RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12247
(119 letters)
>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 = 98.1 bits (245), Expect = 6e-28
Identities = 40/112 (35%), Positives = 65/112 (58%), Gaps = 1/112 (0%)
Query: 5 YTEKYSLEERIKIGENLARNHPNCAFVILERSPSALLPQMPRSNYVVAYEMTVGHFFYLL 64
+ E++ E+R E + +P+ VI+ER P + LP + + Y+V ++TVG F Y++
Sbjct: 1 FKERHPFEKRKAEVERIRAKYPDRIPVIVERYPKSDLPDLDKKKYLVPSDLTVGQFVYII 60
Query: 65 RKKMALRPEEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVYSDVNIF 116
RK++ LRPE+A F F+ + + P S M L + D+DG +YM YS F
Sbjct: 61 RKRIQLRPEKALFLFVNNSLPPT-SATMSQLYEEHKDEDGFLYMTYSSEETF 111
>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 = 92.0 bits (229), Expect = 1e-25
Identities = 38/104 (36%), Positives = 62/104 (59%), Gaps = 1/104 (0%)
Query: 13 ERIKIGENLARNHPNCAFVILERSPSALLPQMPRSNYVVAYEMTVGHFFYLLRKKMALRP 72
+R E + +P+ VI+E++ + LP + + Y+V ++TVG F Y++RK++ LRP
Sbjct: 1 KRQAESEKIREKYPDRIPVIIEKASGSDLPDIDKKKYLVPADLTVGQFIYIIRKRIQLRP 60
Query: 73 EEACFFFIESMIVPADSTRMETLSQRFADKDGLIYMVYSDVNIF 116
E+A F F+ + + P S M L + D+DG +YMVYS N F
Sbjct: 61 EKAIFLFVNNTLPPT-SATMSALYEEEKDEDGFLYMVYSGENTF 103
>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 = 34.6 bits (80), Expect = 0.002
Identities = 12/65 (18%), Positives = 28/65 (43%)
Query: 42 PQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFAD 101
P + + + ++ + LRK++ L+ ++ F +I + P+ + L + F
Sbjct: 13 PILKQKVFKISATQSFQAVIDFLRKRLKLKASDSLFLYINNSFAPSPDENVGNLYRCFGT 72
Query: 102 KDGLI 106
LI
Sbjct: 73 NGELI 77
>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 = 30.8 bits (70), Expect = 0.042
Identities = 12/65 (18%), Positives = 27/65 (41%)
Query: 42 PQMPRSNYVVAYEMTVGHFFYLLRKKMALRPEEACFFFIESMIVPADSTRMETLSQRFAD 101
P + +S + V T L+K + L+ ++ F ++ + P+ + L + F
Sbjct: 13 PILKKSKFKVNPSQTFASVILFLKKFLKLQASDSLFLYVNNSFAPSPDQIVGNLYECFGT 72
Query: 102 KDGLI 106
L+
Sbjct: 73 DGKLV 77
>gnl|CDD|128870 smart00607, FTP, eel-Fucolectin Tachylectin-4 Pentaxrin-1 Domain.
Length = 151
Score = 28.7 bits (64), Expect = 0.58
Identities = 15/47 (31%), Positives = 17/47 (36%), Gaps = 6/47 (12%)
Query: 14 RIKIG---ENLARNHPNCAFVILERSPSALL---PQMPRSNYVVAYE 54
RI IG EN N+PNC+ L P YV Y
Sbjct: 84 RILIGNSLENGGINNPNCSTGGLMAGGETKTFCCPPPMIGRYVTVYL 130
>gnl|CDD|176051 cd08406, C2B_Synaptotagmin-12, C2 domain second repeat present in
Synaptotagmin 12. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Synaptotagmin 12, a member of
class 6 synaptotagmins, is located in the brain. It
functions are unknown. It, like synaptotagmins 8 and
13, do not have any consensus Ca2+ binding sites.
Previously all synaptotagmins were thought to be
calcium sensors in the regulation of neurotransmitter
release and hormone secretion, but it has been shown
that not all of them bind calcium. Of the 17
identified synaptotagmins only 8 bind calcium (1-3,
5-7, 9, 10). The function of the two C2 domains that
bind calcium are: regulating the fusion step of
synaptic vesicle exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
C2 domains fold into an 8-standed beta-sandwich that
can adopt 2 structural arrangements: Type I and Type
II, distinguished by a circular permutation involving
their N- and C-terminal beta strands. Many C2 domains
are Ca2+-dependent membrane-targeting modules that bind
a wide variety of substances including bind
phospholipids, inositol polyphosphates, and
intracellular proteins. Most C2 domain proteins are
either signal transduction enzymes that contain a
single C2 domain, such as protein kinase C, or membrane
trafficking proteins which contain at least two C2
domains, such as synaptotagmin 1. However, there are a
few exceptions to this including RIM isoforms and some
splice variants of piccolo/aczonin and intersectin
which only have a single C2 domain. C2 domains with a
calcium binding region have negatively charged
residues, primarily aspartates, that serve as ligands
for calcium ions. This cd contains the second C2
repeat, C2B, and has a type-I topology.
Length = 136
Score = 28.2 bits (63), Expect = 0.66
Identities = 9/36 (25%), Positives = 20/36 (55%)
Query: 63 LLRKKMALRPEEACFFFIESMIVPADSTRMETLSQR 98
+ +KK +++ ++ F E+MI + ++ LS R
Sbjct: 51 ISKKKTSVKRDDTNPIFNEAMIFSVPAIVLQDLSLR 86
>gnl|CDD|235101 PRK03059, PRK03059, PII uridylyl-transferase; Provisional.
Length = 856
Score = 27.6 bits (62), Expect = 1.6
Identities = 9/34 (26%), Positives = 20/34 (58%)
Query: 80 IESMIVPADSTRMETLSQRFADKDGLIYMVYSDV 113
IE+ + P+ S +++RF +K G++ + D+
Sbjct: 308 IEARLFPSTSGITRVINERFVEKQGMLEIASDDL 341
>gnl|CDD|215803 pfam00225, Kinesin, Kinesin motor domain.
Length = 326
Score = 26.4 bits (59), Expect = 4.1
Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 4/25 (16%)
Query: 82 SMIV---PADSTRMETLSQ-RFADK 102
MI P+DS ETLS RFA +
Sbjct: 298 LMIANISPSDSNYEETLSTLRFASR 322
>gnl|CDD|235483 PRK05467, PRK05467, Fe(II)-dependent oxygenase superfamily protein;
Provisional.
Length = 226
Score = 25.9 bits (58), Expect = 4.8
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 6/35 (17%)
Query: 75 ACFFFIESMIVPADSTR-----METLSQRFADKDG 104
A FF+I+S+ V DS R ++T Q + G
Sbjct: 171 ASFFWIQSL-VRDDSQRELLFDLDTAIQSLLARHG 204
>gnl|CDD|219172 pfam06778, Chlor_dismutase, Chlorite dismutase. This family
contains chlorite dismutase enzymes of bacterial and
archaeal origin. This enzyme catalyzes the
disproportionation of chlorite into chloride and oxygen.
Note that many family members are hypothetical proteins.
Length = 192
Score = 25.8 bits (57), Expect = 5.3
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 4/36 (11%)
Query: 37 PSALLPQMPRSNYVVAYEMTVGHFFYLL----RKKM 68
P+ L P++P Y VAY M +YLL R+++
Sbjct: 90 PAFLKPELPPLRYFVAYPMKKSRDWYLLPFEERRRI 125
>gnl|CDD|235557 PRK05682, flgE, flagellar hook protein FlgE; Validated.
Length = 407
Score = 26.0 bits (58), Expect = 6.3
Identities = 6/12 (50%), Positives = 8/12 (66%)
Query: 101 DKDGLIYMVYSD 112
D DG + VYS+
Sbjct: 299 DDDGTVTAVYSN 310
>gnl|CDD|163562 TIGR03850, bind_CPR_0540, carbohydrate ABC transporter
substrate-binding protein, CPR_0540 family. Members of
this protein are the substrate-binding protein of a
predicted carbohydrate transporter operon, together with
permease subunits of ABC transporter homology families.
This substrate-binding protein frequently co-occurs in
genomes with a family of disaccharide phosphorylases,
TIGR02336, suggesting that the molecule transported will
include
beta-D-galactopyranosyl-(1->3)-N-acetyl-D-glucosamine
and related carbohydrates. Members of this family are
sporadically strain by strain, often in species with a
human host association, including Propionibacterium
acnes and Clostridium perfringens, and Bacillus cereus
[Transport and binding proteins, Carbohydrates, organic
alcohols, and acids].
Length = 437
Score = 25.8 bits (57), Expect = 6.7
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 9/42 (21%)
Query: 77 FFFIESMIVPADSTRMETLSQRFADKDGLIYMVYSD--VNIF 116
+ F E M +PA + + K+ + ++ YSD IF
Sbjct: 320 YTFFEQMWIPAAAKNKD------LAKEFIAFL-YSDEAAKIF 354
>gnl|CDD|225858 COG3321, COG3321, Polyketide synthase modules and related proteins
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 1061
Score = 25.9 bits (57), Expect = 6.9
Identities = 9/36 (25%), Positives = 14/36 (38%), Gaps = 1/36 (2%)
Query: 11 LEERIKIGENLARNHPNCAFVILERSPSALLPQMPR 46
LEE E+ + P V+ ++ L PR
Sbjct: 424 LEEAPPRAESTIPSSP-RLLVLSAKTAERLAATAPR 458
>gnl|CDD|180325 PRK05953, PRK05953, precorrin-8X methylmutase; Validated.
Length = 208
Score = 25.5 bits (56), Expect = 8.6
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 19 ENLARNHPNCAFVILERSPSAL 40
E LAR +P FVI + S +AL
Sbjct: 112 ETLARRYPEAIFVIGQ-SQTAL 132
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 25.3 bits (56), Expect = 9.9
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 23 RNHPNCAFVILERSPSALLP 42
+ C F+I R PS L+P
Sbjct: 151 QYSRTCRFIIATRQPSKLIP 170
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 0.138 0.403
Gapped
Lambda K H
0.267 0.0615 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,182,181
Number of extensions: 546870
Number of successful extensions: 578
Number of sequences better than 10.0: 1
Number of HSP's gapped: 576
Number of HSP's successfully gapped: 26
Length of query: 119
Length of database: 10,937,602
Length adjustment: 82
Effective length of query: 37
Effective length of database: 7,300,574
Effective search space: 270121238
Effective search space used: 270121238
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: 53 (24.4 bits)