RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7717
(113 letters)
>gnl|CDD|217901 pfam04110, APG12, Ubiquitin-like autophagy protein Apg12. In
yeast, 15 Apg proteins coordinate the formation of
autophagosomes. Autophagy is a bulk degradation process
induced by starvation in eukaryotic cells. The Apg12
system is one of the ubiquitin-like protein conjugation
systems conserved in eukaryotes. It was first discovered
in yeast during systematic analyses of the apg mutants
defective in autophagy. Covalent attachment of
Apg12-Apg5 is essential for autophagy.
Length = 87
Score = 123 bits (311), Expect = 2e-38
Identities = 50/87 (57%), Positives = 62/87 (71%)
Query: 27 KVPILLRATGDAPILTKKKWLVHVDQNVASIISFTKKSIKMDPSESLFIYVNQSFAPSPD 86
K+ I LRA GDAPIL K K+ V+ Q AS+I F KK +K+ S+SLF+YVN SFAPSPD
Sbjct: 1 KITIRLRAIGDAPILKKSKFKVNPSQTFASVILFLKKFLKLQASDSLFLYVNNSFAPSPD 60
Query: 87 TTIRALYDSFATNGSLVLNYCKTQAWG 113
+ LY+ F T+G LVLNYC + AWG
Sbjct: 61 QIVGNLYECFGTDGKLVLNYCISVAWG 87
>gnl|CDD|176356 cd01612, APG12_C, Ubiquitin-like domain of APG12. APG12_C The
carboxy-terminal ubiquitin-like domain of APG12.
Autophagy is a process in which cytoplasmic components
are delivered to the lysosome/vacuole for degradation.
Autophagy requires a ubiquitin-like protein conjugation
system, in which APG12 is covalently bound to APG5.
Length = 87
Score = 120 bits (302), Expect = 6e-37
Identities = 40/87 (45%), Positives = 58/87 (66%)
Query: 27 KVPILLRATGDAPILTKKKWLVHVDQNVASIISFTKKSIKMDPSESLFIYVNQSFAPSPD 86
KV I + G APIL +K + + Q+ ++I F +K +K+ S+SLF+Y+N SFAPSPD
Sbjct: 1 KVTIRFKPIGSAPILKQKVFKISATQSFQAVIDFLRKRLKLKASDSLFLYINNSFAPSPD 60
Query: 87 TTIRALYDSFATNGSLVLNYCKTQAWG 113
+ LY F TNG L+++YCKT A+G
Sbjct: 61 ENVGNLYRCFGTNGELIVSYCKTVAFG 87
>gnl|CDD|111837 pfam02991, Atg8, Autophagy protein Atg8 ubiquitin like. Light
chain 3 is proposed to function primarily as a subunit
of microtubule associated proteins 1A and 1B and that
its expression may regulate microtubule binding
activity. Autophagy is generally known as a process
involved in the degradation of bulk cytoplasmic
components that are non-specifically sequestered into
an autophagosome, where they are sequestered into
double-membrane vesicles and delivered to the
degradative organelle, the lysosome/vacuole, for
breakdown and eventual recycling of the resulting
macromolecules. The yeast proteins are involved in the
autophagosome, and Atg8 binds Atg19, via its N-terminus
and the C-terminus of Atg19.
Length = 104
Score = 52.7 bits (127), Expect = 3e-10
Identities = 25/72 (34%), Positives = 43/72 (59%), Gaps = 3/72 (4%)
Query: 27 KVP-ILLRATG-DAPILTKKKWLVHVDQNVASIISFTKKSIKMDPSESLFIYVNQSFAPS 84
++P I+ +A+G D P + KKK+LV D V I +K I++ P +++F++VN + P
Sbjct: 16 RIPVIIEKASGSDLPDIDKKKYLVPADLTVGQFIYIIRKRIQLRPEKAIFLFVNNTL-PP 74
Query: 85 PDTTIRALYDSF 96
T+ ALY+
Sbjct: 75 TSATMSALYEEE 86
>gnl|CDD|176355 cd01611, GABARAP, Ubiquitin domain of GABA-receptor-associated
protein. GABARAP (GABA-receptor-associated protein)
belongs ot a large family of proteins that mediate
intracellular membrane trafficking and/or fusion.
GABARAP binds not only to GABA, type A but also to
tubulin, gephrin, and ULK1. Orthologues of GABARAP
include Gate-16 (golgi-associated ATPase enhancer), LC3
(microtubule-associated protein light chain 3), and
ATG8 (autophagy protein 8). ATG8 is a ubiquitin-like
protein that is conjugated to the membrane
phospholipid, phosphatidylethanolamine as part of a
ubiquitin-like conjugation system essential for
autophagosome-formation.
Length = 112
Score = 50.7 bits (122), Expect = 2e-09
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 3/72 (4%)
Query: 27 KVPILL-RATG-DAPILTKKKWLVHVDQNVASIISFTKKSIKMDPSESLFIYVNQSFAPS 84
++P+++ R D P L KKK+LV D V + +K I++ P ++LF++VN S P+
Sbjct: 24 RIPVIVERYPKSDLPDLDKKKYLVPSDLTVGQFVYIIRKRIQLRPEKALFLFVNNSLPPT 83
Query: 85 PDTTIRALYDSF 96
T+ LY+
Sbjct: 84 -SATMSQLYEEH 94
>gnl|CDD|190308 pfam02434, Fringe, Fringe-like. The drosophila protein fringe
(FNG) is a glucosaminyltransferase that controls the
response of the Notch receptor to specific ligands. FNG
is localised to the Golgi apparatus (not secreted as
previously thought). Modification of Notch occurs
through glycosylation by FNG. The xenopus homologue,
lunatic fringe, has been implicated in a variety of
functions.
Length = 248
Score = 28.4 bits (64), Expect = 0.73
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 30 ILLRATGDAPILTKKKWLVHVD 51
+ D + + KKW HVD
Sbjct: 71 CKMAVEYDRFLESGKKWFCHVD 92
>gnl|CDD|107328 cd06333, PBP1_ABC-type_HAAT_like, Type I periplasmic binding
component of ABC (ATPase Binding Cassette)-type
transport systems that are predicted to be involved in
uptake of amino acids. This subgroup includes the type
I periplasmic binding component of ABC (ATPase Binding
Cassette)-type transport systems that are predicted to
be involved in uptake of amino acids. Members of this
subgroup are sequence-similar to members of the family
of ABC-type hydrophobic amino acid transporters (HAAT),
such as leucine-isoleucine-valine-binding protein
(LIVBP); their ligand specificity has not been
determined experimentally, however.
Length = 312
Score = 27.1 bits (61), Expect = 1.8
Identities = 10/44 (22%), Positives = 18/44 (40%)
Query: 10 PEGSAPSSPSIGAEAKVKVPILLRATGDAPILTKKKWLVHVDQN 53
P + + + K P++ A A + K+KW+ QN
Sbjct: 73 PSTTPATMAVAPVAEEAKTPMISLAPAAAIVEPKRKWVFKTPQN 116
>gnl|CDD|143600 cd07576, R-amidase_like, Pseudomonas sp. MCI3434 R-amidase and
related proteins (putative class 13 nitrilases).
Pseudomonas sp. MCI3434 R-amidase hydrolyzes
(R,S)-piperazine-2-tert-butylcarboxamide to form
(R)-piperazine-2-carboxylic acid. It does so with strict
R-stereoselectively. Its preferred substrates are
carboxamide compounds which have the amino or imino
group connected to their beta- or gamma-carbon. This
subgroup belongs to a larger nitrilase superfamily
comprised of nitrile- or amide-hydrolyzing enzymes and
amide-condensing enzymes, which depend on a Glu-Lys-Cys
catalytic triad. This superfamily has been classified in
the literature based on global and structure based
sequence analysis into thirteen different enzyme classes
(referred to as 1-13), class 13 represents proteins that
at the time were difficult to place in a distinct
similarity group. It has been suggested that this
subgroup represents a new class. Members of the
nitrilase superfamily generally form homomeric
complexes, the basic building block of which is a
homodimer. Native R-amidase however appears to be a
monomer.
Length = 254
Score = 26.4 bits (59), Expect = 3.4
Identities = 8/26 (30%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 91 ALYDS---FATNGSLVLNYCKTQAWG 113
A+Y++ +G+++ NY KT +G
Sbjct: 89 AVYNAAVLIDEDGTVLANYRKTHLFG 114
>gnl|CDD|215612 PLN03169, PLN03169, chalcone synthase family protein;
Provisional.
Length = 391
Score = 26.2 bits (58), Expect = 4.8
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 1 MSEEITDNTPEGSAPSSPSI 20
MS+EI D PE + +P+I
Sbjct: 76 MSKEILDKYPELATEGTPTI 95
>gnl|CDD|172776 PRK14288, PRK14288, chaperone protein DnaJ; Provisional.
Length = 369
Score = 26.2 bits (57), Expect = 5.2
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 8/50 (16%)
Query: 59 SFTKKSIKMDP--------SESLFIYVNQSFAPSPDTTIRALYDSFATNG 100
S+ K ++K P +E F +N+++ D RALYD + G
Sbjct: 23 SYRKLALKYHPDRNAGDKEAEEKFKLINEAYGVLSDEKKRALYDRYGKKG 72
>gnl|CDD|187678 cd09620, CBM9_like_3, DOMON-like type 9 carbohydrate binding
module. Family 9 carbohydrate-binding modules (CBM9)
play a role in the microbial degradation of cellulose
and hemicellulose (materials found in plants). The
domain has previously been called cellulose-binding
domain. The polysaccharide binding sites of CBMs with
available 3D structure have been found to be either
flat surfaces with interactions formed by predominantly
aromatic residues (tryptophan and tyrosine), or
extended shallow grooves. CBM9 domains found in this
uncharacterized heterogeneous subfamily may co-occur
with various other domains.
Length = 200
Score = 25.0 bits (55), Expect = 8.2
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 62 KKSIKMDPSESLFIYVNQSFAPSPDTTIRALYD 94
+ + + P LF+ + P P T +R LYD
Sbjct: 7 EPAWQAAPWVELFVDIGGGPPPKPQTRVRLLYD 39
>gnl|CDD|233851 TIGR02403, trehalose_treC, alpha,alpha-phosphotrehalase. Trehalose
is a glucose disaccharide that serves in many biological
systems as a compatible solute for protection against
hyperosmotic and thermal stress. This family describes
trehalose-6-phosphate hydrolase, product of the treC (or
treA) gene, which is often found together with a
trehalose uptake transporter and a trehalose operon
repressor.
Length = 543
Score = 25.4 bits (56), Expect = 8.6
Identities = 13/51 (25%), Positives = 22/51 (43%)
Query: 56 SIISFTKKSIKMDPSESLFIYVNQSFAPSPDTTIRALYDSFATNGSLVLNY 106
SI F +K I + SE + + F D ++ A ++ LV+N
Sbjct: 448 SIFYFYQKLIALRKSEPVITDGDYQFLLPDDPSVWAYTRTYKNQKLLVINN 498
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
0.313 0.128 0.368
Gapped
Lambda K H
0.267 0.0658 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,518,237
Number of extensions: 445474
Number of successful extensions: 258
Number of sequences better than 10.0: 1
Number of HSP's gapped: 258
Number of HSP's successfully gapped: 18
Length of query: 113
Length of database: 10,937,602
Length adjustment: 77
Effective length of query: 36
Effective length of database: 7,522,344
Effective search space: 270804384
Effective search space used: 270804384
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.3 bits)