: 60 TVWDVGGQDKIRPLWRHYYTNTQGLIFVV----------DSNDRDRIDEAREELHRMLNE 109
Query: 260 RYFREASFILFLNKFDL--------FREKI-LYSGRHLRYYL 292
R+A ++F NK DL EK+ L+S R +Y+
Sbjct: 110 DELRDAVILVFANKQDLPDAMKAAEITEKLGLHSIRDRNWYI 151
>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 = 39.2 bits (92), Expect = 0.001
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 12/80 (15%)
Query: 198 IVNMVDVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSS-VNRLDESLNLFEQV 256
+N+ DVGGQ+S R W F+ A+++VV DSS RL++ +++
Sbjct: 59 KLNIWDVGGQKSLRSYWRNYFESTDALIWVV-----------DSSDRARLEDCKRELQKL 107
Query: 257 VNNRYFREASFILFLNKFDL 276
+ A+ ++F NK DL
Sbjct: 108 LVEERLAGATLLIFANKQDL 127
Score = 27.7 bits (62), Expect = 6.1
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 16/77 (20%)
Query: 25 LTQLSLQEKHVIKILLLGAGESGKSTLVKQMKIIHNDGFTREELESFKPTVMDNL--LSS 82
L + +E+ + +IL+LG +GK+T++K+ F E++ + PT+ N+ L
Sbjct: 5 LRKTKQKEREM-RILMLGLDNAGKTTILKK--------FNGEDISTISPTLGFNIKTLEY 55
Query: 83 MKYVL-----GGMGILR 94
Y L GG LR
Sbjct: 56 NGYKLNIWDVGGQKSLR 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 = 38.5 bits (90), Expect = 0.001
Identities = 21/94 (22%), Positives = 40/94 (42%), Gaps = 12/94 (12%)
Query: 184 TNGIIETNFRLGESIVNMVDVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSS- 242
T G T RL + V + D+GG + R W+ + + +++VV DSS
Sbjct: 30 TVGFTPTKLRLDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVV-----------DSSD 78
Query: 243 VNRLDESLNLFEQVVNNRYFREASFILFLNKFDL 276
+R+ E + +++ + ++ NK D
Sbjct: 79 DDRVQEVKEILRELLQHPRVSGKPILVLANKQDK 112
>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 = 38.2 bits (89), Expect = 0.002
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 12/75 (16%)
Query: 203 DVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSS-VNRLDESLNLFEQVVNNRY 261
DVGGQ R W + F + + +++VV DS+ R+ E+ ++++N
Sbjct: 50 DVGGQDKIRPLWRHYFQNTQGLIFVV-----------DSNDRERIGEAREELQRMLNEDE 98
Query: 262 FREASFILFLNKFDL 276
R+A ++F NK DL
Sbjct: 99 LRDAVLLVFANKQDL 113
>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 = 37.8 bits (88), Expect = 0.003
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 12/78 (15%)
Query: 200 NMVDVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSS-VNRLDESLNLFEQVVN 258
N+ D+GGQR R W F++ ++YV+ DS+ R +E+ +++
Sbjct: 62 NVWDIGGQRKIRPYWRNYFENTDVLIYVI-----------DSADRKRFEEAGQELVELLE 110
Query: 259 NRYFREASFILFLNKFDL 276
++F NK DL
Sbjct: 111 EEKLAGVPVLVFANKQDL 128
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 35.7 bits (82), Expect = 0.016
Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 10/74 (13%)
Query: 203 DVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSSVNRLDESLNLFEQVVNNRYF 262
DVGGQ R W + F + + +++VV + + +R+ E+ + +++N
Sbjct: 67 DVGGQDKIRPLWRHYFQNTQGLIFVV----------DSNDRDRVVEARDELHRMLNEDEL 116
Query: 263 REASFILFLNKFDL 276
R+A ++F NK DL
Sbjct: 117 RDAVLLVFANKQDL 130
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 34.2 bits (79), Expect = 0.052
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 6/33 (18%)
Query: 37 KILLLGAGESGKSTLVKQM------KIIHNDGF 63
KI+L+G+G SGKSTL +Q+ + H D
Sbjct: 3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDAL 35
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 33.7 bits (77), Expect = 0.069
Identities = 25/101 (24%), Positives = 47/101 (46%), Gaps = 19/101 (18%)
Query: 201 MVDVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSSVNRLDESLNLFEQVVNNR 260
M DVGGQ R W + + + +++VV + + R+ ++ E++++
Sbjct: 65 MWDVGGQDKLRPLWRHYYQNTNGLIFVV----------DSNDRERIGDAREELERMLSED 114
Query: 261 YFREASFILFLNKFDL--------FREKI-LYSGRHLRYYL 292
R+A ++F NK DL EK+ L+S R +Y+
Sbjct: 115 ELRDAVLLVFANKQDLPNAMSTTEVTEKLGLHSVRQRNWYI 155
>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 = 33.5 bits (76), Expect = 0.086
Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 10/74 (13%)
Query: 203 DVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSSVNRLDESLNLFEQVVNNRYF 262
DVGG+ R W + + + +AV++V+ + S +R+ E+ + +++ +
Sbjct: 49 DVGGKHKLRPLWKHYYLNTQAVVFVI----------DSSHRDRVSEAHSELAKLLTEKEL 98
Query: 263 REASFILFLNKFDL 276
R+A ++F NK D+
Sbjct: 99 RDALLLIFANKQDV 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 = 31.6 bits (72), Expect = 0.30
Identities = 18/91 (19%), Positives = 30/91 (32%), Gaps = 9/91 (9%)
Query: 199 VNMVDVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSSVNRLDESLNLFEQVVN 258
N++D GQ + V++ L V + V ++E L + +
Sbjct: 53 FNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIV---------ILVLDVEEILEKQTKEII 103
Query: 259 NRYFREASFILFLNKFDLFREKILYSGRHLR 289
+ IL NK DL K+ L
Sbjct: 104 HHAESGVPIILVGNKIDLRDAKLKTHVAFLF 134
Score = 27.3 bits (61), Expect = 8.5
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 6/43 (13%)
Query: 36 IKILLLGAGESGKSTLVKQMKIIHNDGFTREELESFKPTVMDN 78
IKI+++G GKSTL+ +++ N + +KP N
Sbjct: 2 IKIVIVGDPNVGKSTLLN--RLLGNKIS----ITEYKPGTTRN 38
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 31.5 bits (71), Expect = 0.53
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 33 KHVIKILLLGAGESGKSTLVKQMK 56
KI++LG G GK+TL+ ++
Sbjct: 3 MKEFKIVVLGDGGVGKTTLLNRLV 26
>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 = 31.1 bits (70), Expect = 0.62
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 10/73 (13%)
Query: 203 DVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSSVNRLDESLNLFEQVVNNRYF 262
D+GG + RR W F +V ++Y+V YD R ES + ++++
Sbjct: 67 DLGGHQQARRLWKDYFPEVNGIVYLV--DAYDK--------ERFAESKRELDALLSDEEL 116
Query: 263 REASFILFLNKFD 275
F++ NK D
Sbjct: 117 ATVPFLILGNKID 129
Score = 27.6 bits (61), Expect = 9.0
Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 25 LTQLSLQEKHVIKILLLGAGESGKSTLVKQMK 56
L L L KH KIL LG +GK+TL+ +K
Sbjct: 8 LASLGLWNKHA-KILFLGLDNAGKTTLLHMLK 38
>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 = 30.7 bits (70), Expect = 0.82
Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 12/75 (16%)
Query: 203 DVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSS-VNRLDESLNLFEQVVNNRY 261
D+GG RR W F +V ++++V D++ R ES + ++N+
Sbjct: 69 DLGGHEQARRVWKDYFPEVDGIVFLV-----------DAADPERFQESKEELDSLLNDEE 117
Query: 262 FREASFILFLNKFDL 276
++ NK D
Sbjct: 118 LANVPILILGNKIDK 132
>gnl|CDD|192528 pfam10307, DUF2410, Hypothetical protein (DUF2410). This is a
family of proteins conserved in fungi. The function is
not known.There are two characteristic sequence motifs,
GGWW and TGR.
Length = 200
Score = 30.3 bits (69), Expect = 0.97
Identities = 12/32 (37%), Positives = 22/32 (68%)
Query: 24 QLTQLSLQEKHVIKILLLGAGESGKSTLVKQM 55
L +LS+++K + +LL G ESG S L++++
Sbjct: 61 DLAELSMKQKDTLSVLLTGRSESGFSELIERI 92
>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 = 30.0 bits (68), Expect = 1.1
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 12/77 (15%)
Query: 201 MVDVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSS-VNRLDESLNLFEQVVNN 259
M D+GGQ S R W + + AV+ V+ DS+ RL + +++ +
Sbjct: 63 MWDIGGQESLRSSWNTYYTNTDAVILVI-----------DSTDRERLPLTKEELYKMLAH 111
Query: 260 RYFREASFILFLNKFDL 276
R+A ++ NK DL
Sbjct: 112 EDLRKAVLLVLANKQDL 128
>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 = 28.9 bits (65), Expect = 1.6
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 7/59 (11%)
Query: 37 KILLLGAGESGKSTLVKQMKIIHNDGFTREELESFKPTVMDNLLSSMKYVLGGMGILRI 95
K++++G SGKS+L+ Q+ E D L V G G+L I
Sbjct: 1 KVVVIGDKGSGKSSLLSQL-------VGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNI 52
>gnl|CDD|206703 cd04131, Rnd, Rho family GTPase subfamily Rnd includes Rnd1/Rho6,
Rnd2/Rho7, and Rnd3/RhoE/Rho8. The Rnd subfamily
contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8.
These novel Rho family proteins have substantial
structural differences compared to other Rho members,
including N- and C-terminal extensions relative to
other Rhos. Rnd3/RhoE is farnesylated at the C-terminal
prenylation site, unlike most other Rho proteins that
are geranylgeranylated. In addition, Rnd members are
unable to hydrolyze GTP and are resistant to GAP
activity. They are believed to exist only in the
GTP-bound conformation, and are antagonists of RhoA
activity. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho
proteins. Due to the presence of truncated sequences in
this CD, the lipid modification site is not available
for annotation.
Length = 176
Score = 29.3 bits (66), Expect = 1.9
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 7/47 (14%)
Query: 36 IKILLLGAGESGKSTLVKQMKIIHNDGFTREELESFKPTVMDNLLSS 82
KI+L+G + GK+ L +++ D F E++ PTV +N +S
Sbjct: 2 CKIVLVGDSQCGKTAL---LQVFAKDSFP----ENYVPTVFENYTAS 41
>gnl|CDD|130261 TIGR01193, bacteriocin_ABC, ABC-type bacteriocin transporter. This
model describes ABC-type bacteriocin transporter. The
amino terminal domain (pfam03412) processes the
N-terminal leader peptide from the bacteriocin while
C-terminal domains resemble ABC transporter membrane
protein and ATP-binding cassette domain. In general,
bacteriocins are agents which are responsible for
killing or inhibiting the closely related species or
even different strains of the same species. Bacteriocins
are usually encoded by bacterial plasmids. Bacteriocins
are named after the species and hence in literature one
encounters various names e.g., leucocin from Leuconostic
geldium; pedicocin from Pedicoccus acidilactici; sakacin
from Lactobacillus sake etc [Protein fate, Protein and
peptide secretion and trafficking, Protein fate, Protein
modification and repair, Transport and binding proteins,
Other].
Length = 708
Score = 30.1 bits (68), Expect = 2.3
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 22 DKQLTQLSLQEKHVIKILLLGAGESGKSTLVKQM 55
L+ +SL K K ++G SGKSTL K +
Sbjct: 487 SNILSDISLTIKMNSKTTIVGMSGSGKSTLAKLL 520
>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 29.6 bits (67), Expect = 2.3
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 17 RSDEIDKQLTQLSLQEKHVIKILLLGAGESGKSTLVKQMKIIHND 61
R D I+ + +L ++ + ++G G GK+TL KQ I+ND
Sbjct: 1 REDMIEALIEKLLEMSDNLGVVGIVGMGGVGKTTLAKQ---IYND 42
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 29.0 bits (65), Expect = 3.4
Identities = 16/35 (45%), Positives = 24/35 (68%)
Query: 18 SDEIDKQLTQLSLQEKHVIKILLLGAGESGKSTLV 52
S+ I +QL L L EK + +LL+GA +GKS+L+
Sbjct: 22 SERILEQLRMLQLTEKEPVNVLLMGATGAGKSSLI 56
>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 = 28.5 bits (64), Expect = 3.8
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 12/75 (16%)
Query: 203 DVGGQRSQRRKWIYCFDDVKAVLYVVALSGYDMTLLEDSS-VNRLDESLNLFEQVVNNRY 261
D+GGQ S R W + + A++YVV DS+ +RL S + ++
Sbjct: 49 DLGGQTSIRPYWRCYYSNTDAIIYVV-----------DSTDRDRLGISKSELHAMLEEEE 97
Query: 262 FREASFILFLNKFDL 276
++A ++F NK D+
Sbjct: 98 LKDAVLLVFANKQDM 112
>gnl|CDD|206706 cd04134, Rho3, Ras homology family 3 (Rho3) of small guanosine
triphosphatases (GTPases). Rho3 is a member of the Rho
family found only in fungi. Rho3 is believed to
regulate cell polarity by interacting with the
diaphanous/formin family protein For3 to control both
the actin cytoskeleton and microtubules. Rho3 is also
believed to have a direct role in exocytosis that is
independent of its role in regulating actin polarity.
The function in exocytosis may be two-pronged: first,
in the transport of post-Golgi vesicles from the mother
cell to the bud, mediated by myosin (Myo2); second, in
the docking and fusion of vesicles to the plasma
membrane, mediated by an exocyst (Exo70) protein. Most
Rho proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins.
Length = 185
Score = 28.3 bits (63), Expect = 4.2
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 9/43 (20%)
Query: 37 KILLLGAGESGKSTLVKQMKIIHNDGFTREEL-ESFKPTVMDN 78
K+++LG G GK++L+ + FTR + ++PTV +N
Sbjct: 2 KVVVLGDGACGKTSLL--------NVFTRGYFPQVYEPTVFEN 36
>gnl|CDD|187720 cd08651, FMT_core_like_4, Formyl transferase catalytic core domain
found in a group of proteins with unknown functions.
Formyl transferase catalytic core domain found in a
group of proteins with unknown functions. Formyl
transferase catalyzes the transfer of one-carbon groups,
specifically the formyl- or hydroxymethyl- group. This
domain contains a Rossmann fold and it is the catalytic
domain of the enzyme.
Length = 180
Score = 28.4 bits (64), Expect = 4.3
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 299 DFDVDSGALFIQHKFALRNHNSAKVIY 325
D DSG + Q F + ++A +Y
Sbjct: 136 DEGADSGDILSQEPFPIDKDDTANSLY 162
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 28.4 bits (64), Expect = 4.5
Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 4/27 (14%)
Query: 37 KILLLGAGESGKST----LVKQMKIIH 59
+IL+LG +GKST L K++ + H
Sbjct: 2 RILILGPPGAGKSTLAKKLAKKLGLPH 28
>gnl|CDD|200601 cd10979, CE4_PuuE_like, Putative catalytic domain of
uncharacterized prokaryotic polysaccharide deacetylases
similar to bacterial PuuE allantoinases. The family
includes a group of uncharacterized prokaryotic
polysaccharide deacetylases (DCAs) that show high
sequence similarity to the catalytic domain of bacterial
PuuE (purine utilization E) allantoinases. PuuE
allantoinase specifically catalyzes the hydrolysis of
(S)-allantoin into allantoic acid. It functions as a
homotetramer. Its monomer is composed of a 7-stranded
barrel with detectable sequence similarity to the
6-stranded barrel NodB homology domain of DCA-like
proteins in the CE4 superfamily, which removes N-linked
or O-linked acetyl groups from cell wall
polysaccharides. PuuE allantoinase appears to be
metal-independent and acts on a small substrate
molecule, which is distinct from the common feature of
DCAs which are normally metal ion dependent and
recognize multimeric substrates.
Length = 281
Score = 28.7 bits (65), Expect = 4.9
Identities = 17/65 (26%), Positives = 21/65 (32%), Gaps = 18/65 (27%)
Query: 136 DRGVRLAVARG------YEYELNDSALYLFENME------RICDLKYVPNATDVLRARVR 183
D+ L G Y ELND +YL RI D D L A
Sbjct: 176 DQPYWLRTPAGPLLSLPYTLELNDIPIYLVRGHSADEFADRIID------QFDQLYAEGA 229
Query: 184 TNGII 188
+G +
Sbjct: 230 ESGRV 234
>gnl|CDD|185718 cd08772, GH43_62_32_68, Glycosyl hydrolase families: GH43, GH62,
GH32, GH68. Members of the glycosyl hydrolase families
32, 43, 62 and 68 (GH32, GH43, GH62, GH68) all possess
5-bladed beta-propeller domains and comprise clans F and
J, as classified by the carbohydrate-active enzymes
database (CAZY). Clan F consists of families GH43 and
GH62. GH43 includes beta-xylosidases, beta-xylanases,
alpha-L-arabinases, and alpha-L-arabinofuranosidases,
using aryl-glycosides as substrates, while family GH62
contains alpha-L-arabinofuranosidases (EC 3.2.1.55) that
specifically cleave either alpha-1,2 or
alpha-1,3-L-arabinofuranose sidechains from xylans.
These are inverting enzymes (i.e. they invert the
stereochemistry of the anomeric carbon atom of the
substrate) that have an aspartate as the catalytic
general base, a glutamate as the catalytic general acid
and another aspartate that is responsible for pKa
modulation and orienting the catalytic acid. Clan J
consists of families GH32 and GH68. GH32 comprises
sucrose-6-phosphate hydrolases, invertases, inulinases,
levanases, eukaryotic fructosyltransferases, and
bacterial fructanotransferases while GH68 consists of
frucosyltransferases (FTFs) that include levansucrase
(EC 2.4.1.10); beta-fructofuranosidase (EC 3.2.1.26);
inulosucrase (EC 2.4.1.9), while GH68 consists of
frucosyltransferases (FTFs) that include levansucrase
(EC 2.4.1.10); beta-fructofuranosidase (EC 3.2.1.26);
inulosucrase (EC 2.4.1.9), all of which use sucrose as
their preferential donor substrate. Members of this clan
are retaining enzymes (i.e. they retain the
configuration at anomeric carbon atom of the substrate)
that catalyze hydrolysis in two steps involving a
covalent glycosyl enzyme intermediate: an aspartate
located close to the N-terminus acts as the catalytic
nucleophile and a glutamate acts as the general
acid/base; a conserved aspartate residue in the
Arg-Asp-Pro (RDP) motif stabilizes the transition state.
Structures of all families in the two clans manifest a
funnel-shaped active site that comprises two subsites
with a single route for access by ligands.
Length = 286
Score = 28.6 bits (64), Expect = 5.0
Identities = 15/85 (17%), Positives = 23/85 (27%), Gaps = 7/85 (8%)
Query: 264 EASFILFLN-KFDLF----REKILYSGRHLRYYLSDFKGPDFDVDSGALFIQHKFALRNH 318
E +L N K+ LF + S + Y S+ + S +
Sbjct: 180 EGPGLLKKNGKYYLFYSINGTGRVDSTYSIGYARSESDTGPYVPKSDTSGGLSLTGGNDG 239
Query: 319 NSAKVIYPHFTTATDTSNVQTVFHA 343
Y V V+HA
Sbjct: 240 --GVGPYHAAAFNDAGGRVVLVYHA 262
>gnl|CDD|213214 cd03247, ABCC_cytochrome_bd, ATP-binding cassette domain of
CydCD, subfamily C. The CYD subfamily implicated in
cytochrome bd biogenesis. The CydC and CydD proteins
are important for the formation of cytochrome bd
terminal oxidase of E. coli and it has been proposed
that they were necessary for biosynthesis of the
cytochrome bd quinol oxidase and for periplasmic c-type
cytochromes. CydCD were proposed to determine a
heterooligomeric complex important for heme export into
the periplasm or to be involved in the maintenance of
the proper redox state of the periplasmic space. In
Bacillus subtilis, the absence of CydCD does not affect
the presence of halo-cytochrome c in the membrane and
this observation suggests that CydCD proteins are not
involved in the export of heme in this organism.
Length = 178
Score = 28.0 bits (63), Expect = 5.6
Identities = 16/31 (51%), Positives = 20/31 (64%)
Query: 25 LTQLSLQEKHVIKILLLGAGESGKSTLVKQM 55
L LSL+ K KI LLG SGKSTL++ +
Sbjct: 18 LKNLSLELKQGEKIALLGRSGSGKSTLLQLL 48
>gnl|CDD|133377 cd04177, RSR1, RSR1/Bud1p family GTPase. RSR1/Bud1p is a member
of the Rap subfamily of the Ras family that is found in
fungi. In budding yeasts, RSR1 is involved in selecting
a site for bud growth on the cell cortex, which directs
the establishment of cell polarization. The Rho family
GTPase cdc42 and its GEF, cdc24, then establish an axis
of polarized growth by organizing the actin
cytoskeleton and secretory apparatus at the bud site.
It is believed that cdc42 interacts directly with RSR1
in vivo. In filamentous fungi, polar growth occurs at
the tips of hypha and at novel growth sites along the
extending hypha. In Ashbya gossypii, RSR1 is a key
regulator of hyphal growth, localizing at the tip
region and regulating in apical polarization of the
actin cytoskeleton. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras
proteins.
Length = 168
Score = 27.8 bits (62), Expect = 5.6
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 7/41 (17%)
Query: 37 KILLLGAGESGKSTLVKQMKIIHNDGFTREELESFKPTVMD 77
KI++LGAG GKS L Q + N +ES+ PT+ D
Sbjct: 3 KIVVLGAGGVGKSALTVQF--VQN-----VFIESYDPTIED 36
>gnl|CDD|206741 cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc
(COR) domain family. RocCOR (or Roco) protein family
is characterized by a superdomain containing a Ras-like
GTPase domain, called Roc (Ras of complex proteins),
and a characteristic second domain called COR
(C-terminal of Roc). A kinase domain and diverse
regulatory domains are also often found in Roco
proteins. Their functions are diverse; in Dictyostelium
discoideum, which encodes 11 Roco proteins, they are
involved in cell division, chemotaxis and development,
while in human, where 4 Roco proteins (LRRK1, LRRK2,
DAPK1, and MFHAS1) are encoded, these proteins are
involved in epilepsy and cancer. Mutations in LRRK2
(leucine-rich repeat kinase 2) are known to cause
familial Parkinson's disease.
Length = 161
Score = 27.7 bits (62), Expect = 5.7
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 36 IKILLLGAGESGKSTLVKQMK 56
K++L+G G GK++L KQ+
Sbjct: 2 AKLMLVGQGGVGKTSLCKQLI 22
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain
I of the ABC component of a cobalt transport family
found in bacteria, archaea, and eukaryota. The
transition metal cobalt is an essential component of
many enzymes and must be transported into cells in
appropriate amounts when needed. This ABC transport
system of the CbiMNQO family is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most of cobalt (Cbi)
transport systems possess a separate CbiN component,
the cobalt-binding periplasmic protein, and they are
encoded by the conserved gene cluster cbiMNQO. Both the
CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems.
Length = 211
Score = 27.8 bits (63), Expect = 7.6
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 37 KILLLGAGESGKSTLVKQM 55
+L++G SGKSTL++ +
Sbjct: 29 FVLIVGPNGSGKSTLLRLL 47
>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 = 27.5 bits (62), Expect = 7.7
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 9/40 (22%)
Query: 37 KILLLGAGESGKSTLVKQMKIIHNDGFTREE-LESFKPTV 75
K++L+G G GKS+L+ + FT+ + E + PT+
Sbjct: 1 KLVLVGDGGVGKSSLLIR--------FTQNKFPEEYIPTI 32
>gnl|CDD|222302 pfam13666, DUF4151, Domain of unknown function (DUF4151). This
domain is found on dynein heavy chain proteins. The
exact function is not known but it is conserved from
plants to Sch. pombe to human.
Length = 117
Score = 26.6 bits (59), Expect = 8.9
Identities = 6/21 (28%), Positives = 15/21 (71%)
Query: 5 ISLDSEEIKAQRRSDEIDKQL 25
++ + E+ +R++ EID+Q+
Sbjct: 57 VAEEQEDRNVERQTKEIDEQI 77
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
0.323 0.137 0.391
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: 18,094,869
Number of extensions: 1761026
Number of successful extensions: 1991
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1970
Number of HSP's successfully gapped: 63
Length of query: 359
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 261
Effective length of database: 6,590,910
Effective search space: 1720227510
Effective search space used: 1720227510
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 (22.0 bits)
S2: 60 (26.8 bits)